草菇形态建成中差异表达转录因子的筛选及关键基因的功能分析
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摘要
草菇(Volvariella volvacea)是一种生长于热带和亚热带的腐生真菌,具有极其复杂的生活史,在整个生活史中形态发生了明显变化,并且这些形态变化受到相关基因的调控。在实际生产应用中,草菇由于其生长周期短,易开伞等因素,导致草菇采摘后不易存储和保鲜,因此制约了草菇的市场价值,本文通过草菇不同生长发育时期基因表达量的比较研究,发现了在原基期和伸长期差异表达的基因,并对这些差异表达的基因进行了生物信息学分析,旨在能发现调控草菇原基形成和菌柄伸长的转录因子,为后期的功能验证和生产应用提供理论基础,希望能通过基因改造来延长草菇的货架保鲜期,主要试验结果如下：
(1)草菇基因组通过与真菌转录因子数据库进行比对,共鉴定出214个转录因子,分属于30个转录因子家族。
(2)根据同源比对,分析转录因子在不同担子菌和子囊菌中的保守性,比对的真菌包括草菇(V. volvacea),裂褶菌(Schizophyllum commune),双色蜡磨(Laccaria bicolor),灰盖鬼伞(Coprinopsis cinerea),黑粉菌(Ustilago maydis),酿酒酵母(Saccharomyces cerevisiae),瑞氏木霉(Trichoderma reesei),粗糙脉孢菌(Neurospora crassa)和构巢曲霉(Aspergillus nidulans)。比对结果显示草菇中62.6%的转录因子与其他8种真菌具有同源性,其中37%的转录因子只在草菇基因组中有同源基因,46%的转录因子在所比对的担子菌中有同源基因,而仅有16%的转录因子在担子菌和子囊菌中具有同源性,因此,不同真菌间,尤其是担子菌和子囊菌之间,转录因子的同源性很低。虽然转录因子的氨基酸序列不是很保守,但是转录因子绑定DNA的区域却很保守。
(3)分别比较异核菌丝体和原基,蛋形期和伸长期的基因表达量。从异核菌丝体到原基,共得到1503个差异表达基因,其中877个上调表达,626个下调表达；而从蛋形期到伸长期,共得到1367差异表达基因,其中1004个下调表达,仅有363个上调表达。通过对异核菌丝体和原基,蛋形期和伸长期的功能富集研究表明,相较于异核菌丝体,在原基期上调表达的主要功能为对生物的调节作用,主要表现在对细胞和代谢过程的调节,而在原基期下调表达的基因参与的主要生物过程为细胞组分的生物合成和多细胞生物过程。相反,相较于蛋形期,在伸长期下调表达的基因功能主要为对细胞组分以及细胞过程的调节作用,而参与多细胞生物过程则在伸长期上调表达。通过对差异表达基因的功能富集分析,发现调节基因表达的基因在子实体的形成过程中发挥着至关重要的作用。此外,研究还发现14%在原基期和伸长期差异表达的转录因子属于同源异形框家族的转录因子,因此,推测同源异形框转录因子在这两个发育阶段发挥着重要的调节作用。
(4)通过差异表达分析,共得到8个差异表达的同源异形框转录因子,其中有5个(GME10392, GME1763, GME860, GME11623和GME8409)在原基期上调表达,有3个(GME918, GME8013和GME2319)在伸长期下调表达,并且荧光定量结果(qRT-PCR)与表达谱的结果一致,这些差异表达的同源异形框转录因子很可能与子实体的形态建成有关。
(5)克隆测序结果显示,GME918(GenBank accession numbers:JX843776)在两个同核菌丝体PYd15和PYd21中的DNA序列完全相同。通过转录组测序,共得到约2600万个高质量的reads和2,408,000,220nt核苷酸,其中有3,632个reads可以定位到GME918上。通过转录组数据,分析GME918的基因结构,结果显示,GME918全长为2856bp,开放阅读框为1149bp,由四个外显子和三个内含子组成,并且在第一个内含子中存在可变剪切现象。
(6)根据GME918的保守结构域,构建其RNAi载体,经过PCR和酶切验证,证明已经成功构建了GME918的RNAi载体,并通过农杆菌介导的方法将其转化到草菇H1521中,发现经RNAi后的转化子在菌落形态和菌丝生长速度方面都发生了明显变化,因此,试验结果表明GME918对菌落的形态发生和菌丝生长具有重要的调节作用。
The Chinese mushroom, Volvariella volvacea (Bull.:Fr.) Singer, is a tropical and subtropical saprophytic fungus in the family Pluteaceae of the Basidiomycota. The lifecycle of V. volvacea is a complex process that involves a cascade of morphological events in fruiting body development. Several genes are responsible for regulation and control of the morphogenesis of V. volvacea fruiting body formation. In fact, the market value of V. volvacea was limited as difficult to storage and preservation that the short lifecycle resulted in the pileus-opening. The differentially expressed genes were obtained by comparing the gene expression level between two periods, from mycelia to primordia and from egg stage to elongation stage, respectively. Moreover, to identify the transcription factors of V. volvacea involved in primordia formation and stipe elongation, enrichment analysis of functional annotation for the expression profiles were performed. It could provide fundamental basis for functional verification and application in production that the preservation of V. volvacea was prolongated by using gene modification. The mainly results as follow:
(1) In the present work,214putative transcription factors (TFs) belong to30transcription factor families were identified from the genome of V. volvacea via the pipeline of fungal transcription factor database (FTFD).
(2) Compared the conservation of the TFs in different basidiomycetes and ascomycetes fungi, including V. volvacea, Schizophyllum commune, Laccaria bicolor, Coprinopsis cinerea, Ustilago maydis, Saccharomyces cerevisiae, Trichoderma reesei, Neurospora crassa, Aspergillus nidulans, by homology alignment. The results showed that62.6%transcription factors have homology with other eight fungi,37%is specific for V. volvacea, and46%is specific for basidiomycetes fungi. In addition, only16%transcription factors have homology in basidiomycetes and ascomycetes fungi. Therefore, the homology of transcription factors was low between basidiomycetes and ascomycetes fungi. However, the conserved domain of transcription factors among them is similar, although the whole amino acid sequences of transcription factors were not conserved.
(3) To identify the differentially expressed genes in primordia and elongation stage,1503and1367differentially expressed genes were obtained by comparing the gene expression level between two periods, from mycelia to primordia and from egg stage to elongation stage, respectively. Of them,877and626genes were up-regulated and down-regulated expression from mycelia to primordia, respectively. Nevertheless, there have1004genes down-regulated expression, only363genes up-regulated, from egg stage to elongation stage. The enrichment analysis of functional annotation for the expression profiles of the developmental stages defined by mycelia, primordia, egg stage and elongation stage was performed. Functional terms involved in regulation of cellular process and metabolic process, were over-represented in genes up-regulated of primordia. Genes involved in cellular component biogenesis, anatomical structure formation and multicellular organismal process were enriched in the group of genes down-regulated of primordia. However, functional terms involved in regulation of cellular component organization and of cellular process were enriched in the down-regulated genes of elongation stage. Genes encoding anatomical structure formation, multi-organnism process were enriched in the group of genes up-regulated of elongation stage. The enrichment analysis of functional annotation illustrated that the regulation of gene expression played a crucial role in the formation of fruiting body based on the different expression analysis. We found that14%differentially expressed TFs belong to homeobox family in primordia and elongation stage. It may be paly more important role in these processes.
(4) By the differential expression analysis as above mention,8differentially expressed homeobox TFs were obtained, including5up-regulated expressed in the primordia and3down-regulated expressed in the elongation stage of V. volvacea. In fact, quantitative real-time PCR (qRT-PCR) was used to analyze gene expression value in mycelia, primordia, egg stage, elongation stage. The results showed that the gene expression levels of five genes (GME10392, GME1763, GME860, GME11623, and GME8409) were higher in primordia than in mycelia, whereas the gene expression levels of three genes (GME918, GME8013, and GME2319) in elongation stage were lower than in egg stage. The qRT-PCR results were consistant with the gene expression profile, and inferred that these differential expression homeobox TFs may contribute to morphological formation of the fruiting body of V. volvacea.
(5) The molecular cloning and sequencing results of PCR products illustrated that the sequences of GME918(GenBank accession numbers:JX843776) from strains PYd15and PYd21were identical. About26million high-quality reads and2,408,000,220nt nucleotides from transcriptome sequencing. Of them,3,632reads could map to the reference sequence in analysis of gene structure of GME918. GME918spanned2856bp including an open reading frame of1149bp, and composed four exons and three introns. In addition, the alternative splicing in the first intron was found in studying the gene structure.
(6) RNAi vector of GME918was constructed according to its conserved domain. It was evaluated by using polymerse chain reaction (PCR) and restriction enzyme digestion. Moreover, it was transform to V. volvacea strain H1521by Agrobacterium tumefaciens. The results showed that the colonial morphology and mycelial growth rate of transformant changed significantly. Therefore, the results indicate that transcription factor GME918could regulate the colonial morphology and mycelial growth rate of V. volvacea.
(1)草菇基因组通过与真菌转录因子数据库进行比对,共鉴定出214个转录因子,分属于30个转录因子家族。
(2)根据同源比对,分析转录因子在不同担子菌和子囊菌中的保守性,比对的真菌包括草菇(V. volvacea),裂褶菌(Schizophyllum commune),双色蜡磨(Laccaria bicolor),灰盖鬼伞(Coprinopsis cinerea),黑粉菌(Ustilago maydis),酿酒酵母(Saccharomyces cerevisiae),瑞氏木霉(Trichoderma reesei),粗糙脉孢菌(Neurospora crassa)和构巢曲霉(Aspergillus nidulans)。比对结果显示草菇中62.6%的转录因子与其他8种真菌具有同源性,其中37%的转录因子只在草菇基因组中有同源基因,46%的转录因子在所比对的担子菌中有同源基因,而仅有16%的转录因子在担子菌和子囊菌中具有同源性,因此,不同真菌间,尤其是担子菌和子囊菌之间,转录因子的同源性很低。虽然转录因子的氨基酸序列不是很保守,但是转录因子绑定DNA的区域却很保守。
(3)分别比较异核菌丝体和原基,蛋形期和伸长期的基因表达量。从异核菌丝体到原基,共得到1503个差异表达基因,其中877个上调表达,626个下调表达；而从蛋形期到伸长期,共得到1367差异表达基因,其中1004个下调表达,仅有363个上调表达。通过对异核菌丝体和原基,蛋形期和伸长期的功能富集研究表明,相较于异核菌丝体,在原基期上调表达的主要功能为对生物的调节作用,主要表现在对细胞和代谢过程的调节,而在原基期下调表达的基因参与的主要生物过程为细胞组分的生物合成和多细胞生物过程。相反,相较于蛋形期,在伸长期下调表达的基因功能主要为对细胞组分以及细胞过程的调节作用,而参与多细胞生物过程则在伸长期上调表达。通过对差异表达基因的功能富集分析,发现调节基因表达的基因在子实体的形成过程中发挥着至关重要的作用。此外,研究还发现14%在原基期和伸长期差异表达的转录因子属于同源异形框家族的转录因子,因此,推测同源异形框转录因子在这两个发育阶段发挥着重要的调节作用。
(4)通过差异表达分析,共得到8个差异表达的同源异形框转录因子,其中有5个(GME10392, GME1763, GME860, GME11623和GME8409)在原基期上调表达,有3个(GME918, GME8013和GME2319)在伸长期下调表达,并且荧光定量结果(qRT-PCR)与表达谱的结果一致,这些差异表达的同源异形框转录因子很可能与子实体的形态建成有关。
(5)克隆测序结果显示,GME918(GenBank accession numbers:JX843776)在两个同核菌丝体PYd15和PYd21中的DNA序列完全相同。通过转录组测序,共得到约2600万个高质量的reads和2,408,000,220nt核苷酸,其中有3,632个reads可以定位到GME918上。通过转录组数据,分析GME918的基因结构,结果显示,GME918全长为2856bp,开放阅读框为1149bp,由四个外显子和三个内含子组成,并且在第一个内含子中存在可变剪切现象。
(6)根据GME918的保守结构域,构建其RNAi载体,经过PCR和酶切验证,证明已经成功构建了GME918的RNAi载体,并通过农杆菌介导的方法将其转化到草菇H1521中,发现经RNAi后的转化子在菌落形态和菌丝生长速度方面都发生了明显变化,因此,试验结果表明GME918对菌落的形态发生和菌丝生长具有重要的调节作用。
The Chinese mushroom, Volvariella volvacea (Bull.:Fr.) Singer, is a tropical and subtropical saprophytic fungus in the family Pluteaceae of the Basidiomycota. The lifecycle of V. volvacea is a complex process that involves a cascade of morphological events in fruiting body development. Several genes are responsible for regulation and control of the morphogenesis of V. volvacea fruiting body formation. In fact, the market value of V. volvacea was limited as difficult to storage and preservation that the short lifecycle resulted in the pileus-opening. The differentially expressed genes were obtained by comparing the gene expression level between two periods, from mycelia to primordia and from egg stage to elongation stage, respectively. Moreover, to identify the transcription factors of V. volvacea involved in primordia formation and stipe elongation, enrichment analysis of functional annotation for the expression profiles were performed. It could provide fundamental basis for functional verification and application in production that the preservation of V. volvacea was prolongated by using gene modification. The mainly results as follow:
(1) In the present work,214putative transcription factors (TFs) belong to30transcription factor families were identified from the genome of V. volvacea via the pipeline of fungal transcription factor database (FTFD).
(2) Compared the conservation of the TFs in different basidiomycetes and ascomycetes fungi, including V. volvacea, Schizophyllum commune, Laccaria bicolor, Coprinopsis cinerea, Ustilago maydis, Saccharomyces cerevisiae, Trichoderma reesei, Neurospora crassa, Aspergillus nidulans, by homology alignment. The results showed that62.6%transcription factors have homology with other eight fungi,37%is specific for V. volvacea, and46%is specific for basidiomycetes fungi. In addition, only16%transcription factors have homology in basidiomycetes and ascomycetes fungi. Therefore, the homology of transcription factors was low between basidiomycetes and ascomycetes fungi. However, the conserved domain of transcription factors among them is similar, although the whole amino acid sequences of transcription factors were not conserved.
(3) To identify the differentially expressed genes in primordia and elongation stage,1503and1367differentially expressed genes were obtained by comparing the gene expression level between two periods, from mycelia to primordia and from egg stage to elongation stage, respectively. Of them,877and626genes were up-regulated and down-regulated expression from mycelia to primordia, respectively. Nevertheless, there have1004genes down-regulated expression, only363genes up-regulated, from egg stage to elongation stage. The enrichment analysis of functional annotation for the expression profiles of the developmental stages defined by mycelia, primordia, egg stage and elongation stage was performed. Functional terms involved in regulation of cellular process and metabolic process, were over-represented in genes up-regulated of primordia. Genes involved in cellular component biogenesis, anatomical structure formation and multicellular organismal process were enriched in the group of genes down-regulated of primordia. However, functional terms involved in regulation of cellular component organization and of cellular process were enriched in the down-regulated genes of elongation stage. Genes encoding anatomical structure formation, multi-organnism process were enriched in the group of genes up-regulated of elongation stage. The enrichment analysis of functional annotation illustrated that the regulation of gene expression played a crucial role in the formation of fruiting body based on the different expression analysis. We found that14%differentially expressed TFs belong to homeobox family in primordia and elongation stage. It may be paly more important role in these processes.
(4) By the differential expression analysis as above mention,8differentially expressed homeobox TFs were obtained, including5up-regulated expressed in the primordia and3down-regulated expressed in the elongation stage of V. volvacea. In fact, quantitative real-time PCR (qRT-PCR) was used to analyze gene expression value in mycelia, primordia, egg stage, elongation stage. The results showed that the gene expression levels of five genes (GME10392, GME1763, GME860, GME11623, and GME8409) were higher in primordia than in mycelia, whereas the gene expression levels of three genes (GME918, GME8013, and GME2319) in elongation stage were lower than in egg stage. The qRT-PCR results were consistant with the gene expression profile, and inferred that these differential expression homeobox TFs may contribute to morphological formation of the fruiting body of V. volvacea.
(5) The molecular cloning and sequencing results of PCR products illustrated that the sequences of GME918(GenBank accession numbers:JX843776) from strains PYd15and PYd21were identical. About26million high-quality reads and2,408,000,220nt nucleotides from transcriptome sequencing. Of them,3,632reads could map to the reference sequence in analysis of gene structure of GME918. GME918spanned2856bp including an open reading frame of1149bp, and composed four exons and three introns. In addition, the alternative splicing in the first intron was found in studying the gene structure.
(6) RNAi vector of GME918was constructed according to its conserved domain. It was evaluated by using polymerse chain reaction (PCR) and restriction enzyme digestion. Moreover, it was transform to V. volvacea strain H1521by Agrobacterium tumefaciens. The results showed that the colonial morphology and mycelial growth rate of transformant changed significantly. Therefore, the results indicate that transcription factor GME918could regulate the colonial morphology and mycelial growth rate of V. volvacea.
引文
[I]Chang S T, Yau C K. Volvariella volvacea and its life history[J]. American Journal of Botany,1971, 552-561.
[2]Chang S T, Chu S S. Nuclear Behaviour in the Basidium of Volvariella volvacea[J]. Cytologia,1969,34: 293-299.
[3]张树庭,林芳灿.蕈菌遗传与育种[M].北京：中国农业出版社,1997.
[4]傅俊生.草菇遗传规律研究[D].福建：福建农林大学,2010.
[5]Botas J. Control of morphogenesis and differentiation by HOM/Hox genes[J]. Current opinion in cell biology,1993,5:1015-1022.
[6]Jackson D, Veit B, Hake S. Expression of maize KNOTTED1 related homeobox genes in the shoot apical meristem predicts patterns of morphogenesis in the vegetative shoot[J]. Development,1994,120: 405-413.
[7]Kim G T, Shoda K, Tsuge T, Cho K H, Uchimiya H, et al. The ANGUSTIFOLIA gene of Arabidopsis, a plant CtBP gene, regulates leaf-cell expansion, the arrangement of cortical microtubules in leaf cells and expression of a gene involved in cell-wall formation[J]. Science Signalling,2002,21:1267.
[8]Hroudova M, Vojta P, Strnad H, Krejcik Z, Ridl J, et al. Diversity, Phylogeny and Expression Patterns of Pou and Six Homeodomain Transcription Factors in Hydrozoan Jellyfish Craspedacusta sowerbyi[J]. PloS one,2012,7:e36420.
[9]Kues U. Life history and developmental processes in the basidiomycete Coprinus cinereus[J]. Microbiol Mol Biol,2000,64:316-353.
[10]Yasumasa Miyazaki MN, Katsuhiko Babasaki. Molecular cloning of developmentally specific genes by representational difference analysis during the fruiting body formation in the basidiomycete Lentinula edodes[J]. Fungal Genetics and Biology,2005,42:493-505.
[11]Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, et al. Genome sequence of the model mushroom Schizophyllum commune[J]. Nature Biotechnology,2010,28:957-U910.
[12]Ohm R A, de Jong J F, de Bekker C, Wosten H A B, Lugones L G. Transcription factor genes of Schizophyllum commune involved in regulation of mushroom formation[J]. Molecular Microbiology, 2011,81:1433-1445.
[13]Scott M P, Weiner A J. Structural relationships among genes that control development:sequence homology between the Antennapedia, Ultrabithorax, and fushi tarazu loci of Drosophila[J]. Proceedings of the National Academy of Sciences,1984,81:4115-4119.
[14]McGinnis W, Levine M, Hafen E, Kuroiwa A, Gehring W. A conserved DNA sequence in homoeotic genes of the Drosophila antennapedia and bithorax complexes[J]. Nature,1984,308:428.
[15]Gehring W. Homeo boxes in the study of development[J]. Science,1987,236:1245-1252.
[16]Banerjee-Basu S, Baxevanis A D. Molecular evolution of the homeodomain family of transcription factors[J]. Nucleic acids research,2001,29:3258-3269.
[17]Bender W, Lucas M. The Border between the Ultrabithorax and abdominal-A Domains in the Drosophila Bithorax Complex[J]. Genetics,2013, doi:10.1534/genetics.112.146340.
[18]Furlong R F, Younger R, Kasahara M, Reinhardt R, Thorndyke M, et al. A degenerate ParaHox gene cluster in a degenerate vertebrate[J]. Molecular biology and evolution,2007,24:2681-2686.
[19]Hroudova M, Vojta P, Strnad H, Krejcik Z, Ridl J, et al. Diversity, Phylogeny and Expression Patterns of Pou and Six Homeodomain Transcription Factors in Hydrozoan Jellyfish Craspedacusta sowerbyi [J]. PLoS ONE,2012,7:e36420.
[20]Hay A, Tsiantis M. KNOX genes:versatile regulators of plant development and diversity[J]. Development,2010,137:3153-3165.
[21]Hake S, Char B R, Chuck G, Foster T, Long J, et al. Homeobox genes in the functioning of plant meristems[J]. Philosophical Transactions of the Royal Society of London Series B:Biological Sciences,1995,350:45-51.
[22]Long J A, Moan E I, Medford J I, Barton M K. A member of the KNOTTED class of homeodomain proteins encoded by the STM gene of Arabidopsis[J]. Nature,1996,379:66-69.
[23]Belles-Boix E, Hamant O, Witiak S M, Morin H, Traas J, et al. KNAT6:An Arabidopsis homeobox gene involved in meristem activity and organ separation[J]. The Plant Cell Online,2006,18:1900-1907.
[24]Byrne M E, Simorowski J, Martienssen RA. ASYMMETRIC LEAVES1 reveals knox gene redundancy in Arabidopsis[J]. Development,2002,129:1957-1965.
[25]Dockx J, Quaedvlieg N, Keultjes G, Kock P, Weisbeek P, et al. The homeobox gene ATK1 of Arabidopsis thaliana is expressed in the shoot apex of the seedling and in flowers and inflorescence stems of mature plants[J]. Plant molecular biology,1995,28:723-737.
[26]Kues U, Richardson W, Tymon AM, Mutasa ES, Gottgens B, et al. The combination of dissimilar alleles of the A alpha and A beta gene complexes, whose proteins contain homeo domain motifs, determines sexual development in the mushroom Coprinus cinereus[J]. Genes & development,1992,6: 568-577.
[27]Kim S, Park S Y, Kim K S, Rho H S, Chi M H, et al. Homeobox transcription factors are required for conidiation and appressorium development in the rice blast fungus Magnaporthe oryzae[J].PLoS genetics,2009,5:e1000757.
[28]Ohm R A, de Jong J F, Lugones L G, Aerts A, Kothe E, et al. Genome sequence of the model mushroom Schizophyllum commune[J]. Nature biotechnology,2010,28:957-963.
[29]Ohm R A, de Jong J F, de Bekker C, Wosten HA, Lugones LG Transcription factor genes of Schizophyllum commune involved in regulation of mushroom formation[J]. Molecular microbiology, 2011,81:1433-1445.
[30]Antal Z, Rascle C, Cimerman A, Viaud M, Billon-Grand G, et al. The Homeobox BcHOX8 Gene in Botrytis Cinerea Regulates Vegetative Growth and Morphology[J]. PLoS ONE,2012,7:e48134.
[31]Torres-Guzman JC, Dominguez A. HOY1, a homeo gene required for hyphal formation in Yarrowia lipolytica[J]. Molecular and cellular biology,1997,17:6283-6293.
[32]Coppin E, Berteaux-Lecellier V, Bidard F, Brun S, Ruprich-Robert G, et al. Systematic deletion of homeobox genes in Podospora anserina uncovers their roles in shaping the fruiting body[J]. PloS one, 2012,7:e37488.
[33]Arnaise S, Zickler D, Poisier C, Debuchy R. pahl:a homeobox gene involved in hyphal morphology and microconidiogenesis in the filamentous ascomycete Podospora anserina[J]. Mol Microbiol,2001,39: 54-64.
[34]Kim S, Park S Y, Kim K S, Rho H S, Chi M H, et al. Homeobox Transcription Factors Are Required for Conidiation and Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae[J]. PLoS Genet,2009,5:e1000757.
[35]Liu W, Xie S, Zhao X, Chen X, Zheng W, et al. A homeobox gene is essential for conidiogenesis of the rice blast fungus Magnaporthe oryzae[J]. Molecular plant-microbe interactions,2010,23:366-375.
[36]Kim J Y, Kwon E S, Roe J H. A homeobox protein Phxl regulates long-term survival and meiotic sporulation in Schizosaccharomyces pombe[J]. BMC Microbiology,2012,12:86.
[37]Coppin E, Berteaux-Lecellier V, Bidard F, Brun S, Ruprich-Robert G, et al. Systematic Deletion of Homeobox Genes in Podospora anserina Uncovers Their Roles in Shaping the Fruiting Body[J]. PLoS ONE,2012,7:e37488.
[38]Colot H V, Park G, Turner G E, Ringelberg C, Crew C M, et al. A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors[J]. Proceedings of the National Academy of Sciences,2006,103:10352-10357.
[39]Brown A J, Casselton L A. Mating in mushrooms:increasing the chances but prolonging the affair[J]. TRENDS in Genetics,2001,17:393-400.
[40]Zheng W, Zhao X, Xie Q, Huang Q, Zhang C, et al. A Conserved Homeobox Transcription Factor Htfl Is Required for Phialide Development and Conidiogenesis in Fusarium Species[J]. PLoS ONE,2012,7: e45432.
[41]Jason E. Stajich S K W, Dag Ahrenf, Chun Hang Aug, Bruce W. Birrenh, Mark Borodovskyi, Claire Burnsj,, Bjorn Canbackf LAC, C.K. Chengg, Jixin Denge, Fred S. Dietrichd, David C. Fargom, Mark L. Farmann, Allen C. Gathmano JG, Roderic Guigop, Patrick J. Hoeggerq, James B. Hookere, Ashleigh Hugginse, Timothy Y. Jamesr T K, Sreedhar Kilaruq, Chinnapa Kodirah, Ursula Kuesq, Doris Kupfert, H.S. Kwang, Alexandre Lomsadzei WL, Walt W. Lillyo, Li-Jun Mah, Aaron J. Mackeyu, Gerard Manningv, Francis Martinw, et al. Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinerens) [J]. PNAS,2010,107:11889-11894.
[42]Linder M B S G, Nakari-Setala T, Penttila M E. Hydrophobins:the protein-amphiphiles of filamentous fungi[J]. FEMS Microbiol Rev,2005,29:877-896.
[43]Sunde M K A, Templeton M D, Beever R E, Mackay J P. Structural analysis of hydrophobins[J]. Micron, 2008,39:773-784.
[44]Bell-Pedersen D D J, Loros J J. The Neurospora circadian clock-controlled gene, ccg-2, is allelic to eas and encodes a fungal hydrophobin required for formation of the conidial rodlet layer[J]. Genes Dev, 1992,6:2382-2394.
[45]Ma H S L, Tian C, Kaminskyj S G W, Dahms T E S. Fungal surface remodelling visualized by atomic force microscopy[J]. Mycol Res,2006,110:879-886.
[46]Wessels J G H. Hydrophobins, unique fungal proteins[J]. Mycologist,2000,14.
[47]Talbot N J, Kershaw, M J, Wakley, G E, deVries, O M H, Wessels, J G H, Hamer, J E. MPG1 encodes a fungal hydrophobin involved in surface interactions during infection-related development of Magnaporthe grisea[J]. Plant Cell,1996,8:985-999.
[48]WSsten H A B. Hydrophobins:multipurpose proteins[J]. Ann Rev Microbiol,2001,55:625-646.
[49]Wosten H A B, vanWetter, M A, Lugones, L G, van der Mei, H C, Busscher, H J, Wessels, J G H. How a fungus escapes the water to grow into the air[J]. Curr Biol,1999,9:85-88.
[50]Kershaw M J T N. Hydrophobins and repellents:proteins with fundamental roles in fungal morphogenesis[J]. Fungal Genet Biol,1998,23:18-33.
[51]Ma A S L, Wang N, Zheng L, Chen L, Xie B. Characterization of a Pleurotus ostreatus fruiting body-specific hydrophobin gene[J], Po.hyd. J Basic Microbiol,2007,47:317-324.
[52]Penas M M R B, Larraya L M, Ramirez L, Pisabarro A G. Differentially regulated, vegetative-mycelium-specific hydrophobins of the edible basidiomycete Pleurotus ostreatus[J]. Appl Environ Microbiol,2002,68:3891-3898.
[53]Van Wetter, M A W H, Wessels, J G H. SC3 and SC4 hydrophobins have distinct roles in formation of aerial structures in dikaryons of Schizophyllum commune[J]. Mol Microbiol,2000,36:201-210.
[54]Hamer J E T N. Infection-related development in the rice blast fungus Magnaporthe grisea[J]. Curr Opin Microbiol,1998,1:693-697.
[55]Lugones L G W H, Birkenkamp K U, Sjollema K A, Zagers J, Wessels J G H. Hydrophobins line air channels in fruiting bodies of Schizophyllum commune and Agaricus bisporus[J]. Mycol Res,1999, 103:635-640.
[56]Whiteford J R S P. Hydrophobins and the interactions between fungi and plants[J]. Mol Plant Pathol, 2002,3:391-400.
[57]van den Brink H, van Gorcom R F, van den Hondel C A, Punt P J. Cytochrome P450 enzyme systems in fungi[J]. Fungal Genetics and Biology,1998,23:1-17.
[58]Nadeau J A, Zhang X S, Li J, O'Neill S D. Ovule development:identification of stage-specific and tissue-specific cDNAs[J]. The Plant Cell Online,1996,8:213-239.
[59]Kim G T, Tsukaya H, Uchimiya H. The ROTUNDIFOLIA3 gene of Arabidopsis thaliana encodes a new member of the cytochrome P-450 family that is required for the regulated polar elongation of leaf cells[J]. Genes & development,1998,12:2381-2391.
[60]Winkler RG, Helentjaris T. The maize Dwarf3 gene encodes a cytochrome P450-mediated early step in Gibberellin biosynthesis[J]. The Plant Cell Online,1995,7:1307-1317.
[61]Szekeres M, Nemeth K, Koncz-Kalman Z, Mathur J, Kauschmann A, et al. Brassinosteroids rescue the deficiency of CYP90, a cytochrome P450, controlling cell elongation and de-etiolation in Arabidopsis[J]. Cell,1996,85:171-182.
[62]Kamada T, Takemaru T. Stipe elongation during basidiocarp maturation in Coprinus macrorhizus: mechanical properties of stipe cell wall[J]. Plant and cell physiology,1977,18:831-840.
[63]Muraguchi H, Kamada T. A Mutation in the eln2 Gene Encoding a Cytochrome P450 of Coprinus cinereus Affects Mushroom Morphogenesis[J]. Fungal Genetics and Biology,2000,29:49-59.
[64]Akiyama R, Sato Y, Kajiwara S, Shishido K. Cloning and expression of cytochrome P450 genes, belonging to a new P450 family, of the basidiomycete Lentinula edodes[J]. Bioscience, biotechnology, and biochemistry,2002,66:2183-2188.
[65]Kues U J D, Granado K, Kertesz-Chaloupkova' P J, Walser M, Hollenstein E, Polak Y, Liu R P, Boulianne A P F, Bottoli, M. Aebi. Mating types and light are major regulators of development in Coprinus cinereus[M]; In L. J. L. D. Van Griensven and J. Visser (ed.) PotFMotGaCBoB, editor: Mushroom Experimental Station, Horst, The Netherlands.1998,113-118.
[66]Uno I, and Ishikawa T. Effect of glucose on the fruiting body formation and adenosine 3',5'-cyclic monophosphate levels in Coprinus macrorhizus[J]. J Bacteriol,1974,120:96-100.
[67]Uno I, Yamaguchi M, and Ishikawa T. The effect of light on fruiting body formation and adenosine 3',5 cyclic monophosphate metabolism in Coprinus macrorhizus[J]. Proc Natl Acad Sci,1974,71: 479-483.
[68]Elgavish S, Shaanan B. Lectin-carbohydrate interactions:different folds, common recognition principles[J]. Trends in biochemical sciences,1997,22:462-467.
[69]Coulet M, Mustier J, Guillot J. Les hemagglutinines des champignons[J]. Rev Mycologie,1970,35:71.
[70]Liener I E, Sharon N, Goldstein I J. The lectins:properties, functions, and applications in biology and medicine[M]. Academic Press,1986.
[71]Kocourek J, Horejsi V. A Note on the Recent Discussion on Definition of the Term "Lectin"[J]. Lectins: Biology, biochemistry, clinical biochemistry,1983,3:3-6.
[72]Banerjee P, Ghosh A, Sengupta S. Hemagglutinating activity in extracts of mycelia from submerged mushroom cultures[J]. Applied and Environmental Microbiology,1982,44:1009-1011.
[73]Konska G Lectins of Higher Fungi (Macromycetes)-their Occurrence, Physiological Role, and Biological Activity[J]. International Journal of Medicinal Mushrooms,2006,8:19-30.
[74]Ticha M, Dudova V, Kocourek J, Volc J. Studies on lectins. LXII. A nonspecific erythroagglutinating lectin and a blood-group A specific lectin in the mushroom Agrocybe aegerita (Brig.) Sing. Lectins-Biology, Biochemistry, Clinical Biochemistry,1985,4:505-514.
[75]Tsivileva O M, Nikitina V E, Garibova L V, Ignatov V V. Lectin activity of Lentinus edodes[J]. IntMicrobiol,2001,4:41-45.
[76]Schubert W J. Lignin biochemistryp[M].1965.
[77]Leonard T J, Phillips L E. Study of phenoloxidase activity during the reproductive cycle in Schizophyllum commune[J]. Journal of bacteriology,1973,114:7-10.
[78]Wood D. Production, purification and properties of extracellular laccase of Agaricus bisporus[J]. Journal of General Microbiology,1980,117:327-338.
[79]Esser K. Phenol oxidases and morphogenesis in Podospora anserina[J].Genetics,1968,60:281.
[80]Wong A, Willetts H. Polyacrylamide-gel electrophoresis of enzymes during morphogenesis of sclerotia of Sclerotinia sclerotiorum[J]. Journal of General Microbiology,1974,81:101-109.
[81]Daniel J. Metabolism of phenolic precursor of a myxomycete spore pigment[J]. Journal of Cell Biology, 1963,19:18-19.
[82]Leonard T J. Phenoloxidase Activity and Fruiting Body Formation in Schizophyllum commune[J]. Journal of Bacteriology,1971,106:162-167.
[83]Kues U, Liu Y. Fruiting body production in basidiomycetes[J]. Applied Microbiology and Biotechnology, 2000,54(2):141-152.
[84]Kamada T, Sano H, Nakazawa T, Nakahori K. Regulation of fruiting body photomorphogenesis in Coprinopsis cinerea[J]. Fungal Genetics and Biology,2010,47:917-921.
[85]Carlile M. The photoresponses of fungi[J]. Photobiology of microorganisms,1970,309-344.
[86]Tan K. Light-induced fungal development[J]. The filamentous fungi,1978,3:334-357.
[87]Elliott C G, Maheshwari R. Reproduction in fungi:genetical and physiological aspects[J]. Journal of Genetics,1994,73:55.
[88]Kihara J, Kumagai T. Ecotypes of the fungus Bipolaris oryzae with various responses of the mycochrome system[J]. Physiologia Plantarum,1994,92:689-695.
[89]Chebotarev L, Zemlyanukhin A. Effect of visible light and ultraviolet rays on the activity of oxidation enzymes in molds[J]. Microbiology (Mikrobiologiya),1973,42:196.
[90]Cohen R J. Cyclic A M P levels in Phycomyces during a response to light[J]. Nature,1974,251:144-146.
[91]Graafmans W. Effect of blue light on metabolism in Penicillium isariiforme[J]. Journal of General Microbiology,1977,101:157-161.
[92]Linden H. A white collar protein senses blue light[J]. Science,2002,297:777-778.
[93]Dunlap J C. Proteins in the Neurospora circadian clockworks[J]. J Biol Chem,2006,281:28489-28493.
[94]Corrochano L M. Fungal photoreceptors:sensory molecules for fungal development and behaviour[J]. Photochem Photobiol Sci,2007,6:725-736.
[95]Ballario P, Vittorioso P, Magrelli A, Talora C, Cabibbo A, Macino G. White collar-1, a central regulator of blue light responses in Neurospora, is a zinc finger protein[J]. EMBO J,1996,15:1650-1657.
[96]Moore-Landecker E. Physiology and biochemistry of ascocarp induction and development[J]. Mycological Research,1992,96:705-716.
[97]Chang S T, Hayes W A. The Biology and cultivation of edible mushrooms[M].1978.
[98]Moore D. Fungal morphogenesis[M]. Cambridge University Press.2003.
[99]Flegg P B W D. Growth and fruiting[M]. Glegg P B S D, Wood D A, editor. Wiley, London:The biology and technology of the cultivated mushroom.1985.
[100]Niederpruem D J. Role of carbon dioxide in the control of fruiting of Schizophyllum commune[J]. Journal of Bacteriology,1963,85:1300-1308.
[101]Lambert E B. Effect of excess carbon dioxide on growing mushrooms[M]. US Government Printing Office.1933.
[102]Turner E M. Development of excised sporocarps of Agaricus bisporus and its control by CO2 [J]. Transactions of the British Mycological Society,1977,69:183-186.
[103]Berget S M, Moore C, Sharp P A. Spliced segments at the 5'terminus of adenovirus 2 late mRNA[J]. Proceedings of the National Academy of Sciences,1977,74:3171-3175.
[104]Chow L T, Gelinas R E, Broker T R, Roberts R J. An amazing sequence arrangement at the 5' ends of adenovirus 2 messenger RNA[J]. Cell,1977,12:1-8.
[105]Nakayashiki H, Hanada S, Quoc N B, Kadotani N, Tosa Y, et al. RNA silencing as a tool for exploring gene function in ascomycete fungi[J]. Fungal Genetics and Biology,2005,42:275-283.
[106]Napoli C, Lemieux C, Jorgensen R. Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans[J]. The Plant Cell Online,1990,2: 279-289.
[107]Romano N, Macino G Quelling:transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences[J]. Molecular microbiology,1992,6:3343-3353.
[108]Elbashir S M, Lendeckel W, Tuschl T. RNA interference is mediated by 21-and 22-nucleotide RNAs[J]. Genes & development,2001,15:188-200.
[109]Erik J. Sontheimer and Richard W. Carthew. Argonaute journeys into the heart of RISC[J]. Science, 2004,305:1409-1410.
[110]Li R, Zhu H, Ruan J, Qian W, Fang X, et al. De novo assembly of human genomes with massively parallel short read sequencing[J]. Genome Research,2010,20:265-272.
[111]Ter-Hovhannisyan V, Lomsadze A, Chernoff Y O, Borodovsky M. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training[J]. Genome research,2008,18: 1979-1990.
[112]Park J, Park J, Jang S, Kim S, Kong S, et al. FTFD:an informatics pipeline supporting phylogenomic analysis of fungal transcription factors[J]. Bioinformatics,2008,24:1024-1025.
[113]Galagan J E, Calvo S E, Borkovich K A, Selker E U, Read N D, et al. The genome sequence of the filamentous fungus Neurospora crassa[J]. Nature,2003,422:859-868.
[114]Coradetti S T, Craig J P, Xiong Y, Shock T, Tian C, et al. Conserved and essential transcription factors for cellulase gene expression in ascomycete fungi[J]. Proceedings of the National Academy of Sciences,2012,109:7397-7402.
[115]Kothe E. Mating-type genes for basidiomycete strain improvement in mushroom farming[J]. Applied microbiology and biotechnology,2001,56:602-612.
[116]Kues U, Casselton L A. Homeodomains and regulation of sexual development in basidiomycetes[J]. Trends in genetics:TIG,1992,8:154.
[117]Robertson C I, Bartholomew K A, Novotny C P, Ullrich R C. Deletion of the Schizophyllum commune Aa Locus:The Roles of Aα Y and Z Mating-Type Genes[J]. Genetics,1996,144:1437-1444.
[118]Heitman J. Sex in fungi:molecular determination and evolutionary implications[M]. Amer Society for Microbiology.2007.
[119]Kues U, Asante-Owusu RN, Mutasa ES, Tymon AM, Pardo EH, et al. Two classes of homeodomain proteins specify the multiple a mating types of the mushroom Coprinus cinereus[J]. The Plant Cell Online,1994,6:1467-1475.
[120]Shelest E. Transcription factors in fungi[J]. FEMS microbiology letters,2008,286:145-151.
[121]Fillinger S, Chaveroche M K, Shimizu K, Keller N, D'Enfert C. cAMP and ras signalling independently control spore germination in the filamentous fungus Aspergillus nidulans[J]. Molecular microbiology, 2002,44:1001-1016.
[122]Wei H, Requena N, Fischer R. The MAPKK kinase SteC regulates conidiophore morphology and is essential for heterokaryon formation and sexual development in the homothallic fungus Aspergillus nidulans[J]. Molecular microbiology,2003,47:1577-1588.
[123]Miller K Y, Wu J, Miller B L. StuA is required for cell pattern formation in Aspergillus[J]. Genes& development,1992,6:1770-1782.
[124]Han K H, Han K Y, Yu J H, Chae K S, Jahng K Y, et al. The nsdD gene encodes a putative GATA-type transcription factor necessary for sexual development of Aspergillus nidulans[J]. Molecular microbiology,2001,41:299-309.
[125]Vienken K, Fischer R. The Zn (Ⅱ) 2Cys6 putative transcription factor NosA controls fruiting body formation in Aspergillus nidulans[J]. Molecular microbiology,2006,61:544-554.
[126]Pi H, Chien C T, Fields S. Transcriptional activation upon pheromone stimulation mediated by a small domain of Saccharomyces cerevisiae Stel2p[J], Molecular and cellular biology,1997,17:6410-6418.
[127]Vallim M A, Miller K Y, Miller B L. Aspergillus SteA (Sterile 12-like) is a homeodomain-C2/H2-Zn+2 finger transcription factor required for sexual reproduction[J]. Molecular microbiology,2002,36: 290-301.
[128]Morrissy A S, Morin R D, Delaney A, Zeng T, McDonald H, et al. Next-generation tag sequencing for cancer gene expression profiling[J]. Genome research,2009,19:1825-1835.
[129]AC't Hoen P, Ariyurek Y, Thygesen H H, Vreugdenhil E, Vossen R H, et al. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms[J]. Nucleic acids research,2008,36:el41-e141.
[130]Subramanian A, Tamayo P, Mootha V K, Mukherjee S, Ebert B L, et al. Gene set enrichment analysis:a knowledge-based approach for interpreting genome-wide expression profiles[J]. Proceedings of the National Academy of Sciences of the United States of America,2005,102:15545-15550.
[131]Audic S, Claverie J M. The significance of digital gene expression profiles[J]. Genome research,1997,7: 986-995.
[132]Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency[J]. Annals of statistics,2001,1165-1188.
[133]Thompson J D, Higgins D G, Gibson T J. CLUSTAL W:improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice[J]. Nucleic acids research,1994,22:4673-4680.
[134]Kumar S, Tamura K, Jakobsen I B, Nei M. MEGA2:molecular evolutionary genetics analysis software[J]. Bioinformatics,2001,17:1244-1245.
[135]Saitou N, Nei M. The neighbor-joining method:a new method for reconstructing phylogenetic trees[J]. Molecular biology and evolution,1987,4:406-425.
[136]Apweiler R, Attwood T K, Bairoch A, Birney E, Biswas M, et al. InterPro-an integrated documentation resource for protein families, domains and functional sites[J]. Bioinformatics,2000,16:1145-1150.
[137]Coulson R M, Ouzounis C A. The phylogenetic diversity of eukaryotic transcription[J]. Nucleic acids research,2003,31:653-660.
[138]M6ller E, Bahnweg G, Sandermann H, Geiger H. A simple and efficient protocol for isolation of high molecular weight DNA from filamentous fungi, fruit bodies, and infected plant tissues[J]. Nucleic Acids Research,1992,20:6115.
[139]Gray M, Peacock J, Squires E. Characterization of the porcine constitutive androstane receptor (CAR) and its splice variants[J]. Xenobiotica,2009,39:915-930.
[140]Matlin A J, Clark F, Smith C W. Understanding alternative splicing:towards a cellular code[J]. Nature Reviews Molecular Cell Biology,2005,6:386-398.
[141]Li Q, Lee J A, Black D L. Neuronal regulation of alternative pre-mRNA splicing[J]. Nature Reviews Neuroscience,2007,8:819-831.
[142]Wahl MC, Will CL, Luhrmann R. The spliceosome:design principles of a dynamic RNP machine[J]. Cell,2009,136:701-718.
[143]Kelemen O, Convertini P, Zhang Z, Wen Y, Shen M, et al. Function of alternative splicing[J]. Gene, 2013,514:1-30.
[2]Chang S T, Chu S S. Nuclear Behaviour in the Basidium of Volvariella volvacea[J]. Cytologia,1969,34: 293-299.
[3]张树庭,林芳灿.蕈菌遗传与育种[M].北京：中国农业出版社,1997.
[4]傅俊生.草菇遗传规律研究[D].福建：福建农林大学,2010.
[5]Botas J. Control of morphogenesis and differentiation by HOM/Hox genes[J]. Current opinion in cell biology,1993,5:1015-1022.
[6]Jackson D, Veit B, Hake S. Expression of maize KNOTTED1 related homeobox genes in the shoot apical meristem predicts patterns of morphogenesis in the vegetative shoot[J]. Development,1994,120: 405-413.
[7]Kim G T, Shoda K, Tsuge T, Cho K H, Uchimiya H, et al. The ANGUSTIFOLIA gene of Arabidopsis, a plant CtBP gene, regulates leaf-cell expansion, the arrangement of cortical microtubules in leaf cells and expression of a gene involved in cell-wall formation[J]. Science Signalling,2002,21:1267.
[8]Hroudova M, Vojta P, Strnad H, Krejcik Z, Ridl J, et al. Diversity, Phylogeny and Expression Patterns of Pou and Six Homeodomain Transcription Factors in Hydrozoan Jellyfish Craspedacusta sowerbyi[J]. PloS one,2012,7:e36420.
[9]Kues U. Life history and developmental processes in the basidiomycete Coprinus cinereus[J]. Microbiol Mol Biol,2000,64:316-353.
[10]Yasumasa Miyazaki MN, Katsuhiko Babasaki. Molecular cloning of developmentally specific genes by representational difference analysis during the fruiting body formation in the basidiomycete Lentinula edodes[J]. Fungal Genetics and Biology,2005,42:493-505.
[11]Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, et al. Genome sequence of the model mushroom Schizophyllum commune[J]. Nature Biotechnology,2010,28:957-U910.
[12]Ohm R A, de Jong J F, de Bekker C, Wosten H A B, Lugones L G. Transcription factor genes of Schizophyllum commune involved in regulation of mushroom formation[J]. Molecular Microbiology, 2011,81:1433-1445.
[13]Scott M P, Weiner A J. Structural relationships among genes that control development:sequence homology between the Antennapedia, Ultrabithorax, and fushi tarazu loci of Drosophila[J]. Proceedings of the National Academy of Sciences,1984,81:4115-4119.
[14]McGinnis W, Levine M, Hafen E, Kuroiwa A, Gehring W. A conserved DNA sequence in homoeotic genes of the Drosophila antennapedia and bithorax complexes[J]. Nature,1984,308:428.
[15]Gehring W. Homeo boxes in the study of development[J]. Science,1987,236:1245-1252.
[16]Banerjee-Basu S, Baxevanis A D. Molecular evolution of the homeodomain family of transcription factors[J]. Nucleic acids research,2001,29:3258-3269.
[17]Bender W, Lucas M. The Border between the Ultrabithorax and abdominal-A Domains in the Drosophila Bithorax Complex[J]. Genetics,2013, doi:10.1534/genetics.112.146340.
[18]Furlong R F, Younger R, Kasahara M, Reinhardt R, Thorndyke M, et al. A degenerate ParaHox gene cluster in a degenerate vertebrate[J]. Molecular biology and evolution,2007,24:2681-2686.
[19]Hroudova M, Vojta P, Strnad H, Krejcik Z, Ridl J, et al. Diversity, Phylogeny and Expression Patterns of Pou and Six Homeodomain Transcription Factors in Hydrozoan Jellyfish Craspedacusta sowerbyi [J]. PLoS ONE,2012,7:e36420.
[20]Hay A, Tsiantis M. KNOX genes:versatile regulators of plant development and diversity[J]. Development,2010,137:3153-3165.
[21]Hake S, Char B R, Chuck G, Foster T, Long J, et al. Homeobox genes in the functioning of plant meristems[J]. Philosophical Transactions of the Royal Society of London Series B:Biological Sciences,1995,350:45-51.
[22]Long J A, Moan E I, Medford J I, Barton M K. A member of the KNOTTED class of homeodomain proteins encoded by the STM gene of Arabidopsis[J]. Nature,1996,379:66-69.
[23]Belles-Boix E, Hamant O, Witiak S M, Morin H, Traas J, et al. KNAT6:An Arabidopsis homeobox gene involved in meristem activity and organ separation[J]. The Plant Cell Online,2006,18:1900-1907.
[24]Byrne M E, Simorowski J, Martienssen RA. ASYMMETRIC LEAVES1 reveals knox gene redundancy in Arabidopsis[J]. Development,2002,129:1957-1965.
[25]Dockx J, Quaedvlieg N, Keultjes G, Kock P, Weisbeek P, et al. The homeobox gene ATK1 of Arabidopsis thaliana is expressed in the shoot apex of the seedling and in flowers and inflorescence stems of mature plants[J]. Plant molecular biology,1995,28:723-737.
[26]Kues U, Richardson W, Tymon AM, Mutasa ES, Gottgens B, et al. The combination of dissimilar alleles of the A alpha and A beta gene complexes, whose proteins contain homeo domain motifs, determines sexual development in the mushroom Coprinus cinereus[J]. Genes & development,1992,6: 568-577.
[27]Kim S, Park S Y, Kim K S, Rho H S, Chi M H, et al. Homeobox transcription factors are required for conidiation and appressorium development in the rice blast fungus Magnaporthe oryzae[J].PLoS genetics,2009,5:e1000757.
[28]Ohm R A, de Jong J F, Lugones L G, Aerts A, Kothe E, et al. Genome sequence of the model mushroom Schizophyllum commune[J]. Nature biotechnology,2010,28:957-963.
[29]Ohm R A, de Jong J F, de Bekker C, Wosten HA, Lugones LG Transcription factor genes of Schizophyllum commune involved in regulation of mushroom formation[J]. Molecular microbiology, 2011,81:1433-1445.
[30]Antal Z, Rascle C, Cimerman A, Viaud M, Billon-Grand G, et al. The Homeobox BcHOX8 Gene in Botrytis Cinerea Regulates Vegetative Growth and Morphology[J]. PLoS ONE,2012,7:e48134.
[31]Torres-Guzman JC, Dominguez A. HOY1, a homeo gene required for hyphal formation in Yarrowia lipolytica[J]. Molecular and cellular biology,1997,17:6283-6293.
[32]Coppin E, Berteaux-Lecellier V, Bidard F, Brun S, Ruprich-Robert G, et al. Systematic deletion of homeobox genes in Podospora anserina uncovers their roles in shaping the fruiting body[J]. PloS one, 2012,7:e37488.
[33]Arnaise S, Zickler D, Poisier C, Debuchy R. pahl:a homeobox gene involved in hyphal morphology and microconidiogenesis in the filamentous ascomycete Podospora anserina[J]. Mol Microbiol,2001,39: 54-64.
[34]Kim S, Park S Y, Kim K S, Rho H S, Chi M H, et al. Homeobox Transcription Factors Are Required for Conidiation and Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae[J]. PLoS Genet,2009,5:e1000757.
[35]Liu W, Xie S, Zhao X, Chen X, Zheng W, et al. A homeobox gene is essential for conidiogenesis of the rice blast fungus Magnaporthe oryzae[J]. Molecular plant-microbe interactions,2010,23:366-375.
[36]Kim J Y, Kwon E S, Roe J H. A homeobox protein Phxl regulates long-term survival and meiotic sporulation in Schizosaccharomyces pombe[J]. BMC Microbiology,2012,12:86.
[37]Coppin E, Berteaux-Lecellier V, Bidard F, Brun S, Ruprich-Robert G, et al. Systematic Deletion of Homeobox Genes in Podospora anserina Uncovers Their Roles in Shaping the Fruiting Body[J]. PLoS ONE,2012,7:e37488.
[38]Colot H V, Park G, Turner G E, Ringelberg C, Crew C M, et al. A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors[J]. Proceedings of the National Academy of Sciences,2006,103:10352-10357.
[39]Brown A J, Casselton L A. Mating in mushrooms:increasing the chances but prolonging the affair[J]. TRENDS in Genetics,2001,17:393-400.
[40]Zheng W, Zhao X, Xie Q, Huang Q, Zhang C, et al. A Conserved Homeobox Transcription Factor Htfl Is Required for Phialide Development and Conidiogenesis in Fusarium Species[J]. PLoS ONE,2012,7: e45432.
[41]Jason E. Stajich S K W, Dag Ahrenf, Chun Hang Aug, Bruce W. Birrenh, Mark Borodovskyi, Claire Burnsj,, Bjorn Canbackf LAC, C.K. Chengg, Jixin Denge, Fred S. Dietrichd, David C. Fargom, Mark L. Farmann, Allen C. Gathmano JG, Roderic Guigop, Patrick J. Hoeggerq, James B. Hookere, Ashleigh Hugginse, Timothy Y. Jamesr T K, Sreedhar Kilaruq, Chinnapa Kodirah, Ursula Kuesq, Doris Kupfert, H.S. Kwang, Alexandre Lomsadzei WL, Walt W. Lillyo, Li-Jun Mah, Aaron J. Mackeyu, Gerard Manningv, Francis Martinw, et al. Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinerens) [J]. PNAS,2010,107:11889-11894.
[42]Linder M B S G, Nakari-Setala T, Penttila M E. Hydrophobins:the protein-amphiphiles of filamentous fungi[J]. FEMS Microbiol Rev,2005,29:877-896.
[43]Sunde M K A, Templeton M D, Beever R E, Mackay J P. Structural analysis of hydrophobins[J]. Micron, 2008,39:773-784.
[44]Bell-Pedersen D D J, Loros J J. The Neurospora circadian clock-controlled gene, ccg-2, is allelic to eas and encodes a fungal hydrophobin required for formation of the conidial rodlet layer[J]. Genes Dev, 1992,6:2382-2394.
[45]Ma H S L, Tian C, Kaminskyj S G W, Dahms T E S. Fungal surface remodelling visualized by atomic force microscopy[J]. Mycol Res,2006,110:879-886.
[46]Wessels J G H. Hydrophobins, unique fungal proteins[J]. Mycologist,2000,14.
[47]Talbot N J, Kershaw, M J, Wakley, G E, deVries, O M H, Wessels, J G H, Hamer, J E. MPG1 encodes a fungal hydrophobin involved in surface interactions during infection-related development of Magnaporthe grisea[J]. Plant Cell,1996,8:985-999.
[48]WSsten H A B. Hydrophobins:multipurpose proteins[J]. Ann Rev Microbiol,2001,55:625-646.
[49]Wosten H A B, vanWetter, M A, Lugones, L G, van der Mei, H C, Busscher, H J, Wessels, J G H. How a fungus escapes the water to grow into the air[J]. Curr Biol,1999,9:85-88.
[50]Kershaw M J T N. Hydrophobins and repellents:proteins with fundamental roles in fungal morphogenesis[J]. Fungal Genet Biol,1998,23:18-33.
[51]Ma A S L, Wang N, Zheng L, Chen L, Xie B. Characterization of a Pleurotus ostreatus fruiting body-specific hydrophobin gene[J], Po.hyd. J Basic Microbiol,2007,47:317-324.
[52]Penas M M R B, Larraya L M, Ramirez L, Pisabarro A G. Differentially regulated, vegetative-mycelium-specific hydrophobins of the edible basidiomycete Pleurotus ostreatus[J]. Appl Environ Microbiol,2002,68:3891-3898.
[53]Van Wetter, M A W H, Wessels, J G H. SC3 and SC4 hydrophobins have distinct roles in formation of aerial structures in dikaryons of Schizophyllum commune[J]. Mol Microbiol,2000,36:201-210.
[54]Hamer J E T N. Infection-related development in the rice blast fungus Magnaporthe grisea[J]. Curr Opin Microbiol,1998,1:693-697.
[55]Lugones L G W H, Birkenkamp K U, Sjollema K A, Zagers J, Wessels J G H. Hydrophobins line air channels in fruiting bodies of Schizophyllum commune and Agaricus bisporus[J]. Mycol Res,1999, 103:635-640.
[56]Whiteford J R S P. Hydrophobins and the interactions between fungi and plants[J]. Mol Plant Pathol, 2002,3:391-400.
[57]van den Brink H, van Gorcom R F, van den Hondel C A, Punt P J. Cytochrome P450 enzyme systems in fungi[J]. Fungal Genetics and Biology,1998,23:1-17.
[58]Nadeau J A, Zhang X S, Li J, O'Neill S D. Ovule development:identification of stage-specific and tissue-specific cDNAs[J]. The Plant Cell Online,1996,8:213-239.
[59]Kim G T, Tsukaya H, Uchimiya H. The ROTUNDIFOLIA3 gene of Arabidopsis thaliana encodes a new member of the cytochrome P-450 family that is required for the regulated polar elongation of leaf cells[J]. Genes & development,1998,12:2381-2391.
[60]Winkler RG, Helentjaris T. The maize Dwarf3 gene encodes a cytochrome P450-mediated early step in Gibberellin biosynthesis[J]. The Plant Cell Online,1995,7:1307-1317.
[61]Szekeres M, Nemeth K, Koncz-Kalman Z, Mathur J, Kauschmann A, et al. Brassinosteroids rescue the deficiency of CYP90, a cytochrome P450, controlling cell elongation and de-etiolation in Arabidopsis[J]. Cell,1996,85:171-182.
[62]Kamada T, Takemaru T. Stipe elongation during basidiocarp maturation in Coprinus macrorhizus: mechanical properties of stipe cell wall[J]. Plant and cell physiology,1977,18:831-840.
[63]Muraguchi H, Kamada T. A Mutation in the eln2 Gene Encoding a Cytochrome P450 of Coprinus cinereus Affects Mushroom Morphogenesis[J]. Fungal Genetics and Biology,2000,29:49-59.
[64]Akiyama R, Sato Y, Kajiwara S, Shishido K. Cloning and expression of cytochrome P450 genes, belonging to a new P450 family, of the basidiomycete Lentinula edodes[J]. Bioscience, biotechnology, and biochemistry,2002,66:2183-2188.
[65]Kues U J D, Granado K, Kertesz-Chaloupkova' P J, Walser M, Hollenstein E, Polak Y, Liu R P, Boulianne A P F, Bottoli, M. Aebi. Mating types and light are major regulators of development in Coprinus cinereus[M]; In L. J. L. D. Van Griensven and J. Visser (ed.) PotFMotGaCBoB, editor: Mushroom Experimental Station, Horst, The Netherlands.1998,113-118.
[66]Uno I, and Ishikawa T. Effect of glucose on the fruiting body formation and adenosine 3',5'-cyclic monophosphate levels in Coprinus macrorhizus[J]. J Bacteriol,1974,120:96-100.
[67]Uno I, Yamaguchi M, and Ishikawa T. The effect of light on fruiting body formation and adenosine 3',5 cyclic monophosphate metabolism in Coprinus macrorhizus[J]. Proc Natl Acad Sci,1974,71: 479-483.
[68]Elgavish S, Shaanan B. Lectin-carbohydrate interactions:different folds, common recognition principles[J]. Trends in biochemical sciences,1997,22:462-467.
[69]Coulet M, Mustier J, Guillot J. Les hemagglutinines des champignons[J]. Rev Mycologie,1970,35:71.
[70]Liener I E, Sharon N, Goldstein I J. The lectins:properties, functions, and applications in biology and medicine[M]. Academic Press,1986.
[71]Kocourek J, Horejsi V. A Note on the Recent Discussion on Definition of the Term "Lectin"[J]. Lectins: Biology, biochemistry, clinical biochemistry,1983,3:3-6.
[72]Banerjee P, Ghosh A, Sengupta S. Hemagglutinating activity in extracts of mycelia from submerged mushroom cultures[J]. Applied and Environmental Microbiology,1982,44:1009-1011.
[73]Konska G Lectins of Higher Fungi (Macromycetes)-their Occurrence, Physiological Role, and Biological Activity[J]. International Journal of Medicinal Mushrooms,2006,8:19-30.
[74]Ticha M, Dudova V, Kocourek J, Volc J. Studies on lectins. LXII. A nonspecific erythroagglutinating lectin and a blood-group A specific lectin in the mushroom Agrocybe aegerita (Brig.) Sing. Lectins-Biology, Biochemistry, Clinical Biochemistry,1985,4:505-514.
[75]Tsivileva O M, Nikitina V E, Garibova L V, Ignatov V V. Lectin activity of Lentinus edodes[J]. IntMicrobiol,2001,4:41-45.
[76]Schubert W J. Lignin biochemistryp[M].1965.
[77]Leonard T J, Phillips L E. Study of phenoloxidase activity during the reproductive cycle in Schizophyllum commune[J]. Journal of bacteriology,1973,114:7-10.
[78]Wood D. Production, purification and properties of extracellular laccase of Agaricus bisporus[J]. Journal of General Microbiology,1980,117:327-338.
[79]Esser K. Phenol oxidases and morphogenesis in Podospora anserina[J].Genetics,1968,60:281.
[80]Wong A, Willetts H. Polyacrylamide-gel electrophoresis of enzymes during morphogenesis of sclerotia of Sclerotinia sclerotiorum[J]. Journal of General Microbiology,1974,81:101-109.
[81]Daniel J. Metabolism of phenolic precursor of a myxomycete spore pigment[J]. Journal of Cell Biology, 1963,19:18-19.
[82]Leonard T J. Phenoloxidase Activity and Fruiting Body Formation in Schizophyllum commune[J]. Journal of Bacteriology,1971,106:162-167.
[83]Kues U, Liu Y. Fruiting body production in basidiomycetes[J]. Applied Microbiology and Biotechnology, 2000,54(2):141-152.
[84]Kamada T, Sano H, Nakazawa T, Nakahori K. Regulation of fruiting body photomorphogenesis in Coprinopsis cinerea[J]. Fungal Genetics and Biology,2010,47:917-921.
[85]Carlile M. The photoresponses of fungi[J]. Photobiology of microorganisms,1970,309-344.
[86]Tan K. Light-induced fungal development[J]. The filamentous fungi,1978,3:334-357.
[87]Elliott C G, Maheshwari R. Reproduction in fungi:genetical and physiological aspects[J]. Journal of Genetics,1994,73:55.
[88]Kihara J, Kumagai T. Ecotypes of the fungus Bipolaris oryzae with various responses of the mycochrome system[J]. Physiologia Plantarum,1994,92:689-695.
[89]Chebotarev L, Zemlyanukhin A. Effect of visible light and ultraviolet rays on the activity of oxidation enzymes in molds[J]. Microbiology (Mikrobiologiya),1973,42:196.
[90]Cohen R J. Cyclic A M P levels in Phycomyces during a response to light[J]. Nature,1974,251:144-146.
[91]Graafmans W. Effect of blue light on metabolism in Penicillium isariiforme[J]. Journal of General Microbiology,1977,101:157-161.
[92]Linden H. A white collar protein senses blue light[J]. Science,2002,297:777-778.
[93]Dunlap J C. Proteins in the Neurospora circadian clockworks[J]. J Biol Chem,2006,281:28489-28493.
[94]Corrochano L M. Fungal photoreceptors:sensory molecules for fungal development and behaviour[J]. Photochem Photobiol Sci,2007,6:725-736.
[95]Ballario P, Vittorioso P, Magrelli A, Talora C, Cabibbo A, Macino G. White collar-1, a central regulator of blue light responses in Neurospora, is a zinc finger protein[J]. EMBO J,1996,15:1650-1657.
[96]Moore-Landecker E. Physiology and biochemistry of ascocarp induction and development[J]. Mycological Research,1992,96:705-716.
[97]Chang S T, Hayes W A. The Biology and cultivation of edible mushrooms[M].1978.
[98]Moore D. Fungal morphogenesis[M]. Cambridge University Press.2003.
[99]Flegg P B W D. Growth and fruiting[M]. Glegg P B S D, Wood D A, editor. Wiley, London:The biology and technology of the cultivated mushroom.1985.
[100]Niederpruem D J. Role of carbon dioxide in the control of fruiting of Schizophyllum commune[J]. Journal of Bacteriology,1963,85:1300-1308.
[101]Lambert E B. Effect of excess carbon dioxide on growing mushrooms[M]. US Government Printing Office.1933.
[102]Turner E M. Development of excised sporocarps of Agaricus bisporus and its control by CO2 [J]. Transactions of the British Mycological Society,1977,69:183-186.
[103]Berget S M, Moore C, Sharp P A. Spliced segments at the 5'terminus of adenovirus 2 late mRNA[J]. Proceedings of the National Academy of Sciences,1977,74:3171-3175.
[104]Chow L T, Gelinas R E, Broker T R, Roberts R J. An amazing sequence arrangement at the 5' ends of adenovirus 2 messenger RNA[J]. Cell,1977,12:1-8.
[105]Nakayashiki H, Hanada S, Quoc N B, Kadotani N, Tosa Y, et al. RNA silencing as a tool for exploring gene function in ascomycete fungi[J]. Fungal Genetics and Biology,2005,42:275-283.
[106]Napoli C, Lemieux C, Jorgensen R. Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans[J]. The Plant Cell Online,1990,2: 279-289.
[107]Romano N, Macino G Quelling:transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences[J]. Molecular microbiology,1992,6:3343-3353.
[108]Elbashir S M, Lendeckel W, Tuschl T. RNA interference is mediated by 21-and 22-nucleotide RNAs[J]. Genes & development,2001,15:188-200.
[109]Erik J. Sontheimer and Richard W. Carthew. Argonaute journeys into the heart of RISC[J]. Science, 2004,305:1409-1410.
[110]Li R, Zhu H, Ruan J, Qian W, Fang X, et al. De novo assembly of human genomes with massively parallel short read sequencing[J]. Genome Research,2010,20:265-272.
[111]Ter-Hovhannisyan V, Lomsadze A, Chernoff Y O, Borodovsky M. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training[J]. Genome research,2008,18: 1979-1990.
[112]Park J, Park J, Jang S, Kim S, Kong S, et al. FTFD:an informatics pipeline supporting phylogenomic analysis of fungal transcription factors[J]. Bioinformatics,2008,24:1024-1025.
[113]Galagan J E, Calvo S E, Borkovich K A, Selker E U, Read N D, et al. The genome sequence of the filamentous fungus Neurospora crassa[J]. Nature,2003,422:859-868.
[114]Coradetti S T, Craig J P, Xiong Y, Shock T, Tian C, et al. Conserved and essential transcription factors for cellulase gene expression in ascomycete fungi[J]. Proceedings of the National Academy of Sciences,2012,109:7397-7402.
[115]Kothe E. Mating-type genes for basidiomycete strain improvement in mushroom farming[J]. Applied microbiology and biotechnology,2001,56:602-612.
[116]Kues U, Casselton L A. Homeodomains and regulation of sexual development in basidiomycetes[J]. Trends in genetics:TIG,1992,8:154.
[117]Robertson C I, Bartholomew K A, Novotny C P, Ullrich R C. Deletion of the Schizophyllum commune Aa Locus:The Roles of Aα Y and Z Mating-Type Genes[J]. Genetics,1996,144:1437-1444.
[118]Heitman J. Sex in fungi:molecular determination and evolutionary implications[M]. Amer Society for Microbiology.2007.
[119]Kues U, Asante-Owusu RN, Mutasa ES, Tymon AM, Pardo EH, et al. Two classes of homeodomain proteins specify the multiple a mating types of the mushroom Coprinus cinereus[J]. The Plant Cell Online,1994,6:1467-1475.
[120]Shelest E. Transcription factors in fungi[J]. FEMS microbiology letters,2008,286:145-151.
[121]Fillinger S, Chaveroche M K, Shimizu K, Keller N, D'Enfert C. cAMP and ras signalling independently control spore germination in the filamentous fungus Aspergillus nidulans[J]. Molecular microbiology, 2002,44:1001-1016.
[122]Wei H, Requena N, Fischer R. The MAPKK kinase SteC regulates conidiophore morphology and is essential for heterokaryon formation and sexual development in the homothallic fungus Aspergillus nidulans[J]. Molecular microbiology,2003,47:1577-1588.
[123]Miller K Y, Wu J, Miller B L. StuA is required for cell pattern formation in Aspergillus[J]. Genes& development,1992,6:1770-1782.
[124]Han K H, Han K Y, Yu J H, Chae K S, Jahng K Y, et al. The nsdD gene encodes a putative GATA-type transcription factor necessary for sexual development of Aspergillus nidulans[J]. Molecular microbiology,2001,41:299-309.
[125]Vienken K, Fischer R. The Zn (Ⅱ) 2Cys6 putative transcription factor NosA controls fruiting body formation in Aspergillus nidulans[J]. Molecular microbiology,2006,61:544-554.
[126]Pi H, Chien C T, Fields S. Transcriptional activation upon pheromone stimulation mediated by a small domain of Saccharomyces cerevisiae Stel2p[J], Molecular and cellular biology,1997,17:6410-6418.
[127]Vallim M A, Miller K Y, Miller B L. Aspergillus SteA (Sterile 12-like) is a homeodomain-C2/H2-Zn+2 finger transcription factor required for sexual reproduction[J]. Molecular microbiology,2002,36: 290-301.
[128]Morrissy A S, Morin R D, Delaney A, Zeng T, McDonald H, et al. Next-generation tag sequencing for cancer gene expression profiling[J]. Genome research,2009,19:1825-1835.
[129]AC't Hoen P, Ariyurek Y, Thygesen H H, Vreugdenhil E, Vossen R H, et al. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms[J]. Nucleic acids research,2008,36:el41-e141.
[130]Subramanian A, Tamayo P, Mootha V K, Mukherjee S, Ebert B L, et al. Gene set enrichment analysis:a knowledge-based approach for interpreting genome-wide expression profiles[J]. Proceedings of the National Academy of Sciences of the United States of America,2005,102:15545-15550.
[131]Audic S, Claverie J M. The significance of digital gene expression profiles[J]. Genome research,1997,7: 986-995.
[132]Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency[J]. Annals of statistics,2001,1165-1188.
[133]Thompson J D, Higgins D G, Gibson T J. CLUSTAL W:improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice[J]. Nucleic acids research,1994,22:4673-4680.
[134]Kumar S, Tamura K, Jakobsen I B, Nei M. MEGA2:molecular evolutionary genetics analysis software[J]. Bioinformatics,2001,17:1244-1245.
[135]Saitou N, Nei M. The neighbor-joining method:a new method for reconstructing phylogenetic trees[J]. Molecular biology and evolution,1987,4:406-425.
[136]Apweiler R, Attwood T K, Bairoch A, Birney E, Biswas M, et al. InterPro-an integrated documentation resource for protein families, domains and functional sites[J]. Bioinformatics,2000,16:1145-1150.
[137]Coulson R M, Ouzounis C A. The phylogenetic diversity of eukaryotic transcription[J]. Nucleic acids research,2003,31:653-660.
[138]M6ller E, Bahnweg G, Sandermann H, Geiger H. A simple and efficient protocol for isolation of high molecular weight DNA from filamentous fungi, fruit bodies, and infected plant tissues[J]. Nucleic Acids Research,1992,20:6115.
[139]Gray M, Peacock J, Squires E. Characterization of the porcine constitutive androstane receptor (CAR) and its splice variants[J]. Xenobiotica,2009,39:915-930.
[140]Matlin A J, Clark F, Smith C W. Understanding alternative splicing:towards a cellular code[J]. Nature Reviews Molecular Cell Biology,2005,6:386-398.
[141]Li Q, Lee J A, Black D L. Neuronal regulation of alternative pre-mRNA splicing[J]. Nature Reviews Neuroscience,2007,8:819-831.
[142]Wahl MC, Will CL, Luhrmann R. The spliceosome:design principles of a dynamic RNP machine[J]. Cell,2009,136:701-718.
[143]Kelemen O, Convertini P, Zhang Z, Wen Y, Shen M, et al. Function of alternative splicing[J]. Gene, 2013,514:1-30.