棉花FAR1/FHY3基因家族的全基因组分析
|
摘要
【目的】FAR1/FHY3是1类起源于转座子酶的转录因子,在光敏色素A(phyA)信号通路的启动中起到非常重要的作用。通过对FAR1/FHY3家族进行全基因组学分析,为深入研究FAR1/FHY3在棉花光信号通路中的分子调控机理提供基础。【方法】利用生物信息学方法对亚洲棉(Gossypium arboreum L.)、雷蒙德氏棉(Gossypium raimondii Ulbrich)和陆地棉(Gossypium hirsutum L.)中的FAR1/FHY3基因进行了全基因组鉴定和分析。【结果】共鉴定出88个FAR1/FHY3基因,其中陆地棉中数量最少。聚类分析将所有成员分为3个亚组。Ka/Ks值表明大部分基因都经历了负选择过程。转录组数据分析发现,大部分FAR1/FHY3基因在棉花叶片中表达,少数在茎、花瓣和花托中表达。陆地棉中的Gh FAR14在4种组织中均有较高水平的表达,且与拟南芥FHY3具有较高的同源性,推测其在陆地棉phyA信号通路的启动过程中可能起到关键作用。【结论】该研究结果有助于了解棉花FAR1/FHY3基因家族的进化与功能,为下一步深入研究该基因家族在棉花生长发育和响应红光信号通路中的分子调控机理提供基础。
[Objective] FAR1/FHY3,a class of transcription factors derived from mutator-like transposases,plays an important role in the phytochrome A signaling pathway.Genome-wide analysis of FAR1/FHY3 is helpful to understand the evolutionary history and molecular mechanism of the FAR1/FHY3 family in light signaling pathways in cotton.[Method] We identified the members of the FAR1/FHY3 family in the genomes of three cotton species using bioinformatics methods.[Result] Eighty-eight FAR1/FHY3 genes were identified in the three cotton species.The least number of FAR1/FHY3 genes was observed in Gossypium hirsutum L.The genes were divided into three groups by phylogenetic analysis.The Ka/Ksratio of the majority of orthologs was less than 1,which indicated that most of the genes had likely undergone purifying selection.Using online published transcriptome data,we established that the majority of FAR1/FHY3 genes were expressed in the leaf,whereas a small number of genes were expressed in the stem,petal,and torus.GhFAR14 of upland cotton,a homolog of Arabidopsis thaliana FHY3,was highly expressed in all of the four tissues,and might play an important role in phytochrome A signaling and regulation of plant growth and development.[Conclusion] The results provide a foundation for future studies of the functions and regulatory mechanisms of FAR1/FHY3 family members in light signaling pathways.
[Objective] FAR1/FHY3,a class of transcription factors derived from mutator-like transposases,plays an important role in the phytochrome A signaling pathway.Genome-wide analysis of FAR1/FHY3 is helpful to understand the evolutionary history and molecular mechanism of the FAR1/FHY3 family in light signaling pathways in cotton.[Method] We identified the members of the FAR1/FHY3 family in the genomes of three cotton species using bioinformatics methods.[Result] Eighty-eight FAR1/FHY3 genes were identified in the three cotton species.The least number of FAR1/FHY3 genes was observed in Gossypium hirsutum L.The genes were divided into three groups by phylogenetic analysis.The Ka/Ksratio of the majority of orthologs was less than 1,which indicated that most of the genes had likely undergone purifying selection.Using online published transcriptome data,we established that the majority of FAR1/FHY3 genes were expressed in the leaf,whereas a small number of genes were expressed in the stem,petal,and torus.GhFAR14 of upland cotton,a homolog of Arabidopsis thaliana FHY3,was highly expressed in all of the four tissues,and might play an important role in phytochrome A signaling and regulation of plant growth and development.[Conclusion] The results provide a foundation for future studies of the functions and regulatory mechanisms of FAR1/FHY3 family members in light signaling pathways.
引文
[1]Deng X W,Quail P H.Signalling in light-controlled development[J].Seminars in Cell&Developmental Biology,1999,10(2):121-129.
[2]Casal J J.Phytochromes,cryptochromes,phototropin:photoreceptor interactions in plants[J].Photochemistry&Photobiology,2000,71(1):1-11.
[3]Heijde M,Ulm R.UV-B photoreceptor-mediated signalling in plants[J].Trends in Plant Science,2012,17(4):230-237.
[4]刘圈炜,何云,齐胜利,等.光敏色素研究进展[J].中国农学通报,2005,21(5):237-241.Liu Quanwei,He Yun,Qi Shengli,et al.Advances in researches on phytochrome[J].Chinese Agricultural Science Bulletin,2005,21(5):237-241.
[5]Furuya M.Phytochromes:their molecular species,gene families,and functions[J].Annual Review of Plant Physiology and Plant Molecular Biology,1993,44(1):617-645.
[6]陈芳,邓兴旺.远红光受体伴侣蛋白FHY1在介导基因表达和植物生长发育过程中的独特作用[J].遗传,2014,36(9):958.Chen Fang,Deng Xingwang.Far red light receptor chaperone FHY1 plays a unique role in mediating gene expression and plant growth and development[J].Hereditas(Beijing),2014,36(9):958.
[7]Lamparter T.Evolution of cyanobacterial and plant phytochromes[J].FEBS Letters,2004,573(1-3):1-5.
[8]Kircher S,Kozma-Bognar L,Kim L,et al.Light quality-dependent nuclear import of the plant photoreceptors phytochrome A and B[J].Plant Cell,1999,11(8):1445-1456.
[9]Tepperman J M,Zhu T,Chang H S,et al.Multiple transcription-factor genes are early targets of phytochrome A signaling[J].Proceedings of the National Academy of Sciences of the United States of America,2001,98(16):9437-9442.
[10]Lin R C,Ding L,Casola C,et al.Transposase-derived transcription factors regulate light signaling in Arabidopsis[J].Science,2007,318(5854):1302-1305.
[11]Hiltbrunner A.FHY1 and FHL act together to mediate nuclear accumulation of the phytochrome A photoreceptor[J].Plant&Cell Physiology,2006,47(8):1023-1034.
[12]Hudson M E,Lisch D R,Quail P H.The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway[J].The Plant Journal,2003,34(4):453-471.
[13]Xu Z N,Dooner H K.Jittery,a mutator distant relative with a paradoxical mobile behavior:Excision without reinsertion[J].Plant Cell,2004,16(5):1105-1114.
[14]Lin R C,Wang H Y.Arabidopsis FHY3/FAR1 gene family and distinct roles of its members in light control of Arabidopsis development[J].Plant Physiology,2004,136(4):4010-4022.
[15]Lin R C,Teng Y B,Park H J,et al.Discrete and essential roles of the multiple domains of Arabidopsis FHY3 in mediating phytochrome A signal transduction[J].Plant Physiology,2008,148(2):981-992.
[16]马燕斌,吴霞,张林水,等.利用光敏色素基因改良棉花农艺经济性状的探讨[C]//中国棉花学会2011年年会论文汇编.安阳:中国棉花杂志社,2011:71-73.Ma Yanbin,Wu Xia,Zhang Linshui,et al.Improvement of agronomic and economic characteristics of cotton by phytochrome genes[C]//The 2011 Annual Conference of China Society of Cotton Sci-Tech.Anyang:China Cotton Magazine House,2011:71-73.
[17]Thiele A,Herold M,Lenk I,et al.Heterologous expression of Arabidopsis phytochrome B in transgenic potato influences photosynthetic performance and tuber development[J].Plant Physiology,1999,120(1):73-82.
[18]Garg A K,Sawers R J,Wang H,et al.Light-regulated overexpression of an Arabidopsis phytochrome A gene in rice alters plant architecture and increases grain yield[J].Planta,2006,223(4):627-636.
[19]Wang K B,Wang Z W,Li F G,et al.The draft genome of a diploid cotton Gossypium raimondii[J].Nature Genetics,2012,44(10):1098-1103.
[20]Li F G,Fan G Y,Wang K B,et al.Genome sequence of the cultivated cotton Gossypium arboreum[J].Nature Genetics,2014,46(6):567-572.
[21]Li F G,Fan G Y,Lu C R,et al.Genome sequence of cultivated upland cotton(Gossypium hirsutum TM-1)provides insights into genome evolution[J].Nature Biotechnology,2015,33(5):524-530.
[22]Zhang T Z,Hu Y,Jiang W K,et al.Sequencing of allotetraploid cotton(Gossypium hirsutum L.acc.TM-1)provides a resource for fiber improvement[J].Nature Biotechnology,2015,33(5):531-537.
[23]郭安源,朱其慧,陈新,等.GSDS:基因结构显示系统[J].遗传,2007,29(8):1023-1026.Guo Anyuan,Zhu Qihui,Chen Xin et al.GSDS:a gene structure display server[J].Hereditas(Beijing),2007,29(8):1023-1026.
[24]Kumar S,Stecher G,Tamura K.MEGA7:molecular evolutionary genetics analysis version 7.0 for bigger datasets[J].Molecular Biology&Evolution,2016,33(7):1870-1874.
[25]Adobe C.Adobe illustrator CS3[M].San Francisco:Adobe Press,2007.
[26]O'Brien K P,Remm M,Sonnhammer E L.Inparanoid:A com prehensive database of eukaryotic orthologs[J].Nucleic Acids Research,2005,33(Database issue):476-480.
[27]Wang D,Zhang Y,Zhang Z,et al.Ka Ks_calculator 2.0:A toolkit incorporating gamma-series methods and sliding window strategies[J].Genomics Proteomics Bioinformatics,2010,8(1):77-80.
[28]Trapnell C,Pachter L,Salzberg S L.Top Hat:Discovering splice junctions with RNA-Seq[J].Bioinformatics,2009,25(9):1105-1111.
[29]Trapnell C,Roberts A,Goff L,et al.Differential gene and transcript expression analysis of RNA-seq experiments with Top Hat and Cufflinks[J].Nature Protocols,2012,7(3):562-578.
[30]Deng W K,Wang Y B,Liu Z X,et al.Hem I:A toolkit for illustrating heatmaps[J/OL].PLo S ONE,2014,9(11):e111988[2017-1-30].https://doi.org/10.1371/journal.pone.0111988.
[31]Quail P H.Phytochrome-regulated gene expression[J].Journal of Integrative Plant Biology,2007,49(1):11-20.
[32]Jiao Y,Lau O S,Deng X W.Light-regulated transcriptional networks in higher plants[J].Nature Reviews Genetics,2007,8(3):217-230.
[33]Ouyang X H,Li J G,Li G,et al.Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development[J].Plant Cell,2011,23(7):2514-2535.
[34]Hurst L D.The Ka/Ksratio:Diagnosing the form of sequence evolution[J].Trends in Genetics,2002,18(9):486-487.
[35]Zhao L,Zhang N,Ma P F,et al.Phylogenomic analyses of nuclear genes reveal the evolutionary relationships within the BEP clade and the evidence of positive selection in Poaceae[J/OL].PLo S ONE,2013,8(5):e64642[2017-1-30].https://doi.org/10.1371/journal.pone.0064642.
[2]Casal J J.Phytochromes,cryptochromes,phototropin:photoreceptor interactions in plants[J].Photochemistry&Photobiology,2000,71(1):1-11.
[3]Heijde M,Ulm R.UV-B photoreceptor-mediated signalling in plants[J].Trends in Plant Science,2012,17(4):230-237.
[4]刘圈炜,何云,齐胜利,等.光敏色素研究进展[J].中国农学通报,2005,21(5):237-241.Liu Quanwei,He Yun,Qi Shengli,et al.Advances in researches on phytochrome[J].Chinese Agricultural Science Bulletin,2005,21(5):237-241.
[5]Furuya M.Phytochromes:their molecular species,gene families,and functions[J].Annual Review of Plant Physiology and Plant Molecular Biology,1993,44(1):617-645.
[6]陈芳,邓兴旺.远红光受体伴侣蛋白FHY1在介导基因表达和植物生长发育过程中的独特作用[J].遗传,2014,36(9):958.Chen Fang,Deng Xingwang.Far red light receptor chaperone FHY1 plays a unique role in mediating gene expression and plant growth and development[J].Hereditas(Beijing),2014,36(9):958.
[7]Lamparter T.Evolution of cyanobacterial and plant phytochromes[J].FEBS Letters,2004,573(1-3):1-5.
[8]Kircher S,Kozma-Bognar L,Kim L,et al.Light quality-dependent nuclear import of the plant photoreceptors phytochrome A and B[J].Plant Cell,1999,11(8):1445-1456.
[9]Tepperman J M,Zhu T,Chang H S,et al.Multiple transcription-factor genes are early targets of phytochrome A signaling[J].Proceedings of the National Academy of Sciences of the United States of America,2001,98(16):9437-9442.
[10]Lin R C,Ding L,Casola C,et al.Transposase-derived transcription factors regulate light signaling in Arabidopsis[J].Science,2007,318(5854):1302-1305.
[11]Hiltbrunner A.FHY1 and FHL act together to mediate nuclear accumulation of the phytochrome A photoreceptor[J].Plant&Cell Physiology,2006,47(8):1023-1034.
[12]Hudson M E,Lisch D R,Quail P H.The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway[J].The Plant Journal,2003,34(4):453-471.
[13]Xu Z N,Dooner H K.Jittery,a mutator distant relative with a paradoxical mobile behavior:Excision without reinsertion[J].Plant Cell,2004,16(5):1105-1114.
[14]Lin R C,Wang H Y.Arabidopsis FHY3/FAR1 gene family and distinct roles of its members in light control of Arabidopsis development[J].Plant Physiology,2004,136(4):4010-4022.
[15]Lin R C,Teng Y B,Park H J,et al.Discrete and essential roles of the multiple domains of Arabidopsis FHY3 in mediating phytochrome A signal transduction[J].Plant Physiology,2008,148(2):981-992.
[16]马燕斌,吴霞,张林水,等.利用光敏色素基因改良棉花农艺经济性状的探讨[C]//中国棉花学会2011年年会论文汇编.安阳:中国棉花杂志社,2011:71-73.Ma Yanbin,Wu Xia,Zhang Linshui,et al.Improvement of agronomic and economic characteristics of cotton by phytochrome genes[C]//The 2011 Annual Conference of China Society of Cotton Sci-Tech.Anyang:China Cotton Magazine House,2011:71-73.
[17]Thiele A,Herold M,Lenk I,et al.Heterologous expression of Arabidopsis phytochrome B in transgenic potato influences photosynthetic performance and tuber development[J].Plant Physiology,1999,120(1):73-82.
[18]Garg A K,Sawers R J,Wang H,et al.Light-regulated overexpression of an Arabidopsis phytochrome A gene in rice alters plant architecture and increases grain yield[J].Planta,2006,223(4):627-636.
[19]Wang K B,Wang Z W,Li F G,et al.The draft genome of a diploid cotton Gossypium raimondii[J].Nature Genetics,2012,44(10):1098-1103.
[20]Li F G,Fan G Y,Wang K B,et al.Genome sequence of the cultivated cotton Gossypium arboreum[J].Nature Genetics,2014,46(6):567-572.
[21]Li F G,Fan G Y,Lu C R,et al.Genome sequence of cultivated upland cotton(Gossypium hirsutum TM-1)provides insights into genome evolution[J].Nature Biotechnology,2015,33(5):524-530.
[22]Zhang T Z,Hu Y,Jiang W K,et al.Sequencing of allotetraploid cotton(Gossypium hirsutum L.acc.TM-1)provides a resource for fiber improvement[J].Nature Biotechnology,2015,33(5):531-537.
[23]郭安源,朱其慧,陈新,等.GSDS:基因结构显示系统[J].遗传,2007,29(8):1023-1026.Guo Anyuan,Zhu Qihui,Chen Xin et al.GSDS:a gene structure display server[J].Hereditas(Beijing),2007,29(8):1023-1026.
[24]Kumar S,Stecher G,Tamura K.MEGA7:molecular evolutionary genetics analysis version 7.0 for bigger datasets[J].Molecular Biology&Evolution,2016,33(7):1870-1874.
[25]Adobe C.Adobe illustrator CS3[M].San Francisco:Adobe Press,2007.
[26]O'Brien K P,Remm M,Sonnhammer E L.Inparanoid:A com prehensive database of eukaryotic orthologs[J].Nucleic Acids Research,2005,33(Database issue):476-480.
[27]Wang D,Zhang Y,Zhang Z,et al.Ka Ks_calculator 2.0:A toolkit incorporating gamma-series methods and sliding window strategies[J].Genomics Proteomics Bioinformatics,2010,8(1):77-80.
[28]Trapnell C,Pachter L,Salzberg S L.Top Hat:Discovering splice junctions with RNA-Seq[J].Bioinformatics,2009,25(9):1105-1111.
[29]Trapnell C,Roberts A,Goff L,et al.Differential gene and transcript expression analysis of RNA-seq experiments with Top Hat and Cufflinks[J].Nature Protocols,2012,7(3):562-578.
[30]Deng W K,Wang Y B,Liu Z X,et al.Hem I:A toolkit for illustrating heatmaps[J/OL].PLo S ONE,2014,9(11):e111988[2017-1-30].https://doi.org/10.1371/journal.pone.0111988.
[31]Quail P H.Phytochrome-regulated gene expression[J].Journal of Integrative Plant Biology,2007,49(1):11-20.
[32]Jiao Y,Lau O S,Deng X W.Light-regulated transcriptional networks in higher plants[J].Nature Reviews Genetics,2007,8(3):217-230.
[33]Ouyang X H,Li J G,Li G,et al.Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development[J].Plant Cell,2011,23(7):2514-2535.
[34]Hurst L D.The Ka/Ksratio:Diagnosing the form of sequence evolution[J].Trends in Genetics,2002,18(9):486-487.
[35]Zhao L,Zhang N,Ma P F,et al.Phylogenomic analyses of nuclear genes reveal the evolutionary relationships within the BEP clade and the evidence of positive selection in Poaceae[J/OL].PLo S ONE,2013,8(5):e64642[2017-1-30].https://doi.org/10.1371/journal.pone.0064642.