陆地棉ZF-HD蛋白的全基因组分析
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摘要
ZF-HD(Zinc finger-homeodomain)蛋白属于同源异型盒蛋白家族,在动植物发育过程中起重要的作用。利用生物信息学的手段,研究陆地棉标准系TM-1基因组中ZF-HD蛋白的数目、亚细胞定位、染色体分布、基序、进化关系和组织表达情况。TM-1中共有35个Gh ZHD蛋白成员,且大部分成员定位到细胞核内;分布在20条染色体和2条Scaffold上,且具有11对直系同源基因;进化树分析表明,TM-1基因组中的ZF-HD蛋白大致分为6个小组,每个小组成员间具有类似的基序类型和排列顺序;大部分Gh ZHD基因在胚珠和纤维组织中表达,还有部分基因在根、茎、花、蕾和分生区中表达,在叶和愈伤组织中表达的基因最少。
The Zinc finger-homeodomain(ZF-HD) protein family of homeobox genes plays a vital role during the development processes of plants and animals. The number, subcellular localization, chromosome distribution, motif, evolutionary relationships and tissue-expression patterns of the ZF-HD protein family were studied in the genome of Gossypium hirsutum L. acc.'TM-1' using bioinformatics methods. In total, 35 Gh ZHD genes were identified in the 'TM-1' genome, and a majority of the members are located in nucleus. The family members were distributed on 20 chromosomes and two scaffolds, and 11 pairs were orthologous genes. The family could be divided into six groups based on the phylogenetic analysis, and there were similar motif types and arrangements in each group. Most Gh ZHD genes were expressed in ovules and fibers, some were expressed in roots,stems, buds and flowers, and a fraction were expressed in leaves and calli.
The Zinc finger-homeodomain(ZF-HD) protein family of homeobox genes plays a vital role during the development processes of plants and animals. The number, subcellular localization, chromosome distribution, motif, evolutionary relationships and tissue-expression patterns of the ZF-HD protein family were studied in the genome of Gossypium hirsutum L. acc.'TM-1' using bioinformatics methods. In total, 35 Gh ZHD genes were identified in the 'TM-1' genome, and a majority of the members are located in nucleus. The family members were distributed on 20 chromosomes and two scaffolds, and 11 pairs were orthologous genes. The family could be divided into six groups based on the phylogenetic analysis, and there were similar motif types and arrangements in each group. Most Gh ZHD genes were expressed in ovules and fibers, some were expressed in roots,stems, buds and flowers, and a fraction were expressed in leaves and calli.
引文
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[17]倪万潮,巩元勇,徐珍珍,等.陆地棉Gh ZIP基因家族全基因组分析[J].华北农学报,2015,30(6):8-16.Ni Wanchao,Gong Yuanyong,Xu Zhenzhen,et al.Gemome wide analysis of the Gh ZIP gene family in upland cotton[J].Acta Agriculturae Boreali-Sinica,2015,30(6):8-16.
[18]张新宇,林书岱,张涛,等.棉花C2H2类型锌指蛋白基因GhSIZ1的克隆及表达分析[J].棉花学报,2015,27(3):189-197.Zhang Xinyu,Lin Shudai,Zhang Tao,et al.Cloning and expression analysis of Gh SIZ1,encoding a C2H2 zinc finger protein in cotton(Gossypium hirsutum)[J].Cotton Science,2015,27(3):189-197.
[19]杨郁文,周建武,张保龙,等.棉花SUPERMAN类锌指蛋白基因GZFP的启动子及功能分析[J].棉花学报,2011,23(6):483-489.Yang Yuwen,Zhou Jianwu,Zhang Baolong,et al.Functional analysis of the SUPERMAN-like zinc finger protein gene GZFP and its promoter[J].Cotton Science,2011,23(6):483-489.●
[2]Johannesson N,Wang Y,Engstrm P.DNA-binding and dimerization preferences of Arabidopsis homeodomain-leucine zipper transcription factors in vitro[J].Plant Molecular Biology,2001,45(1):63-73.
[3]Huter C S,Rhodes S J.LIM-homeodomain genes in mammalian development and human disease[J].Molecular Biology Reports,2005,32(2):67-77
[4]Akin Z N,Nazarali A J.Hox genes and their candidate down-stream targets in developing central nervous system[J].Cellular and Molecular Neurobiology,2005,25(3/4):697-741.
[5]Ariel F D,Manavella P A,Dezar C A,et al.The true story of the HD-Zip family[J].Trends in Plant Science,2007,12(9):419-426.
[6]张大勇,王长彪,易金鑫,等.大豆ZF-HD蛋白家族的全基因组序列特征分析[J].江苏农业学报,2011,27(3):675-677.Zhang Dayong,Wang Changbiao,Yi Jinxin,et al.Characterization of complete genome sequence of ZF-HD protein family in soybean(Glycine max L.)[J].Jiangsu Journal of Agricultural Sciences,2011,27(3):675-677.
[7]Windhovel A,Hein I,Dabrowa R,et al.Characterization of a novel class of plant homeodomain proteins that bind to the C4phosphoenolpyruvate carboxylase gene of Flaveria trinervia[J].Plant Molecular Biology,2001,45(2):201-214.
[8]Tan Q K,Irish V F.The Arabidopsis zinc finger-homeodomain genes encode proteins with unique biochemical properties that are coordinately expressed during floral development[J].Plant Physiology,2006,140(3):1095-1108.
[9]Jennifer S H,Hye Ran K,John D N,et al.Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium[J].Genome Research,2006,16(10):1252-1261
[10]Wang Kunbo,Wang Zhiwen,Li Fuguang,et al.The draft genome of a diploid cotton Gossypium raimondii[J].Nature Genetics,2012,44(10):1098-1103.
[11]Parerson A H,Wendel J F,Gundlach H,et al.Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres[J].Nature,2012,492(7429):423-427.
[12]Li Fuguang,Fan Guangyi,Wang Kunbo,et al.Genome sequence of the cultivated cotton Gossypium arboreum[J].Nature Genetics,2014,46(6):562-574.
[13]Li Fuguang,Fan Guangyi,Lu Cairui,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.
[14]Zhang Tianzhen,Hu Yan,Jiang Wenkai,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.
[15]Hu Lei,Claude W D,Ma Hong.Phylogenetic analysis of the plant-specific Zinc finger-homeobox and mini Zinc finger gene families[J].Journal of Integrative Plant Biology,2008,50(8):1031-1045.
[16]张毓婷,王敏华,陈家栋,等.雷蒙德氏棉HSP70基因家族的进化分析及其同源基因在陆地棉中的表达分析[J].遗传,2014,36(9):921-933.Zhang Yuting,Wang Minhua,Chen Jiadong,et al.Genomewide analysis of HSP70 superfamily in Gossypium raimondii and the expression of orthologs in Gossypium hirsutum[J].Hereditas,2014,36(9):921-933.
[17]倪万潮,巩元勇,徐珍珍,等.陆地棉Gh ZIP基因家族全基因组分析[J].华北农学报,2015,30(6):8-16.Ni Wanchao,Gong Yuanyong,Xu Zhenzhen,et al.Gemome wide analysis of the Gh ZIP gene family in upland cotton[J].Acta Agriculturae Boreali-Sinica,2015,30(6):8-16.
[18]张新宇,林书岱,张涛,等.棉花C2H2类型锌指蛋白基因GhSIZ1的克隆及表达分析[J].棉花学报,2015,27(3):189-197.Zhang Xinyu,Lin Shudai,Zhang Tao,et al.Cloning and expression analysis of Gh SIZ1,encoding a C2H2 zinc finger protein in cotton(Gossypium hirsutum)[J].Cotton Science,2015,27(3):189-197.
[19]杨郁文,周建武,张保龙,等.棉花SUPERMAN类锌指蛋白基因GZFP的启动子及功能分析[J].棉花学报,2011,23(6):483-489.Yang Yuwen,Zhou Jianwu,Zhang Baolong,et al.Functional analysis of the SUPERMAN-like zinc finger protein gene GZFP and its promoter[J].Cotton Science,2011,23(6):483-489.●