棉花CAD基因家族的生物信息学分析

Bioinformatic Analysis of the CAD Gene Family in Cotton

苯丙烷代谢是植物重要的次生代谢途径之一,其代谢产物在植物的生长发育中发挥着重要作用。肉桂酸脱氢酶(cinnamyl alcohol dehydrogenase,CAD)是苯丙烷代谢途径的关键酶之一,在棉花纤维品质形成中起着十分重要的调节作用。为了更好地了解CAD基因家族在二倍体雷蒙德氏棉(D5)和亚洲棉(A2)、四倍体陆地棉(AD1)和海岛棉(AD2)基因组中的数量和分布情况,通过生物信息学方法,在雷蒙德氏棉、亚洲棉、陆地棉和海岛棉全基因组中分别鉴定出16、16、28和25个CAD基因家族成员,进一步分析了这些CAD家族成员进行基因结构、染色体定位、保守域、进化关系及CAD基因在陆地棉不同器官组织中的表达等。结果表明,4个棉种全基因组分别编码16、16、28和25个CAD基因。亚细胞定位将这些棉花CAD基因的表达产物均定位于细胞质。雷蒙德氏棉有14个CAD成员基因分布在5条染色体上,亚洲棉有13个CAD成员基因分布在5条染色体上,陆地棉28个CAD成员基因、海岛棉25个CAD基因分别分布在10条染色体上;内含子/外显子结构分析表明,CAD基因结构较为复杂,均含有内含子和外显子;功能结构域分析发现,有棉花CAD蛋白具有高度保守的ADH_N和ADH_zinc_N 2个功能域;根据系统发育分析结果,将CAD基因家族分成3个亚类。大部分CAD基因在陆地棉的不同器官中均有表达,部分在棉花纤维中表达量较高。分析结果为进一步研究棉花CAD基因家族各成员的功能奠定了理论基础。

Phenylpropane metabolism is an important secondary metabolic pathway,and its metabolites play important roles in plant growth and development.Cinnamic acid dehydrogenase(CAD)is one of the key enzymes in phenylpropane metabolism,which plays a very important role in the regulation of cotton fiber quality.The genome of diploid cotton Gossypium raimondii(D5)and Gossypium arboretum(A2),the tetraploid cotton Gossypium hirsutum(AD1)and Gossypium barbadense(AD2)were analyzed to better understand the quantity and distribution of CAD gene family.By bioinformatics methods,16,16,28 and 25 CAD gene family members were identified from the Gossypium raimondii,Gossypium arboretum,Gossypium hirsutum and Gossypium bar⁃badense genome databases,respectively.The genetic structure,gene localization,subcellular localization,conserved domain and phylogenetic relationship of CAD families were analyzed.The expression of CAD gene in different organs and tissues of Gossy⁃pium hirsutum was analyzed.The results showed that 16,16,28 and 25 CAD genes were encoded in the whole genome of four cotton varieties.The subcellular localization of the cotton CAD proteins were in the cytoplasm.Gossypium raimondii had 14 CAD member genes distributed on the 5 chromosomes.Gossypium arboretum had 13 CAD member genes distributed on the 5 chromo-somes.Gossypium hirsutum had 25 CAD member genes distributed on the 10 chromosomes.Gossypium barbadense had 28 CAD member genes distributed on the 10 chromosomes.The analysis of intron/exon structure showed that the structures of CAD genes were complex,including intron and exon.Through functional domain analysis,it was found that cotton CAD protein contain two functional domains of ADH_N and ADH_zinc_N,which are the conserved domains for most CAD proteins.According to the re-sults of phylogenetic analysis,the CAD gene family was divided into three subfamilies.Most of CAD genes were expressed in dif-ferent organs of Gossypium hirsutum,and some of them were highly expressed in cotton fiber.The results laid a theoretical founda-tion for further research on the functions of cotton CAD gene family members.