摘要
栽培种西番莲是中国南方广泛种植的果树,但是其基因组信息尚不清楚,严重制约了西番莲分子遗传学研究。本研究利用高通量测序得到的14.1 Gb原始数据及165.7 Mb组装到Scaffold水平、代表栽培种西番莲基因组的序列进行生物信息学分析。结果表明,西番莲基因组中含有大量的简单序列重复(simple sequence repeats,SSR)。通过与木薯和桃树基因组比对,西番莲基因组有23053个预测基因。利用NR、Swiss Port、KEGG、InterPro、Pfam和GO数据库,西番莲预测基因能比对到282个植物基因组上。利用GO数据对注释基因的功能进行归类,即Biological process、Cellular component和Molecular function,再细化为41个二级功能,大部分基因与碳水化合物、有机酸、脂等代谢途径相关。KEGG通路富集将基因功能分为5大类19个二级功能,众多基因与新陈代谢通路相关,其中最大一类是碳水化合物代谢相关基因。通过基因家族的聚类分析,栽培种西番莲12767个基因可以聚类到9868个基因家族中,平均每个家族包含有1.29个基因,同时有291个特有基因家族。在进化关系中,栽培种西番莲与毛果杨和蓖麻的亲缘关系较近。本研究为西番莲的基因功能研究和分子育种奠定基础。
Cultivated passion fruit is a fruit tree widely cultivated in southern China,but little is known about its genomics,which seriously restricts the molecular genetics research of Passiflora edulis.In this study,we conducted bioinformatics analysis of the 14.1 Gb raw sequencing data of Passiflora edulis and its 165.7 Mb representative genome sequences that have been assembled at the scaffold level.The results showed that the Passiflora edulis genome contained a large number of simple sequence repeats(SSR).Compared to the cassava and peach genomes,the Passiflora edulis genome has 23053 predicted genes.These genes can be aligned to 282 plant genomes through the NR,SwissPort,KEGG,InterPro,Pfam and GO databases.GO annotation indicated that these genes are involved in the biological processes,cellular components and molecular functions,and related to 41 secondary functions with most genes involved in metabolic pathways of carbohydrates,organic acids,lipids and other molecules.KEGG pathway enrichment assigned these genes into five major categories and 19 secondary functions with most of the genes involved in metabolic pathways,especially carbohydrate metabolism.Cluster analysis of gene families showed that 12767 genes of the Passiflora edulis could be clustered into 9868 gene families with an average of 1.29 genes in each family and 291 unique gene families.On the evolutionary relationship,the Passiflora edulis is closely related to Populus trichocarpa and Ricinus communis,but the rate of evolution is slower.Overall,this study laid the foundation for the genetic function research and molecular breeding of Passiflora edulis.
作者
吴艳艳
刘洁云
田青兰
黄永才
黄伟华
夏秀忠
杨行海
牟海飞
Wu Yanyan;Liu Jieyun;Tian Qinglan;Huang Yongcai;Huang Weihua;Xia Xiuzhong;Yang Xinghai;Mou Haifei(Biotechnology Research Institute,Guangxi Academy of Agricultural Sciences;Rice research Institute,Guangxi Academy of Agricultural Sciences,Nanning,530007)
出处
《基因组学与应用生物学》
CAS
CSCD
北大核心
2020年第5期2103-2110,共8页
Genomics and Applied Biology
基金
广西自然科学基金(2018GXNSFBA281024)
广西农业科学院优势学科团队项目(2018YT19)
广西浦北百香果试验站项目(桂TS2016010)共同资助。
关键词
栽培种西番莲
基因组
基因注释
系统进化
生物信息学
Cultivated passion fruit(Passiflora edulis)
Genome
Gene annotation
Phyletic evolution
Bioinformatics
