西方蜜蜂的基因注释信息优化及新基因鉴定
投稿时间:2017-10-15    点此下载全文
引用本文:郭睿,张璐,熊翠玲,郑燕珍,付中民,陈大福.西方蜜蜂的基因注释信息优化及新基因鉴定[J].《上海交通大学学报》(农业科学版),2018,(3):39-44
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作者单位E-mail
郭睿 福建农林大学 蜂学学院,福州350002 ruiguo@fafu.edu.cn 
张璐 福建农林大学 蜂学学院,福州350002 m17805949180@163.com 
熊翠玲 福建农林大学 蜂学学院,福州350002  
郑燕珍 福建农林大学 蜂学学院,福州350002  
付中民 福建农林大学 蜂学学院,福州350002  
陈大福 福建农林大学 蜂学学院,福州350002  
基金项目:国家自然科学基金(31702190);现代农业产业技术体系建设专项资金(CARS-44-KXJ7);福建农林大学科技创新专项基金项目(CXZX2017342,CXZX2017343)
中文摘要:西方蜜蜂(Apis mellifera)全基因组序列早在2006年就已公布,但其基因注释信息并不完善。本研究利用前期获得的意蜂幼虫肠道RNA-seq数据对西方蜜蜂基因组的已知基因进行结构优化,对新基因进行预测、鉴定和分析。利用 Cufflink 软件进行转录本重构,进而与参考转录本序列进行比较,共对4 177个已公布西方蜜蜂基因的测序结果进行了优化,其中5′端延长、3′端延长、5′和3′端都延长的基因分别有2 383、2 392和2 384个。利用Cuffcompare软件将重构转录本与参考基因组进行比对,共预测出197个西方蜜蜂新基因,随机挑选20个新基因进行RT-PCR验证,有18对引物成功扩增出符合预期的目的片段。GO分类结果显示这些新基因涉及运输和代谢、能量代谢和信号分子和交互等21个GO terms。KEGG 代谢通路(pathway)富集分析结果显示这些新基因富集于13个pathways,其中基因富集数最多的是细胞进程、单一有机体和结合。本研究为西方蜜蜂基因组信息提供了有益的补充和完善,也为新基因的功能研究打下了基础。
中文关键词:西方蜜蜂  意大利蜜蜂  幼虫肠道  基因结构优化  新基因鉴定
 
Optimization of annotated genes′ information and identification of novel genes in Apis mellifera
Abstract:The genome of Apis mellifera was published in 2006,but the gene annotation information is not complete.Based on the previously obtained RNA-seq data of Apis mellifera ligustica larval guts,optimization of annotated genes,prediction,identification and analysis of novel genes were performed in this study.Cufflink software was used to re-built transcripts,which were compared with transcript sequences in the reference genome,a total of 4 177 genes’ structure of A.mellifera were optimized,and 2 383,2 392 and 2 384 genes were prolonged at 5′ terminal,3′ terminal,both 5′ and 3′ terminals,respectively.Cuffcompare software was used to conduct mapping of these re-built transcripts with the genome of A.mellifera and 197 novel genes were predicted.Twenty of them were selected for RT-PCR identification,and expected bands were amplified from 18 primer pairs.GO classification demonstrated that the novel genes were in 21 GO terms,including transport and metabolism,energy metabolism,signal molecule and interaction and so forth.KEGG pathway analysis suggested that the novel genes were engaged in 13 pathways,among them the largest ones were cellular process,single organism and binding.Our results provide some beneficial improvement to A.mellifera genome and some basis for functional investigation of the novel genes.
keywords:Apis mellifera  Apis mellifera ligustica  larval gut  gene structure optimization  novel gene identification
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