不同组装软件在系统发育基因组学中的应用比较  

Comparison of application of assemblers in phylogenomics

作　　者：王耀卓 张文强 张俊霞[1] WANG Yaozhuo;ZHANG Wenqiang;ZHANG Junxia(Key Laboratory of Zoological Systematics and Application of Hebei Province,Institute of Life Science and Green Development,College of Life Sciences,Hebei University,Baoding 071002,China)

机构地区：[1]河北大学生命科学学院,生命科学与绿色发展研究院,河北省动物系统学与应用重点实验室,河北保定071002

出　　处：《河北大学学报（自然科学版）》2023年第2期171-178,共8页Journal of Hebei University(Natural Science Edition)

基　　金：国家自然科学基金资助项目(32070422);河北大学高层次人才科研启动项目(521000981324)。

摘　　要：为了筛选出最适合于超级保守元件(ultra-conserved elements,UCE)序列组装的软件,分别使用5款组装软件SPAdes、ABySS、Velvet、Trinity和Minia对17个UCE捕获测序文库进行组装.结果发现:5款组装软件对UCE数据的组装结果不同,Trinity组装所耗时间明显比其他软件长;SPAdes和Trinity的组装结果较好,得到的可观长度的重叠群(contigs)总数较多,产生的长片段(>250 bp)contigs较其他3款软件更多,但是SPAdes捕获到的UCE数量最多,因此,相比于其他4款组装软件,SPAdes更适合UCE数据的组装.本研究为基于UCE的系统发育基因组学分析提供了参考.To select the most suitable assembler for ultra-conserved elements(UCE)phylogenomic practice,five different assembly softwares,SPAdes,ABySS,Velvet,Trinity and Minia were applied,to assemble 17 UCE captured sequencing libraries,respectively.The results showed that among the five assemblers,Trinity consumed significantly longer computational time than the others;SPAdes and Trinity both assembled more contigs and obtained more longer contigs(>250 bp)than the other three assemblers,but SPAdes captured the highest number of UCE loci.Therefore,SPAdes is more suitable for the assembly of UCE data than the other assembly softwares.This study provides a technical reference for the practice of UCE-based phylogenomic studies.

关 键 词：数据分析 超级保守元件 系统发育基因组学 

分 类 号：Q951[生物学—动物学]