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

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.