Are Differences in Genomic Data Sets due to True Biological Variants or Errors in Genome Assembly: An Example from Two Chloroplast Genomes

2015-06-11

作 者:Wu ZQ*, Tembrock LR, Ge S

影响因子: 3.534

刊物名称: Plos One

出版年份: 2015

卷: 10 期: 2 页码: e0118019

文章摘要 :

  DNA sequencing has been revolutionized by the development of high-throughput sequencing technologies. Plummeting costs and the massive throughput capacities of second and third generation sequencing platforms have transformed many fields of biological research. Concurrently, new data processing pipelines made rapid de novo genome assemblies possible. However, high quality data are critically important for all investigations in the genomic era. We used chloroplast genomes of one Oryza species (O. australiensis) to compare differences in sequence quality: one genome (GU592209) was obtained through Illumina sequencing and reference-guided assembly and the other genome (KJ830774) was obtained via target enrichment libraries and shotgun sequencing. Based on the whole genome alignment, GU592209 was more similar to the reference genome (O. sativa: AY522330) with 99.2% sequence identity (SI value) compared with the 98.8% SI values in the KJ830774 genome; whereas the opposite result was obtained when the SI values in coding and noncoding regions of GU592209 and KJ830774 were compared. Additionally, the junctions of two single copies and repeat copies in the chloroplast genome exhibited differences. Phylogenetic analyses were conducted using these sequences, and the different data sets yielded dissimilar topologies: phylogenetic replacements of the two individuals were remarkably different based on whole genome sequencing or SNP data and insertions and deletions (indels) data. Thus, we concluded that the genomic composition of GU592209 was heterogeneous in coding and non-coding regions. These findings should impel biologists to carefully consider the quality of sequencing and assembly when working with next-generation data.

全文链接


附件下载:

位于北京西部香山脚下的中国科学院植物研究所是我国系统与进化生物学领域的第一个国家重点实验室

版权所有 © 系统与进化植物学国家重点实验室[中国科学院植物研究所]
ICP备16067583号-12 网站管理 技术支持:青云软件

联系我们

  • 地址:北京市海淀区 香山南辛村20号
  • 邮编:100093
  • 电话:010-6283 6086
  • 传真:010-6283 6095
  • 电邮:lseb@ibcas.ac.cn

语言切换