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Are Differences in Genomic Data Sets due to True Biological Variants or Errors in Genome Assembly: An Example from Two Chloroplast Genomes | |
Wu, Zhiqiang; Tembrock, Luke R.; Ge, Song | |
2015 | |
发表期刊 | PLOS ONE |
ISSN | 1932-6203 |
卷号 | 10期号:2 |
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. |
学科领域 | Multidisciplinary Sciences |
DOI | 10.1371/journal.pone.0118019 |
收录类别 | SCI |
语种 | 英语 |
WOS关键词 | PHYLOGENETIC ANALYSIS ; GENE ORGANIZATION ; DNA ; SEQUENCE ; INDELS ; DIVERSIFICATION ; IDENTIFICATION ; TRANSFORMATION ; CHALLENGES ; EVOLUTION |
WOS研究方向 | Science Citation Index Expanded (SCI-EXPANDED) |
WOS记录号 | WOS:000349444900251 |
出版者 | PUBLIC LIBRARY SCIENCE |
文献子类 | Article |
出版地 | SAN FRANCISCO |
资助机构 | National Natural Science Foundation of China [30990240] |
作者邮箱 | wu.zhiqiang.1020@gmail.com |
作品OA属性 | Green Published, Green Submitted, gold |
引用统计 | |
文献类型 | 期刊论文 |
条目标识符 | http://ir.ibcas.ac.cn/handle/2S10CLM1/26022 |
专题 | 系统与进化植物学国家重点实验室 |
作者单位 | 1.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China 2.Wu, Zhiqiang; Tembrock, Luke R.] Colorado State Univ, Dept Biol, Ft Collins, CO 80523 USA |
推荐引用方式 GB/T 7714 | Wu, Zhiqiang,Tembrock, Luke R.,Ge, Song. Are Differences in Genomic Data Sets due to True Biological Variants or Errors in Genome Assembly: An Example from Two Chloroplast Genomes[J]. PLOS ONE,2015,10(2). |
APA | Wu, Zhiqiang,Tembrock, Luke R.,&Ge, Song.(2015).Are Differences in Genomic Data Sets due to True Biological Variants or Errors in Genome Assembly: An Example from Two Chloroplast Genomes.PLOS ONE,10(2). |
MLA | Wu, Zhiqiang,et al."Are Differences in Genomic Data Sets due to True Biological Variants or Errors in Genome Assembly: An Example from Two Chloroplast Genomes".PLOS ONE 10.2(2015). |
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Wu-2015-Are Differen(1144KB) | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | 浏览 请求全文 |
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