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PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes
文献类型：期刊论文
| 作者 | Qu, Xiao-Jian1,2 ; Moore, Michael J.3; Li, De-Zhu1; Yi, Ting-Shuang1
|
| 刊名 | PLANT METHODS
 |
| 出版日期 | 2019-05-21 |
| 卷号 | 15页码:12 |
| 关键词 | PGA Plastome Batch annotation Accuracy BLAST Software Algorithms |
| ISSN号 | 1746-4811 |
| DOI | 10.1186/s13007-019-0435-7 |
| 通讯作者 | Li, De-Zhu(DZL@mail.kib.ac.cn) ; Yi, Ting-Shuang(tingshuangyi@mail.kib.ac.cn) |
| 英文摘要 | BackgroundPlastome (plastid genome) sequences provide valuable information for understanding the phylogenetic relationships and evolutionary history of plants. Although the rapid development of high-throughput sequencing technology has led to an explosion of plastome sequences, annotation remains a significant bottleneck for plastomes. User-friendly batch annotation of multiple plastomes is an urgent need.ResultsWe introduce Plastid Genome Annotator (PGA), a standalone command line tool that can perform rapid, accurate, and flexible batch annotation of newly generated target plastomes based on well-annotated reference plastomes. In contrast to current existing tools, PGA uses reference plastomes as the query and unannotated target plastomes as the subject to locate genes, which we refer to as the reverse query-subject BLAST search approach. PGA accurately identifies gene and intron boundaries as well as intron loss. The program outputs GenBank-formatted files as well as a log file to assist users in verifying annotations. Comparisons against other available plastome annotation tools demonstrated the high annotation accuracy of PGA, with little or no post-annotation verification necessary. Likewise, we demonstrated the flexibility of reference plastomes within PGA by annotating the plastome of Rosa roxburghii using that of Amborella trichopoda as a reference. The program, user manual and example data sets are freely available at https://github.com/quxiaojian/PGA.ConclusionsPGA facilitates rapid, accurate, and flexible batch annotation of plastomes across plants. For projects in which multiple plastomes are generated, the time savings for high-quality plastome annotation are especially significant. |
| WOS研究方向 | Biochemistry & Molecular Biology ; Plant Sciences |
| 语种 | 英语 |
| WOS记录号 | WOS:000470655100001 |
| 源URL | [http://ir.kib.ac.cn/handle/151853/67336]  |
| 专题 | 昆明植物研究所_中国西南野生生物种质资源库 |
| 通讯作者 | Li, De-Zhu; Yi, Ting-Shuang |
| 作者单位 | 1.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, 132 Lanhei Rd, Kunming 650204, Yunnan, Peoples R China 2.Shandong Normal Univ, Coll Life Sci, Inst Biomed Sci, Shandong Prov Key Lab Anim Resistance Biol, Jinan, Shandong, Peoples R China 3.Oberlin Coll, Dept Biol, Oberlin, OH 44074 USA |
| 推荐引用方式 GB/T 7714 | Qu, Xiao-Jian,Moore, Michael J.,Li, De-Zhu,et al. PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes[J]. PLANT METHODS,2019,15:12. |
| APA | Qu, Xiao-Jian,Moore, Michael J.,Li, De-Zhu,&Yi, Ting-Shuang.(2019).PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes.PLANT METHODS,15,12. |
| MLA | Qu, Xiao-Jian,et al."PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes".PLANT METHODS 15(2019):12. |
入库方式： OAI收割
来源：昆明植物研究所
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