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PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes
Qu, Xiao-Jian1,2; Moore, Michael J.3; Li, De-Zhu1; Yi, Ting-Shuang1
Corresponding AuthorLi, De-Zhu(DZL@mail.kib.ac.cn) ; Yi, Ting-Shuang(tingshuangyi@mail.kib.ac.cn)
2019-05-21
Source PublicationPLANT METHODS
ISSN1746-4811
Volume15Pages:12
AbstractBackgroundPlastome (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.
KeywordPGA Plastome Batch annotation Accuracy BLAST Software Algorithms
DOI10.1186/s13007-019-0435-7
Indexed BySCI
Language英语
WOS Research AreaBiochemistry & Molecular Biology ; Plant Sciences
WOS SubjectBiochemical Research Methods ; Plant Sciences
WOS IDWOS:000470655100001
Citation statistics
Cited Times:4[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.kib.ac.cn/handle/151853/67337
Collection中国西南野生生物种质资源库
Corresponding AuthorLi, De-Zhu; Yi, Ting-Shuang
Affiliation1.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
Recommended Citation
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.
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