PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes

doi:10.1186/s13007-019-0435-7

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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
刊名	PLANT METHODS
	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
内容类型	期刊论文
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.