PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes
PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes
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DOI：
10.1186/s13007-019-0435-7
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发表时间：
2019-05-21
期刊：
影响因子：
5.1
通讯作者：
Yi, Ting-Shuang
中科院分区：
文献类型：
--
作者：
Qu, Xiao-Jian;Moore, Michael J.;Yi, Ting-Shuang
背景质体体基因组序列为了解植物的系统发育关系和进化历史提供了有价值的信息。尽管高通量测序技术的快速发展导致了质体组序列的爆炸性增长，但注释仍然是质体组的一个重要瓶颈。结果介绍了一个独立的命令行工具plettid Genome Annotator(PGA)，它可以基于标注良好的参考质体对新生成的目标质体进行快速、准确和灵活的批量注释。与现有工具不同，PGA使用参考质体体作为查询，以未注释的目标质体体作为主题来定位基因，我们称之为反向查询主题BLAST搜索方法。PGA准确识别基因和内含子边界以及内含子丢失。该程序输出GenBank格式的文件以及日志文件，以帮助用户验证注释。与其他可用的质体组注释工具的比较表明，PGA具有很高的注释准确性，几乎不需要注释后验证。同样，我们通过以毛足目Amborella的质体组为参照对刺梨的质体组进行注释，展示了PGA中参照质体体的灵活性。程序、用户手册和示例数据集在https://github.com/quxiaojian/PGA.ConclusionsPGA上免费提供，有助于快速、准确和灵活地对植物中的质体体进行批量注释。对于产生多个质粒体的项目，高质量质粒组注释的时间节省尤其显著。
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.