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

Abstract

Background Plastome (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. Results We 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 . Conclusions PGA 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.

The complete chloroplast genome sequences of Anoectochilus nandanensis and A. calcareus

“…DNA data were sequenced using the Illumina Hiseq 2500 platform (Illumina, San Diego, CA, USA). Subsequently, chloroplast genome assembly using GetOrganelle (Jin et al 2018) and the annotation was performed with PGA (Qu et al 2019), then confirmed manually. Finally, the complete chloroplast genome was deposited in GenBank (accessible numbers: MT021458 and MT021459).…”

Assembly and phylogenetic analysis of the complete chloroplast genome sequence of Epimedium simplicifolium (Berberidaceae), an endangered species endemic to China

“…In this pipeline, the complete cp genome reads were extracted from total genomic reads and were subsequently assembled using SPAdes version 3.10 (Bankevich et al 2012). The genes were annotated using PGA (Qu et al 2019) and Geneious 11.0.3 (Kearse et al 2012) with the published complete cp genome of E. lishihchenii (GenBank accession number: NC_029944) as the reference. Transfer RNAs (tRNAs) were confirmed by their specific structure predicted by tRNAscan-SE 2.0 (Lowe and Chan 2016).…”

Chloroplast genome features and phylogenomic placement of Lespedeza bicolor (Fabaceae)

“…Plastome assembly was performed with Organelle Genome Assembler (OGA) as described in Qu, Fan, et al (2019). Plastome annotation was performed with Plastid Genome Annotator (PGA) (Qu, Moore, et al 2019), with manual correction with Geneious v9.1.4. The annotated complete plastome was submitted to GenBank under accession number MT083894.…”