CPGAVAS2, an integrated plastome sequence annotator and analyzer

Abstract

We previously developed a web server CPGAVAS for annotation, visualization and GenBank submission of plastome sequences. Here, we upgrade the server into CPGAVAS2 to address the following challenges: (i) inaccurate annotation in the reference sequence likely causing the propagation of errors; (ii) difficulty in the annotation of small exons of genes petB, petD and rps16 and trans-splicing gene rps12; (iii) lack of annotation for other genome features and their visualization, such as repeat elements; and (iv) lack of modules for diversity analysis of plastomes. In particular, CPGAVAS2 provides two reference datasets for plastome annotation. The first dataset contains 43 plastomes whose annotation have been validated or corrected by RNA-seq data. The second one contains 2544 plastomes curated with sequence alignment. Two new algorithms are also implemented to correctly annotate small exons and trans-splicing genes. Tandem and dispersed repeats are identified, whose results are displayed on a circular map together with the annotated genes. DNA-seq and RNA-seq data can be uploaded for identification of single-nucleotide polymorphism sites and RNA-editing sites. The results of two case studies show that CPGAVAS2 annotates better than several other servers. CPGAVAS2 will likely become an indispensible tool for plastome research and can be accessed from http://www.herbalgenomics.org/cpgavas2.

Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica)

“…Geneious R8.1 de novo assembler (Kearse et al, 2012) was used to order the selected contigs for final assembly. The genome sequence was annotated using GeSeq (Tillich et al, 2017) and CPGAVAS2 (Shi et al, 2019). Following de novo annotation, start/stop codons and the position of introns were manually inspected and curated.…”

Assembly and Analysis of the Complete Mitochondrial Genome of Capsella bursa-pastoris

“…Capsella bursa-pastoris mitogenome was annotated using a MITOFY web server [44], and the chloroplast genome was annotated using a CPGAVAS2 web server [45], with subsequent manual verification and, if necessary, correction of the found gene boundaries by comparison of nucleotide and amino acid sequences with corresponding ortholog sequences in A. thaliana and C. rubella. The annotated mitochondrial and chloroplast genomes of C. bursa-pastoris were submitted to the NCBI GenBank database (assigned accessions MN746809 and MT040199, respectively).…”

The complete chloroplast genome of Epimedium qingchengshanense G. Y. Zhong et B. L. Guo (Berberidaceae), an endangered species endemic to China

“…DNA library preparations were sequenced, and 150 bp pairedend reads were generated on an Illumina Novaseq PE150 platform. The clean reads were assembled using the program GetOrganelle v1.5 (Jin et al 2018) with the reference chloroplast genome of E. acuminatum (GenBank accession number: KU522469), the chloroplast genome annotation was performed through the online program CPGAVAS2 (Shi et al 2019) and GeSeq (Tillich et al 2017), followed by manual correction. The annotated genomic sequence has been registered in GenBank with an accession number (MN815805).…”