ArticleNucleic acids research2019
CPGAVAS2, an integrated plastome sequence annotator and analyzer.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 917 papers.
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917 citing papers in PubMed.
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- Comparative plastome analyses of Lewinskya (Orthotrichaceae): insights into genome structure, molecular evolution, and phylogenetic relationships.BMC plant biology · 2026Article
- Rubus chingii chloroplast genome sequences: a comparative analysis with other Rubus L.chloroplast genomes.BMC genomics · 2026Article
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- Integrating plastome comparison and phylogenetic analyses reveals the phylogenetic relationships of Pachypleurum (Apiaceae).BMC plant biology · 2026Article
- Genetic and metabolite diversity of Sundaland Heptapleurum (Araliaceae) insight into evolutionary and specialized metabolite.BMC plant biology · 2026Article
- Characterisation of the chloroplast genome of Macrotyloma species: comparative analysis and phylogenomic insights.Scientific reports · 2026Article
- Assembly and Comparative Analysis of the Complete Mitochondrial Genome ofCurrent issues in molecular biology · 2026Article
- Chloroplast Phylogenomics and Evolutionary History of the Alpine EndemicInternational journal of molecular sciences · 2026Article
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7 authors.
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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.
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