ArticlePloS one2019
Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 43 citations in OpenAlex.
- Refined chloroplast annotations, repeat profiles, and phylogenomic evidence reveal maternal lineage shifts and independent evolution in the Triticum-Aegilops complex.BMC plant biology · 2026Article
- The complete chloroplast genome sequence ofMitochondrial DNA. Part B, Resources · 2024Article
- The complete chloroplast genome sequence and phylogenetic analysis ofMitochondrial DNA. Part B, Resources · 2024Article
- The evolutionary history of three Baracoffea species from western Madagascar revealed by chloroplast and nuclear genomes.PloS one · 2024Article
- A comprehensive genus-level phylogeny and biogeographical history of the Lythraceae based on whole plastome sequences.Annals of botany · 2023Article
- The chloroplast protein HCF164 is predicted to be associated with Coffea SScientific reports · 2023Article
- Article
- Progress, challenge and prospect of plant plastome annotation.Frontiers in plant science · 2023Review
- The complete mitochondrial genome ofMitochondrial DNA. Part B, Resources · 2023Article
- Chloroplast Genome Annotation Tools: Prolegomena to the Identification of Inverted Repeats.International journal of molecular sciences · 2022Article
- Comparison of Magnoliaceae Plastomes: Adding NeotropicalPlants (Basel, Switzerland) · 2022Article
- Phylogenetic relationships in the Sorghum genus based on sequencing of the chloroplast and nuclear genes.The plant genome · 2021Article
- airpg: automatically accessing the inverted repeats of archived plastid genomes.BMC bioinformatics · 2021Article
- Towards the Well-Tempered Chloroplast DNA Sequences.Plants (Basel, Switzerland) · 2021Article
- CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA.PLoS computational biology · 2021Article
- Long-read assemblies reveal structural diversity in genomes of organelles - an example withGigaByte (Hong Kong, China) · 2021Article
- Chloroplast genome analysis of Angiosperms and phylogenetic relationships among Lamiaceae members with particular reference to teak (Journal of biosciences · 2021Article
- WCSdb: a database of wild Coffea species.Database : the journal of biological databases and curation · 2020Article
- Two divergent chloroplast genome sequence clades captured in the domesticated rice gene pool may have significance for rice production.BMC plant biology · 2020Article
- Chloroplast genomes of Rubiaceae: Comparative genomics and molecular phylogeny in subfamily Ixoroideae.PloS one · 2020Article
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Authors and funding
8 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chloroplast sequences are widely used for phylogenetic analysis due to their high degree of conservation in plants. Whole chloroplast genomes can now be readily obtained for plant species using new sequencing methods, giving invaluable data for plant evolution However new annotation methods are required for the efficient analysis of this data to deliver high quality phylogenetic analyses. In this study, the two main tools for chloroplast genome annotation were compared. More consistent detection and annotation of genes were produced with GeSeq when compared to the currently used Dogma. This suggests that the annotation of most of the previously annotated chloroplast genomes should now be updated. GeSeq was applied to species related to coffee, including 16 species of the Coffea and Psilanthus genera to reconstruct the ancestral chloroplast genomes and to evaluate their phylogenetic relationships. Eight genes in the plant chloroplast pan genome (consisting of 92 genes) were always absent in the coffee species analyzed. Notably, the two main cultivated coffee species (i.e. Arabica and Robusta) did not group into the same clade and differ in their pattern of gene evolution. While Arabica coffee (Coffea arabica) belongs to the Coffea genus, Robusta coffee (Coffea canephora) is associated with the Psilanthus genus. A more extensive survey of related species is required to determine if this is a unique attribute of Robusta coffee or a more widespread feature of coffee tree species.
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