This result was congruent with earlier findings for a collection of 99 chloroplast genomes of photosynthetic Eucaryotic lineages that asked: which are the genes shared by all the species of a collection (‘core genome’, 106 genes in ) and conversely, which are all the genes found considering the species of the collection (‘pan genome’, the 126 genes in )? Therefore, among the 126 genes found in a large set of angiosperm chloroplast genomes (272 species, including gymnosperms, eudicots, monocots, and basal angiosperms), 106 were shared by 245 species (90%) and 13 were present in only 27 species (9.9%). In terms of gene content and order, conservation is observed for the majority of genes. In consequence complete chloroplast sequences are more and more widely used and provide invaluable data for doubtful phylogenies, plant evolution, barcoding and for a better understanding of patterns of gene loss or of adaptive changes in relation to photosynthesis. The development of low-cost high-throughput sequencing has permitted huge amounts of raw data of both nuclear and plastid sequences to be obtained. įor several decades, plastid sequences polymorphisms have been used to assess with more or less accuracy maternal phylogenetic relationships between orders, families, tribes, genera and species. This organization is generally highly conserved with some exceptions reported such as loss of inverted repeats in gymnosperms. In plants, the chloroplast genome is circular with generally a quadripartite structure including two copies of a large inverted repeat (IR) separated by large and small single-copy regions (LSC and SSC, respectively). This does not alter our adherence to all the PLOS ONE policies on sharing data and materials. There are no patents, products in development or marketed products to declare. The specific role of this author is articulated in the ‘author contributions’ section.Ĭompeting interests: Dominique Crouzillat is employed by Nestlé Centre Tours. Nestlé Centre Tours provided support in the form of salary for author DC, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. Author Dominique Crouzillat is employed by Nestlé Centre Tours. arabica (accession NC_008535) sequence at ( ). This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: The data underlying this study are available in the NCBI repository from the C. Received: NovemAccepted: ApPublished: June 12, 2019Ĭopyright: © 2019 Guyeux et al. PLoS ONE 14(6):Įditor: Tzen-Yuh Chiang, National Cheng Kung University, TAIWAN (2019) Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species. 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.Ĭitation: Guyeux C, Charr J-C, Tran HTM, Furtado A, Henry RJ, Crouzillat D, et al. While Arabica coffee ( Coffea arabica) belongs to the Coffea genus, Robusta coffee ( Coffea canephora) is associated with the Psilanthus genus. Arabica and Robusta) did not group into the same clade and differ in their pattern of gene evolution. Notably, the two main cultivated coffee species (i.e. Eight genes in the plant chloroplast pan genome (consisting of 92 genes) were always absent in the coffee species analyzed. 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. This suggests that the annotation of most of the previously annotated chloroplast genomes should now be updated. More consistent detection and annotation of genes were produced with GeSeq when compared to the currently used Dogma. In this study, the two main tools for chloroplast genome annotation were compared. 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. Chloroplast sequences are widely used for phylogenetic analysis due to their high degree of conservation in plants.
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