ArticleBMC plant biology2022
Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution.
Article in BMC plant biology, 2022. 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.
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- Deciphering the Plastome and Molecular Identities of Six Medicinal "Doukou" Species.International journal of molecular sciences · 2024Article
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- The complete chloroplast genome sequence ofMitochondrial DNA. Part B, Resources · 2024Article
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- The complete chloroplast genome of Cicer reticulatum and comparative analysis against relative Cicer species.Scientific reports · 2023Article
- Plastome evolution and phylogenomic insights into the evolution of Lysimachia (Primulaceae: Myrsinoideae).BMC plant biology · 2023Article
- Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae).BMC genomics · 2023Article
- The Complete Chloroplast Genome of AnGenes · 2023Article
- Comparative and phylogenetic analysis of the complete chloroplast genomes ofFrontiers in plant science · 2023Article
- Comparative chloroplast genome analysis ofFrontiers in plant science · 2023Article
- Plastome phylogenomics provide new perspective into the phylogeny and evolution of Betulaceae (Fagales).BMC plant biology · 2022Article
- The Complete Chloroplast Genome ofGenes · 2022Article
- Comparative Genomics and Phylogenetic Analysis of the Chloroplast Genomes in Three MedicinalInternational journal of molecular sciences · 2022Article
- The complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2022Article
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7 authors.
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Abstract
backgroundThe large and diverse Coffeeae alliance clade of subfamily Ixoroideae (Rubiaceae) consists of 10 tribes, > 90 genera, and > 2000 species. Previous molecular phylogenetics using limited numbers of markers were often unable to fully resolve the phylogenetic relationships at tribal and generic levels. Also, the structural variations of plastomes (PSVs) within the Coffeeae alliance tribes have been poorly investigated in previous studies. To fully understand the phylogenetic relationships and PSVs within the clade, highly reliable and sufficient sampling with superior next-generation analysis techniques is required. In this study, 71 plastomes (40 newly sequenced and assembled and the rest from the GenBank) were comparatively analyzed to decipher the PSVs and resolve the phylogenetic relationships of the Coffeeae alliance using four molecular data matrices.
resultsAll plastomes are typically quadripartite with the size ranging from 153,055 to 155,908 bp and contained 111 unique genes. The inverted repeat (IR) regions experienced multiple contraction and expansion; five repeat types were detected but the most abundant was SSR. The size of the Coffeeae alliance clade plastomes and its elements are affected by the IR boundary shifts and the repeat types. However, the emerging PSVs had no taxonomic and phylogenetic implications. Eight highly divergent regions were identified within the plastome regions ndhF, ccsA, ndhD, ndhA, ndhH, ycf1, rps16-trnQ-UUG, and psbM-trnD. These highly variable regions may be potential molecular markers for further species delimitation and population genetic analyses for the clade. Our plastome phylogenomic analyses yielded a well-resolved phylogeny tree with well-support at the tribal and generic levels within the Coffeeae alliance.
conclusionsPlastome data could be indispensable in resolving the phylogenetic relationships of the Coffeeae alliance tribes. Therefore, this study provides deep insights into the PSVs and phylogenetic relationships of the Coffeeae alliance and the Rubiaceae family as a whole.
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