Plastome phylogenomics of the diverse neotropical orchid genus Lepanthes with emphasis on subgenus Marsipanthes (Pleurothallidinae: Orchidaceae)
Abstract Well-resolved phylogenetic relationships within the diverse Neotropical orchid genus Lepanthes are presented based on a genome skimming approach that yielded nine newly sequenced chloroplast genomes. We complemented this with 17–86 plastome coding genes for 26 species retrieved from GenBank...
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BMC
2025-08-01
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| Series: | BMC Ecology and Evolution |
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| Online Access: | https://doi.org/10.1186/s12862-025-02396-6 |
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| author | Tatiana Arias Juan Sebastian Moreno Sebastian Reyes Martin Llano Almario Alejandra Serna-Sánchez Gabriel A. Iturralde Janice Valencia Luis Baquero Alejandro Zuluaga |
| author_facet | Tatiana Arias Juan Sebastian Moreno Sebastian Reyes Martin Llano Almario Alejandra Serna-Sánchez Gabriel A. Iturralde Janice Valencia Luis Baquero Alejandro Zuluaga |
| author_sort | Tatiana Arias |
| collection | DOAJ |
| description | Abstract Well-resolved phylogenetic relationships within the diverse Neotropical orchid genus Lepanthes are presented based on a genome skimming approach that yielded nine newly sequenced chloroplast genomes. We complemented this with 17–86 plastome coding genes for 26 species retrieved from GenBank, alongside amplified matK and rITS regions. The Lepanthes plastomes (157,185—158,260 bp, 37.15% GC content) contained 136 annotated genes, including 86 protein-coding, 42 tRNA, and 8 rRNA genes. We identified six hypervariable regions, including parts of the ycf1 gene, as potential DNA barcodes. Phylogenetic analyses revealed that Carl Luer’s subgeneric classifications are non-monophyletic, a finding confirmed by PCA of continuous morphological traits, reflecting significant morphological homoplasy. Six major clades were identified, though resolution for the phylogenetic backbone remains unresolved at two nodes. Subgenus Marsipanthes is not monophyletic as currently circumscribed, with two subclades recovered in distinct positions within the phylogeny. An early-diverging lineage, comprising species restricted to the eastern Andean slopes from southern Colombia to Peru, includes members of both Marsipanthes and Lepanthes. A derived clade, consisting of species from both subgenera, confined to the Chocó biogeographic region, forms an unresolved polytomy. Although only a subset of Lepanthes diversity was sampled, this study captures significant taxonomic, geographic, and morphological variation. It provides foundational insights into the genu's evolutionary history, along with tools and hypotheses that can be expanded upon in future research to further refine our understanding of its biogeographic history. |
| format | Article |
| id | doaj-art-aabf9310bf4b428fb8517233a46cc3b1 |
| institution | DOAJ |
| issn | 2730-7182 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Ecology and Evolution |
| spelling | doaj-art-aabf9310bf4b428fb8517233a46cc3b12025-08-20T03:04:07ZengBMCBMC Ecology and Evolution2730-71822025-08-0125112010.1186/s12862-025-02396-6Plastome phylogenomics of the diverse neotropical orchid genus Lepanthes with emphasis on subgenus Marsipanthes (Pleurothallidinae: Orchidaceae)Tatiana Arias0Juan Sebastian Moreno1Sebastian Reyes2Martin Llano Almario3Alejandra Serna-Sánchez4Gabriel A. Iturralde5Janice Valencia6Luis Baquero7Alejandro Zuluaga8Marie Selby Botanical GardensJardín Botánico de Cali-FZCPrograma de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de CaldasDepartamento de Biología, Universidad del ValleCentro de Investigación Jardín Botánico Lankester, Universidad de Costa RicaGrupo de Investigación en Biodiversidad, Medio Ambiente y Salud (BIOMAS), Carrera de Ingeniería Agroindustrial, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas UDLAFacultad de Ingeniería, Max Planck Tandem Group, Universidad Nacional de ColombiaGrupo de Investigación en Biodiversidad, Medio Ambiente y Salud (BIOMAS), Carrera de Ingeniería Agroindustrial, Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas UDLADepartamento de Biología, Universidad del ValleAbstract Well-resolved phylogenetic relationships within the diverse Neotropical orchid genus Lepanthes are presented based on a genome skimming approach that yielded nine newly sequenced chloroplast genomes. We complemented this with 17–86 plastome coding genes for 26 species retrieved from GenBank, alongside amplified matK and rITS regions. The Lepanthes plastomes (157,185—158,260 bp, 37.15% GC content) contained 136 annotated genes, including 86 protein-coding, 42 tRNA, and 8 rRNA genes. We identified six hypervariable regions, including parts of the ycf1 gene, as potential DNA barcodes. Phylogenetic analyses revealed that Carl Luer’s subgeneric classifications are non-monophyletic, a finding confirmed by PCA of continuous morphological traits, reflecting significant morphological homoplasy. Six major clades were identified, though resolution for the phylogenetic backbone remains unresolved at two nodes. Subgenus Marsipanthes is not monophyletic as currently circumscribed, with two subclades recovered in distinct positions within the phylogeny. An early-diverging lineage, comprising species restricted to the eastern Andean slopes from southern Colombia to Peru, includes members of both Marsipanthes and Lepanthes. A derived clade, consisting of species from both subgenera, confined to the Chocó biogeographic region, forms an unresolved polytomy. Although only a subset of Lepanthes diversity was sampled, this study captures significant taxonomic, geographic, and morphological variation. It provides foundational insights into the genu's evolutionary history, along with tools and hypotheses that can be expanded upon in future research to further refine our understanding of its biogeographic history.https://doi.org/10.1186/s12862-025-02396-6AndesChloroplastColombiaEastern AndesChocó Biogeographic RegionEcuador |
| spellingShingle | Tatiana Arias Juan Sebastian Moreno Sebastian Reyes Martin Llano Almario Alejandra Serna-Sánchez Gabriel A. Iturralde Janice Valencia Luis Baquero Alejandro Zuluaga Plastome phylogenomics of the diverse neotropical orchid genus Lepanthes with emphasis on subgenus Marsipanthes (Pleurothallidinae: Orchidaceae) BMC Ecology and Evolution Andes Chloroplast Colombia Eastern Andes Chocó Biogeographic Region Ecuador |
| title | Plastome phylogenomics of the diverse neotropical orchid genus Lepanthes with emphasis on subgenus Marsipanthes (Pleurothallidinae: Orchidaceae) |
| title_full | Plastome phylogenomics of the diverse neotropical orchid genus Lepanthes with emphasis on subgenus Marsipanthes (Pleurothallidinae: Orchidaceae) |
| title_fullStr | Plastome phylogenomics of the diverse neotropical orchid genus Lepanthes with emphasis on subgenus Marsipanthes (Pleurothallidinae: Orchidaceae) |
| title_full_unstemmed | Plastome phylogenomics of the diverse neotropical orchid genus Lepanthes with emphasis on subgenus Marsipanthes (Pleurothallidinae: Orchidaceae) |
| title_short | Plastome phylogenomics of the diverse neotropical orchid genus Lepanthes with emphasis on subgenus Marsipanthes (Pleurothallidinae: Orchidaceae) |
| title_sort | plastome phylogenomics of the diverse neotropical orchid genus lepanthes with emphasis on subgenus marsipanthes pleurothallidinae orchidaceae |
| topic | Andes Chloroplast Colombia Eastern Andes Chocó Biogeographic Region Ecuador |
| url | https://doi.org/10.1186/s12862-025-02396-6 |
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