The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage
Abstract Organellar genomes of liverworts are considered as one of the most stable among plants, with rare events of gene loss and structural rearrangements. However, not all lineages of liverworts are equally explored in the field of organellar genomics, and subclass Pellidae is one of the less kno...
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| Format: | Article |
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Nature Portfolio
2023-05-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-35269-3 |
| _version_ | 1827939953778098176 |
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| author | Łukasz Paukszto Piotr Górski Katarzyna Krawczyk Mateusz Maździarz Monika Szczecińska Monika Ślipiko Jakub Sawicki |
| author_facet | Łukasz Paukszto Piotr Górski Katarzyna Krawczyk Mateusz Maździarz Monika Szczecińska Monika Ślipiko Jakub Sawicki |
| author_sort | Łukasz Paukszto |
| collection | DOAJ |
| description | Abstract Organellar genomes of liverworts are considered as one of the most stable among plants, with rare events of gene loss and structural rearrangements. However, not all lineages of liverworts are equally explored in the field of organellar genomics, and subclass Pellidae is one of the less known. Hybrid assembly, using both short- and long-read technologies enabled the assembly of repeat-rich mitogenomes of Pellia and Apopellia revealing extraordinary reduction of length in the latter which impacts only intergenic spacers. The mitogenomes of Apopellia were revealed to be the smallest among all known liverworts—109 k bp, despite retaining all introns. The study also showed the loss of one tRNA gene in Apopellia mitogenome, although it had no impact on the codon usage pattern of mitochondrial protein coding genes. Moreover, it was revealed that Apopellia and Pellia differ in codon usage by plastome CDSs, despite identical tRNA gene content. Molecular identification of species is especially important where traditional taxonomic methods fail, especially within Pellidae where cryptic speciation is well recognized. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. Application of super-barcodes, based on complete mitochondrial or plastid genomes sequences enable identification of all cryptic lineages within Apopellia and Pellia genera, however in some particular cases, mitogenomes were more efficient in species delimitation than plastomes. |
| first_indexed | 2024-03-13T09:02:20Z |
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| id | doaj.art-1b3909ee13fa48ce90b0972070f622e2 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-13T09:02:20Z |
| publishDate | 2023-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-1b3909ee13fa48ce90b0972070f622e22023-05-28T11:14:54ZengNature PortfolioScientific Reports2045-23222023-05-0113111710.1038/s41598-023-35269-3The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineageŁukasz Paukszto0Piotr Górski1Katarzyna Krawczyk2Mateusz Maździarz3Monika Szczecińska4Monika Ślipiko5Jakub Sawicki6Department of Botany and Nature Protection, University of Warmia and Mazury in OlsztynDepartment of Botany, Poznań University of Life SciencesDepartment of Botany and Nature Protection, University of Warmia and Mazury in OlsztynDepartment of Botany and Nature Protection, University of Warmia and Mazury in OlsztynDepartment of Ecology and Environmental Protection, University of Warmia and Mazury in OlsztynDepartment of Botany and Nature Protection, University of Warmia and Mazury in OlsztynDepartment of Botany and Nature Protection, University of Warmia and Mazury in OlsztynAbstract Organellar genomes of liverworts are considered as one of the most stable among plants, with rare events of gene loss and structural rearrangements. However, not all lineages of liverworts are equally explored in the field of organellar genomics, and subclass Pellidae is one of the less known. Hybrid assembly, using both short- and long-read technologies enabled the assembly of repeat-rich mitogenomes of Pellia and Apopellia revealing extraordinary reduction of length in the latter which impacts only intergenic spacers. The mitogenomes of Apopellia were revealed to be the smallest among all known liverworts—109 k bp, despite retaining all introns. The study also showed the loss of one tRNA gene in Apopellia mitogenome, although it had no impact on the codon usage pattern of mitochondrial protein coding genes. Moreover, it was revealed that Apopellia and Pellia differ in codon usage by plastome CDSs, despite identical tRNA gene content. Molecular identification of species is especially important where traditional taxonomic methods fail, especially within Pellidae where cryptic speciation is well recognized. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. Application of super-barcodes, based on complete mitochondrial or plastid genomes sequences enable identification of all cryptic lineages within Apopellia and Pellia genera, however in some particular cases, mitogenomes were more efficient in species delimitation than plastomes.https://doi.org/10.1038/s41598-023-35269-3 |
| spellingShingle | Łukasz Paukszto Piotr Górski Katarzyna Krawczyk Mateusz Maździarz Monika Szczecińska Monika Ślipiko Jakub Sawicki The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage Scientific Reports |
| title | The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage |
| title_full | The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage |
| title_fullStr | The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage |
| title_full_unstemmed | The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage |
| title_short | The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage |
| title_sort | organellar genomes of pellidae marchantiophyta the evidence of cryptic speciation conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage |
| url | https://doi.org/10.1038/s41598-023-35269-3 |
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