Background: The plastid is a semiautonomous organelle with its own genome. Plastid genomes have been widely used as models for studying phylogeny, speciation and adaptive evolution. However, most studies focus on comparisons of plastid genome evolution at high taxonomic levels, and comparative studies of the process of plastome evolution at the infrageneric or intraspecific level remain elusive. Holcoglossum is a small genus of Orchidaceae, consisting of approximately 20 species of recent radiation. This made it an ideal group to explore the plastome mutation mode at the infrageneric or intraspecific level.
Results: In this paper, we reported 15 complete plastid genomes from 12 species of Holcoglossum and 1 species of Vanda. The plastid genomes of Holcoglossum have a total length range between 145 kb and 148 kb, encoding a set of 102 genes. The whole set of ndh-gene families in Holcoglossum have been truncated or pseudogenized. Hairpin inversion in the coding region of the plastid gene ycf2 has been found.
Conclusions: Using a comprehensive comparative plastome analysis, we found that all the indels between different individuals of the same species resulted from the copy number variation of the short repeat sequence, which may be caused by replication slippage. Annotation of tandem repeats shows that the variation introduced by tandem repeats is widespread in plastid genomes. The hairpin inversion found in the plastid gene ycf2 occurred randomly in the Orchidaceae.
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http://dx.doi.org/10.1186/s12862-019-1384-5 | DOI Listing |
Sci Rep
January 2025
Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
Peucedanum japonicum (PJ), a member of the Apiaceae family, is widely distributed and cultivated in East Asian countries for edible and functional foods. In this study, we compared the plastid genomes (plastomes) and 45S nuclear ribosomal DNA (45S nrDNA) simultaneously from 10 PJ collections. Plastome-based phylogenetic analysis showed that the PJ accessions were monophyletic within the genus Peucedanum.
View Article and Find Full Text PDFFunct Integr Genomics
December 2024
Department of Agricultural and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, Brazil.
Mimosa tenuiflora, popularly known as "Jurema-Preta", is a perennial tree or shrub native to the tropical regions of the Americas, particularly among Afro-Brazilian and Indigenous Brazilian communities. Known for producing N,N-Dimethyltryptamine, a psychedelic compound with profound psychological effects, Jurema-Preta has been studied for its therapeutic potential in mental health. This study offers a comprehensive analysis of the plastid (ptDNA) and mitochondrion (mtDNA) genomes of M.
View Article and Find Full Text PDFBMC Plant Biol
December 2024
Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China.
Background: The genus Lithocarpus is a species-rich dominant woody lineage in East Asian evergreen broad-leaved forests. Despite its ecological and economic significance, the plastome structure and evolutionary history of the genus remain poorly understood. In this study, we comprehensively analyzed the 34 plastomes representing 33 Lithocarpus species.
View Article and Find Full Text PDFMol Phylogenet Evol
December 2024
Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
In plants, cellular function is orchestrated by three distinct genomes located within the nucleus, mitochondrion, and plastid. These genomes are interdependent, requiring tightly coordinated maintenance and expression. Plastids host several multisubunit protein complexes encoded by both the plastid and nuclear genomes.
View Article and Find Full Text PDFBMC Plant Biol
December 2024
International Biological Material Research Center (IBMRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, South Korea.
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