Assembly and Comparative Analysis of Complete Mitochondrial Genome Sequence of Endangered Medicinal Plant <i>Trichopus zeylanicus</i>
Plant mitochondrial genomes exhibit extensive size variability and structural complexity. Here, we report the complete mitochondrial genome of <i>Trichopus zeylanicus</i>, an endemic medicinal plant from the Western Ghats. The mitochondrial genome was assembled using a combination of Ill...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-07-01
|
| Series: | Current Issues in Molecular Biology |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1467-3045/47/7/553 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849246332778184704 |
|---|---|
| author | Biju Vadakkemukadiyil Chellappan P. R. Shidhi Anu Sasi Rashid Ismael Hag Ibrahim Hamad Abu Zahra |
| author_facet | Biju Vadakkemukadiyil Chellappan P. R. Shidhi Anu Sasi Rashid Ismael Hag Ibrahim Hamad Abu Zahra |
| author_sort | Biju Vadakkemukadiyil Chellappan |
| collection | DOAJ |
| description | Plant mitochondrial genomes exhibit extensive size variability and structural complexity. Here, we report the complete mitochondrial genome of <i>Trichopus zeylanicus</i>, an endemic medicinal plant from the Western Ghats. The mitochondrial genome was assembled using a combination of Illumina short-read and PacBio long-read sequencing technologies, followed by extensive annotation and comparative analysis. The circular mitogenome spans 709,127 bp with a GC content of 46%, encoding 32 protein-coding genes, 17 tRNAs, and three rRNAs. Comparative analysis with other monocot mitochondrial genomes revealed conserved gene clusters but also significant lineage-specific rearrangements. Despite genome size similarities, <i>T. zeylanicus</i> displayed marked divergence in gene order, suggesting that genome size does not necessarily correlate with structural conservation. The genome contains 6.7% chloroplast-derived sequences and 324 predicted RNA-editing sites, predominantly in the first and second codon positions. Phylogenetic analysis based on mitochondrial genes placed <i>T. zeylanicus</i> as a distinct lineage within Dioscoreales, supporting its evolutionary uniqueness. This work provides the first mitogenomic resource for Dioscoreales and advances our understanding of mitochondrial diversity and evolution in monocots. |
| format | Article |
| id | doaj-art-84bf06fda1bc4bdca17bed9fdd1158ff |
| institution | Kabale University |
| issn | 1467-3037 1467-3045 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Current Issues in Molecular Biology |
| spelling | doaj-art-84bf06fda1bc4bdca17bed9fdd1158ff2025-08-20T03:58:31ZengMDPI AGCurrent Issues in Molecular Biology1467-30371467-30452025-07-0147755310.3390/cimb47070553Assembly and Comparative Analysis of Complete Mitochondrial Genome Sequence of Endangered Medicinal Plant <i>Trichopus zeylanicus</i>Biju Vadakkemukadiyil Chellappan0P. R. Shidhi1Anu Sasi2Rashid Ismael Hag Ibrahim3Hamad Abu Zahra4Department of Biological Sciences, College of Science, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi ArabiaDepartment of Zoology, University of Kerala, Kariyavattom Campus, Thiruvananthapuram 695581, Kerala, IndiaDepartment of Computational Biology and Bioinformatics, University of Kerala, Kariyavattom Campus, Thiruvananthapuram 695581, Kerala, IndiaDepartment of Biological Sciences, College of Science, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi ArabiaDepartment of Biological Sciences, College of Science, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi ArabiaPlant mitochondrial genomes exhibit extensive size variability and structural complexity. Here, we report the complete mitochondrial genome of <i>Trichopus zeylanicus</i>, an endemic medicinal plant from the Western Ghats. The mitochondrial genome was assembled using a combination of Illumina short-read and PacBio long-read sequencing technologies, followed by extensive annotation and comparative analysis. The circular mitogenome spans 709,127 bp with a GC content of 46%, encoding 32 protein-coding genes, 17 tRNAs, and three rRNAs. Comparative analysis with other monocot mitochondrial genomes revealed conserved gene clusters but also significant lineage-specific rearrangements. Despite genome size similarities, <i>T. zeylanicus</i> displayed marked divergence in gene order, suggesting that genome size does not necessarily correlate with structural conservation. The genome contains 6.7% chloroplast-derived sequences and 324 predicted RNA-editing sites, predominantly in the first and second codon positions. Phylogenetic analysis based on mitochondrial genes placed <i>T. zeylanicus</i> as a distinct lineage within Dioscoreales, supporting its evolutionary uniqueness. This work provides the first mitogenomic resource for Dioscoreales and advances our understanding of mitochondrial diversity and evolution in monocots.https://www.mdpi.com/1467-3045/47/7/553genetic diversitycomparative genomicscodon usage biasmitochondrial repetitive elements |
| spellingShingle | Biju Vadakkemukadiyil Chellappan P. R. Shidhi Anu Sasi Rashid Ismael Hag Ibrahim Hamad Abu Zahra Assembly and Comparative Analysis of Complete Mitochondrial Genome Sequence of Endangered Medicinal Plant <i>Trichopus zeylanicus</i> Current Issues in Molecular Biology genetic diversity comparative genomics codon usage bias mitochondrial repetitive elements |
| title | Assembly and Comparative Analysis of Complete Mitochondrial Genome Sequence of Endangered Medicinal Plant <i>Trichopus zeylanicus</i> |
| title_full | Assembly and Comparative Analysis of Complete Mitochondrial Genome Sequence of Endangered Medicinal Plant <i>Trichopus zeylanicus</i> |
| title_fullStr | Assembly and Comparative Analysis of Complete Mitochondrial Genome Sequence of Endangered Medicinal Plant <i>Trichopus zeylanicus</i> |
| title_full_unstemmed | Assembly and Comparative Analysis of Complete Mitochondrial Genome Sequence of Endangered Medicinal Plant <i>Trichopus zeylanicus</i> |
| title_short | Assembly and Comparative Analysis of Complete Mitochondrial Genome Sequence of Endangered Medicinal Plant <i>Trichopus zeylanicus</i> |
| title_sort | assembly and comparative analysis of complete mitochondrial genome sequence of endangered medicinal plant i trichopus zeylanicus i |
| topic | genetic diversity comparative genomics codon usage bias mitochondrial repetitive elements |
| url | https://www.mdpi.com/1467-3045/47/7/553 |
| work_keys_str_mv | AT bijuvadakkemukadiyilchellappan assemblyandcomparativeanalysisofcompletemitochondrialgenomesequenceofendangeredmedicinalplantitrichopuszeylanicusi AT prshidhi assemblyandcomparativeanalysisofcompletemitochondrialgenomesequenceofendangeredmedicinalplantitrichopuszeylanicusi AT anusasi assemblyandcomparativeanalysisofcompletemitochondrialgenomesequenceofendangeredmedicinalplantitrichopuszeylanicusi AT rashidismaelhagibrahim assemblyandcomparativeanalysisofcompletemitochondrialgenomesequenceofendangeredmedicinalplantitrichopuszeylanicusi AT hamadabuzahra assemblyandcomparativeanalysisofcompletemitochondrialgenomesequenceofendangeredmedicinalplantitrichopuszeylanicusi |