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| Main Authors: | , , , , , , , , , |
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| Format: | Artículo científico |
| Language: | en |
| Published: |
Biomolecules
2026
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| Subjects: | |
| Online Access: | https://pubmed.ncbi.nlm.nih.gov/41750256/ |
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| _version_ | 1868266079693832194 |
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| author | Wujdi, Arief Putra, Angkasa Aini, Sarifah Bang, Gyurim Go, Yunji Kim, Ah Ran Lee, Soo Rin Kang, Kyoungmi Kim, Hyun-Woo Kundu, Shantanu |
| author_facet | Wujdi, Arief Putra, Angkasa Aini, Sarifah Bang, Gyurim Go, Yunji Kim, Ah Ran Lee, Soo Rin Kang, Kyoungmi Kim, Hyun-Woo Kundu, Shantanu Wujdi, Arief Putra, Angkasa Aini, Sarifah Bang, Gyurim Go, Yunji Kim, Ah Ran Lee, Soo Rin Kang, Kyoungmi Kim, Hyun-Woo Kundu, Shantanu |
| collection | PubMed - marine biology |
| contents | Mitogenomic Insights into the Hampala Barb () from Sumatra, Indonesia: Characterization, Phylogenetic Placement, and Genetic Diversity. Wujdi, Arief Putra, Angkasa Aini, Sarifah Bang, Gyurim Go, Yunji Kim, Ah Ran Lee, Soo Rin Kang, Kyoungmi Kim, Hyun-Woo Kundu, Shantanu Animals Phylogeny Indonesia Genome, Mitochondrial Genetic Variation Cyprinidae Despite its ecological and economic importance, (Cyprinidae: Smiliogastrinae) remains taxonomically debated, having undergone historical reclassifications across multiple taxonomic ranks. These challenges highlight the urgent need for integrative genomic analyses to resolve its phylogeny and assess genome-wide diversity, establishing a baseline for effective management and conservation. In this study, the newly assembled mitogenome of from within its native range in Lake Dibawah, West Sumatra, Indonesia, was sequenced. The mitogenome spanned 17,104 bp, encoded 37 genes and a control region, and exhibited a nucleotide composition biased toward adenine and thymine. The protein-coding genes (PCGs) predominantly utilized ATG as the initiation codon and showed a higher proportion of hydrophobic compared to hydrophilic amino acids. The nonsynonymous (Ka) and synonymous (Ks) substitution ratios were below '1', which indicates negative selection on most of the PCGs within and other Smiliogastrinae species. Mitogenome-wide analysis revealed overall high intraspecific genetic diversity (≥2.7%) in the native Indonesian population compared to mainland populations in Southeast Asia. The Bayesian and maximum-likelihood phylogenetic analyses elucidated matrilineal evolutionary relationships within the subfamily Smiliogastrinae, with the species forming a monophyletic cluster. The present mitogenome-based phylogenetic topologies also supported the taxonomic placement of several species in the revised classification, which previously were classified under the genera and , respectively. Additionally, the investigation of partial mitochondrial and genes further elucidated the population genetic structure of across Southeast and East Asia. The observed genetic divergence (0-4.2% in and 0-4.5% in ), together with well-resolved phylogenetic clustering and the presence of both shared and distinct haplotypes among Indonesian samples, provides strong evidence for long-term population isolation and local adaptation. These patterns are most plausibly driven by historical hydrological dynamics, paleo-drainage connectivity, and persistent geographic barriers that have structured population divergence over time. In addition, this study emphasizes the need to generate mitogenomes of seven additional species from Southeast Asia to better understand their evolutionary patterns. Further, broader sampling of wild populations across their biogeographical range will be essential to strengthen understanding of their genetic diversity and guide effective conservation strategies. |
| format | Artículo científico |
| id | pubmed_41750256 |
| institution | PubMed |
| language | en |
| publishDate | 2026 |
| publisher | Biomolecules |
| record_format | pubmed |
| spellingShingle | Mitogenomic Insights into the Hampala Barb () from Sumatra, Indonesia: Characterization, Phylogenetic Placement, and Genetic Diversity. Wujdi, Arief Putra, Angkasa Aini, Sarifah Bang, Gyurim Go, Yunji Kim, Ah Ran Lee, Soo Rin Kang, Kyoungmi Kim, Hyun-Woo Kundu, Shantanu Animals Phylogeny Indonesia Genome, Mitochondrial Genetic Variation Cyprinidae Mitogenomic Insights into the Hampala Barb () from Sumatra, Indonesia: Characterization, Phylogenetic Placement, and Genetic Diversity. Wujdi, Arief Putra, Angkasa Aini, Sarifah Bang, Gyurim Go, Yunji Kim, Ah Ran Lee, Soo Rin Kang, Kyoungmi Kim, Hyun-Woo Kundu, Shantanu Animals Phylogeny Indonesia Genome, Mitochondrial Genetic Variation Cyprinidae Despite its ecological and economic importance, (Cyprinidae: Smiliogastrinae) remains taxonomically debated, having undergone historical reclassifications across multiple taxonomic ranks. These challenges highlight the urgent need for integrative genomic analyses to resolve its phylogeny and assess genome-wide diversity, establishing a baseline for effective management and conservation. In this study, the newly assembled mitogenome of from within its native range in Lake Dibawah, West Sumatra, Indonesia, was sequenced. The mitogenome spanned 17,104 bp, encoded 37 genes and a control region, and exhibited a nucleotide composition biased toward adenine and thymine. The protein-coding genes (PCGs) predominantly utilized ATG as the initiation codon and showed a higher proportion of hydrophobic compared to hydrophilic amino acids. The nonsynonymous (Ka) and synonymous (Ks) substitution ratios were below '1', which indicates negative selection on most of the PCGs within and other Smiliogastrinae species. Mitogenome-wide analysis revealed overall high intraspecific genetic diversity (≥2.7%) in the native Indonesian population compared to mainland populations in Southeast Asia. The Bayesian and maximum-likelihood phylogenetic analyses elucidated matrilineal evolutionary relationships within the subfamily Smiliogastrinae, with the species forming a monophyletic cluster. The present mitogenome-based phylogenetic topologies also supported the taxonomic placement of several species in the revised classification, which previously were classified under the genera and , respectively. Additionally, the investigation of partial mitochondrial and genes further elucidated the population genetic structure of across Southeast and East Asia. The observed genetic divergence (0-4.2% in and 0-4.5% in ), together with well-resolved phylogenetic clustering and the presence of both shared and distinct haplotypes among Indonesian samples, provides strong evidence for long-term population isolation and local adaptation. These patterns are most plausibly driven by historical hydrological dynamics, paleo-drainage connectivity, and persistent geographic barriers that have structured population divergence over time. In addition, this study emphasizes the need to generate mitogenomes of seven additional species from Southeast Asia to better understand their evolutionary patterns. Further, broader sampling of wild populations across their biogeographical range will be essential to strengthen understanding of their genetic diversity and guide effective conservation strategies. |
| title | Mitogenomic Insights into the Hampala Barb () from Sumatra, Indonesia: Characterization, Phylogenetic Placement, and Genetic Diversity. |
| topic | Animals Phylogeny Indonesia Genome, Mitochondrial Genetic Variation Cyprinidae |
| url | https://pubmed.ncbi.nlm.nih.gov/41750256/ |