Assembly, Characterization, and Phylogenetic Relationships of Mitogenomes of Two Species of Mexican Trout (<i>Oncorhynchus chrysogaster</i> and <i>O. mykiss nelsoni</i>)
In this study, the complete mitochondrial genomes of the Mexican golden trout, <i>Oncorhynchus chrysogaster</i>, and Nelson’s trout, <i>O. mykiss nelsoni</i>, were assembled and characterized. The mitogenomes were 16,655 bp and 16,661 bp long, respectively, and were composed...
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MDPI AG
2023-03-01
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| Series: | Fishes |
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| Online Access: | https://www.mdpi.com/2410-3888/8/4/178 |
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| author | Angélica Colín Miguel A. Del Río-Portilla Fabiola Lafarga-De la Cruz Genoveva Ingle-De la Mora Francisco J. García-De León |
| author_facet | Angélica Colín Miguel A. Del Río-Portilla Fabiola Lafarga-De la Cruz Genoveva Ingle-De la Mora Francisco J. García-De León |
| author_sort | Angélica Colín |
| collection | DOAJ |
| description | In this study, the complete mitochondrial genomes of the Mexican golden trout, <i>Oncorhynchus chrysogaster</i>, and Nelson’s trout, <i>O. mykiss nelsoni</i>, were assembled and characterized. The mitogenomes were 16,655 bp and 16,661 bp long, respectively, and were composed of 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes (all with typical ‘cloverleaf’ secondary structures). The length of the D-loop regions was among the longest found in Salmonids, and mitochondrial synteny in both species was identical to that reported in other Salmonids. Selective pressure analysis in the PCGs indicated that purifying selection, mainly among <i>cox</i> and <i>nd</i> genes families, likely generated the main differences between the two studied species. Nine tRNA genes showed slight differences relative to other <i>O. mykiss</i> subspecies, which were identical between the two study taxa. The origin of the light-strand replication has a loop that was especially large in <i>O. mykiss nelsoni</i>. Phylogenetic analysis indicated that <i>O. chrysogaster</i> and <i>O. mykiss nelsoni</i> are sister species, contrary to the expectation that <i>O. chrysogaster</i> would cluster with <i>O. gilae</i>. As previous studies have suggested, <i>O. chrysogaster</i> and <i>O. mykiss nelsoni</i> share common ancestry with North American trout species. |
| first_indexed | 2024-03-11T05:02:27Z |
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| id | doaj.art-c5fae70c4c424c7f9aff9f6dc62d0b00 |
| institution | Directory Open Access Journal |
| issn | 2410-3888 |
| language | English |
| last_indexed | 2024-03-11T05:02:27Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Fishes |
| spelling | doaj.art-c5fae70c4c424c7f9aff9f6dc62d0b002023-11-17T19:12:20ZengMDPI AGFishes2410-38882023-03-018417810.3390/fishes8040178Assembly, Characterization, and Phylogenetic Relationships of Mitogenomes of Two Species of Mexican Trout (<i>Oncorhynchus chrysogaster</i> and <i>O. mykiss nelsoni</i>)Angélica Colín0Miguel A. Del Río-Portilla1Fabiola Lafarga-De la Cruz2Genoveva Ingle-De la Mora3Francisco J. García-De León4Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas del Noroeste, Instituto Politécnico Nacional, No. 195, Col. Playa Palo de Santa Rita, La Paz CP 23096, Baja California Sur, MexicoDepartamento de Acuicultura, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana, No. 3918, Zona Playitas, Ensenada CP 22860, Baja California, MexicoDepartamento de Acuicultura, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana, No. 3918, Zona Playitas, Ensenada CP 22860, Baja California, MexicoInstituto Nacional de Pesca y Acuacultura, Secretaría de Agricultura y Desarrollo Rural (SADER), Avenida México, No. 190, Col del Carmen, Coyoacán CP 04100, Ciudad de México, MexicoLaboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas del Noroeste, Instituto Politécnico Nacional, No. 195, Col. Playa Palo de Santa Rita, La Paz CP 23096, Baja California Sur, MexicoIn this study, the complete mitochondrial genomes of the Mexican golden trout, <i>Oncorhynchus chrysogaster</i>, and Nelson’s trout, <i>O. mykiss nelsoni</i>, were assembled and characterized. The mitogenomes were 16,655 bp and 16,661 bp long, respectively, and were composed of 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes (all with typical ‘cloverleaf’ secondary structures). The length of the D-loop regions was among the longest found in Salmonids, and mitochondrial synteny in both species was identical to that reported in other Salmonids. Selective pressure analysis in the PCGs indicated that purifying selection, mainly among <i>cox</i> and <i>nd</i> genes families, likely generated the main differences between the two studied species. Nine tRNA genes showed slight differences relative to other <i>O. mykiss</i> subspecies, which were identical between the two study taxa. The origin of the light-strand replication has a loop that was especially large in <i>O. mykiss nelsoni</i>. Phylogenetic analysis indicated that <i>O. chrysogaster</i> and <i>O. mykiss nelsoni</i> are sister species, contrary to the expectation that <i>O. chrysogaster</i> would cluster with <i>O. gilae</i>. As previous studies have suggested, <i>O. chrysogaster</i> and <i>O. mykiss nelsoni</i> share common ancestry with North American trout species.https://www.mdpi.com/2410-3888/8/4/178SalmonidaeMexican golden troutNelson’s troutmitochondrial genometaxonomic statusfish |
| spellingShingle | Angélica Colín Miguel A. Del Río-Portilla Fabiola Lafarga-De la Cruz Genoveva Ingle-De la Mora Francisco J. García-De León Assembly, Characterization, and Phylogenetic Relationships of Mitogenomes of Two Species of Mexican Trout (<i>Oncorhynchus chrysogaster</i> and <i>O. mykiss nelsoni</i>) Fishes Salmonidae Mexican golden trout Nelson’s trout mitochondrial genome taxonomic status fish |
| title | Assembly, Characterization, and Phylogenetic Relationships of Mitogenomes of Two Species of Mexican Trout (<i>Oncorhynchus chrysogaster</i> and <i>O. mykiss nelsoni</i>) |
| title_full | Assembly, Characterization, and Phylogenetic Relationships of Mitogenomes of Two Species of Mexican Trout (<i>Oncorhynchus chrysogaster</i> and <i>O. mykiss nelsoni</i>) |
| title_fullStr | Assembly, Characterization, and Phylogenetic Relationships of Mitogenomes of Two Species of Mexican Trout (<i>Oncorhynchus chrysogaster</i> and <i>O. mykiss nelsoni</i>) |
| title_full_unstemmed | Assembly, Characterization, and Phylogenetic Relationships of Mitogenomes of Two Species of Mexican Trout (<i>Oncorhynchus chrysogaster</i> and <i>O. mykiss nelsoni</i>) |
| title_short | Assembly, Characterization, and Phylogenetic Relationships of Mitogenomes of Two Species of Mexican Trout (<i>Oncorhynchus chrysogaster</i> and <i>O. mykiss nelsoni</i>) |
| title_sort | assembly characterization and phylogenetic relationships of mitogenomes of two species of mexican trout i oncorhynchus chrysogaster i and i o mykiss nelsoni i |
| topic | Salmonidae Mexican golden trout Nelson’s trout mitochondrial genome taxonomic status fish |
| url | https://www.mdpi.com/2410-3888/8/4/178 |
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