Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species
Abstract Fish mitochondrial genome have been largely studied worldwide for evolutionary and other genetic purposes and the structure and gene organization are commonly conservative. However, several studies have demonstrated that this scenario may present variations in some taxa, showing differentia...
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| Format: | Article |
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Nature Portfolio
2024-02-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-024-52979-4 |
| _version_ | 1797274573018759168 |
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| author | Valdemiro Muhala Aurycéia Guimarães-Costa Adam Rick Bessa-Silva Luan Pinto Rabelo Jeferson Carneiro Isadola Eusébio Macate Luciana Watanabe Oscar David Balcázar Grazielle Evangelista Gomes Marcelo Vallinoto Iracilda Sampaio |
| author_facet | Valdemiro Muhala Aurycéia Guimarães-Costa Adam Rick Bessa-Silva Luan Pinto Rabelo Jeferson Carneiro Isadola Eusébio Macate Luciana Watanabe Oscar David Balcázar Grazielle Evangelista Gomes Marcelo Vallinoto Iracilda Sampaio |
| author_sort | Valdemiro Muhala |
| collection | DOAJ |
| description | Abstract Fish mitochondrial genome have been largely studied worldwide for evolutionary and other genetic purposes and the structure and gene organization are commonly conservative. However, several studies have demonstrated that this scenario may present variations in some taxa, showing differentiation on the gene rearrangement. In this study, the complete mitogenome of terrestrial fish Boleophthalmus dussumieri was generated and compared with other species of the Exudercidae fishes. The newly complete mitogenome generated is circular and 16,685 bp of length, and it contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNAs), 22 transfer RNA genes (tRNAs), and one control region (CR), with high conservative structure, like other Mudskippers. Most of the PCG showed similar codon usage bias. The gene length was found to be different specially for the CR, 12S rRNA gene and ND5 gene in some taxon. All the Boleophthalmus species showed a gene duplication in the CR, except for B. dussumieri, and they presented a long intergenic spacer specially on the tRNA-Pro/ OH Tandem duplication/random loss (TDRL) and dimer-mitogenome and nonrandom loss (DMNL) are suitable to explain the mitogenome rearrangement observed in this study. The phylogenetic analysis well supported the monophyly of all mudskipper species and the analysis positioned the Periophthalmus clade as the most basal of the terrestrial fishes. This finding provides basis and brings insights for gene variation, gene rearrangements and replications showing evidence for variety of mitochondrial structure diversity within mudskippers. |
| first_indexed | 2024-03-07T15:01:16Z |
| format | Article |
| id | doaj.art-5132cdb25df64b3480ca9dede4e6fee4 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-07T15:01:16Z |
| publishDate | 2024-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-5132cdb25df64b3480ca9dede4e6fee42024-03-05T19:09:03ZengNature PortfolioScientific Reports2045-23222024-02-0114111710.1038/s41598-024-52979-4Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper speciesValdemiro Muhala0Aurycéia Guimarães-Costa1Adam Rick Bessa-Silva2Luan Pinto Rabelo3Jeferson Carneiro4Isadola Eusébio Macate5Luciana Watanabe6Oscar David Balcázar7Grazielle Evangelista Gomes8Marcelo Vallinoto9Iracilda Sampaio10Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do ParáLaboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do ParáLaboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do ParáLaboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do ParáLaboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do ParáLaboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do ParáLaboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do ParáLaboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do ParáLaboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do ParáLaboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do ParáLaboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do ParáAbstract Fish mitochondrial genome have been largely studied worldwide for evolutionary and other genetic purposes and the structure and gene organization are commonly conservative. However, several studies have demonstrated that this scenario may present variations in some taxa, showing differentiation on the gene rearrangement. In this study, the complete mitogenome of terrestrial fish Boleophthalmus dussumieri was generated and compared with other species of the Exudercidae fishes. The newly complete mitogenome generated is circular and 16,685 bp of length, and it contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNAs), 22 transfer RNA genes (tRNAs), and one control region (CR), with high conservative structure, like other Mudskippers. Most of the PCG showed similar codon usage bias. The gene length was found to be different specially for the CR, 12S rRNA gene and ND5 gene in some taxon. All the Boleophthalmus species showed a gene duplication in the CR, except for B. dussumieri, and they presented a long intergenic spacer specially on the tRNA-Pro/ OH Tandem duplication/random loss (TDRL) and dimer-mitogenome and nonrandom loss (DMNL) are suitable to explain the mitogenome rearrangement observed in this study. The phylogenetic analysis well supported the monophyly of all mudskipper species and the analysis positioned the Periophthalmus clade as the most basal of the terrestrial fishes. This finding provides basis and brings insights for gene variation, gene rearrangements and replications showing evidence for variety of mitochondrial structure diversity within mudskippers.https://doi.org/10.1038/s41598-024-52979-4 |
| spellingShingle | Valdemiro Muhala Aurycéia Guimarães-Costa Adam Rick Bessa-Silva Luan Pinto Rabelo Jeferson Carneiro Isadola Eusébio Macate Luciana Watanabe Oscar David Balcázar Grazielle Evangelista Gomes Marcelo Vallinoto Iracilda Sampaio Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species Scientific Reports |
| title | Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species |
| title_full | Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species |
| title_fullStr | Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species |
| title_full_unstemmed | Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species |
| title_short | Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species |
| title_sort | comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species |
| url | https://doi.org/10.1038/s41598-024-52979-4 |
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