Comparative Mitochondrial Genomes between the Genera <i>Amiota</i> and <i>Phortica</i> (Diptera: Drosophilidae) with Evolutionary Insights into D-Loop Sequence Variability
To address the limited number of mitochondrial genomes (mitogenomes) in the subfamily Steganinae (Diptera: Drosophilidae), we assembled 12 complete mitogenomes for six representative species in the genus <i>Amiota</i> and six representative species in the genus <i>Phortica</i>...
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MDPI AG
2023-06-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/6/1240 |
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| author | Caihong Zhang Yalian Wang Hongwei Chen Jia Huang |
| author_facet | Caihong Zhang Yalian Wang Hongwei Chen Jia Huang |
| author_sort | Caihong Zhang |
| collection | DOAJ |
| description | To address the limited number of mitochondrial genomes (mitogenomes) in the subfamily Steganinae (Diptera: Drosophilidae), we assembled 12 complete mitogenomes for six representative species in the genus <i>Amiota</i> and six representative species in the genus <i>Phortica</i>. We performed a series of comparative and phylogenetic analyses for these 12 Steganinae mitogenomes, paying special attention to the commonalities and differences in the D-loop sequences. Primarily determined by the lengths of the D-loop regions, the sizes of the <i>Amiota</i> and <i>Phortica</i> mitogenomes ranged from 16,143–16,803 bp and 15,933–16,290 bp, respectively. Our results indicated that the sizes of genes and intergenic nucleotides (IGNs), codon usage and amino acid usage, compositional skewness levels, evolutionary rates of protein-coding genes (PCGs), and D-loop sequence variability all showed unambiguous genus-specific characteristics and provided novel insights into the evolutionary implications between and within <i>Amiota</i> and <i>Phortica</i>. Most of the consensus motifs were found downstream of the D-loop regions, and some of them showed distinct genus-specific patterns. In addition, the D-loop sequences were phylogenetically informative as the data sets of PCGs and/or rRNAs, especially within the genus <i>Phortica</i>. |
| first_indexed | 2024-03-11T02:25:15Z |
| format | Article |
| id | doaj.art-4a1cd227173844ddaf11276fb630456a |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T02:25:15Z |
| publishDate | 2023-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-4a1cd227173844ddaf11276fb630456a2023-11-18T10:34:45ZengMDPI AGGenes2073-44252023-06-01146124010.3390/genes14061240Comparative Mitochondrial Genomes between the Genera <i>Amiota</i> and <i>Phortica</i> (Diptera: Drosophilidae) with Evolutionary Insights into D-Loop Sequence VariabilityCaihong Zhang0Yalian Wang1Hongwei Chen2Jia Huang3Department of Entomology, South China Agricultural University, 483 Wushan-Lu, Guangzhou 510642, ChinaDepartment of Entomology, South China Agricultural University, 483 Wushan-Lu, Guangzhou 510642, ChinaDepartment of Entomology, South China Agricultural University, 483 Wushan-Lu, Guangzhou 510642, ChinaDepartment of Entomology, South China Agricultural University, 483 Wushan-Lu, Guangzhou 510642, ChinaTo address the limited number of mitochondrial genomes (mitogenomes) in the subfamily Steganinae (Diptera: Drosophilidae), we assembled 12 complete mitogenomes for six representative species in the genus <i>Amiota</i> and six representative species in the genus <i>Phortica</i>. We performed a series of comparative and phylogenetic analyses for these 12 Steganinae mitogenomes, paying special attention to the commonalities and differences in the D-loop sequences. Primarily determined by the lengths of the D-loop regions, the sizes of the <i>Amiota</i> and <i>Phortica</i> mitogenomes ranged from 16,143–16,803 bp and 15,933–16,290 bp, respectively. Our results indicated that the sizes of genes and intergenic nucleotides (IGNs), codon usage and amino acid usage, compositional skewness levels, evolutionary rates of protein-coding genes (PCGs), and D-loop sequence variability all showed unambiguous genus-specific characteristics and provided novel insights into the evolutionary implications between and within <i>Amiota</i> and <i>Phortica</i>. Most of the consensus motifs were found downstream of the D-loop regions, and some of them showed distinct genus-specific patterns. In addition, the D-loop sequences were phylogenetically informative as the data sets of PCGs and/or rRNAs, especially within the genus <i>Phortica</i>.https://www.mdpi.com/2073-4425/14/6/1240mitogenomephylogenycontrol regionSteganinae |
| spellingShingle | Caihong Zhang Yalian Wang Hongwei Chen Jia Huang Comparative Mitochondrial Genomes between the Genera <i>Amiota</i> and <i>Phortica</i> (Diptera: Drosophilidae) with Evolutionary Insights into D-Loop Sequence Variability Genes mitogenome phylogeny control region Steganinae |
| title | Comparative Mitochondrial Genomes between the Genera <i>Amiota</i> and <i>Phortica</i> (Diptera: Drosophilidae) with Evolutionary Insights into D-Loop Sequence Variability |
| title_full | Comparative Mitochondrial Genomes between the Genera <i>Amiota</i> and <i>Phortica</i> (Diptera: Drosophilidae) with Evolutionary Insights into D-Loop Sequence Variability |
| title_fullStr | Comparative Mitochondrial Genomes between the Genera <i>Amiota</i> and <i>Phortica</i> (Diptera: Drosophilidae) with Evolutionary Insights into D-Loop Sequence Variability |
| title_full_unstemmed | Comparative Mitochondrial Genomes between the Genera <i>Amiota</i> and <i>Phortica</i> (Diptera: Drosophilidae) with Evolutionary Insights into D-Loop Sequence Variability |
| title_short | Comparative Mitochondrial Genomes between the Genera <i>Amiota</i> and <i>Phortica</i> (Diptera: Drosophilidae) with Evolutionary Insights into D-Loop Sequence Variability |
| title_sort | comparative mitochondrial genomes between the genera i amiota i and i phortica i diptera drosophilidae with evolutionary insights into d loop sequence variability |
| topic | mitogenome phylogeny control region Steganinae |
| url | https://www.mdpi.com/2073-4425/14/6/1240 |
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