Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of <i>Aythya marila</i>
<i>Aythya marila</i> is a large diving duck belonging to the family Anatidae. However, the phylogenetic relationship among these <i>Aythya</i> species remains unclear due to the presence of extensive interspecific hybridization events within the <i>Aythya</i> genu...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-05-01
|
| Series: | Genes |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-4425/14/6/1205 |
| _version_ | 1797594682881998848 |
|---|---|
| author | Lei Zhang Tian Xia Xiaodong Gao Xiufeng Yang Guolei Sun Chao Zhao Guangshuai Liu Honghai Zhang |
| author_facet | Lei Zhang Tian Xia Xiaodong Gao Xiufeng Yang Guolei Sun Chao Zhao Guangshuai Liu Honghai Zhang |
| author_sort | Lei Zhang |
| collection | DOAJ |
| description | <i>Aythya marila</i> is a large diving duck belonging to the family Anatidae. However, the phylogenetic relationship among these <i>Aythya</i> species remains unclear due to the presence of extensive interspecific hybridization events within the <i>Aythya</i> genus. Here, we sequenced and annotated the complete mitochondrial genome of <i>A. marila</i>, which contained 22 tRNAs, 13 protein-coding genes (PCGs), 2 ribosomal RNAs, and 1 D-loop, with a length of 16,617 bp. The sizes of the PCGs ranged from 297 to 1824 bp and were all, except for <i>ND6</i>, located on the heavy chain (H). ATG and TAA were the most common start and termination codons of the 13 PCGs, respectively. The fastest- and slowest-evolving genes were <i>ATP8</i> and <i>COI</i>, respectively. Codon usage analysis indicated that CUA, AUC, GCC, UUC, CUC, and ACC were the six most frequent codons. The nucleotide diversity values indicated a high level of genetic diversity in <i>A. marila</i>. <i>F</i><sub>ST</sub> analysis suggested a widespread gene exchange between <i>A. baeri</i> and <i>A. nyroca</i>. Moreover, phylogenetic reconstructions using the mitochondrial genomes of all available Anatidae species showed that, in addition to <i>A. marila</i>, four major clades among the Anatidae (Dendrocygninae, Oxyurinae, Anserinae, and Anatinae) were closely related to <i>A. fuligula</i>. Overall, this study provides valuable information on the evolution of <i>A. marila</i> and new insights into the phylogeny of Anatidae. |
| first_indexed | 2024-03-11T02:25:45Z |
| format | Article |
| id | doaj.art-c59a324297324c289cd9a3a49b73f192 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T02:25:45Z |
| publishDate | 2023-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-c59a324297324c289cd9a3a49b73f1922023-11-18T10:34:15ZengMDPI AGGenes2073-44252023-05-01146120510.3390/genes14061205Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of <i>Aythya marila</i>Lei Zhang0Tian Xia1Xiaodong Gao2Xiufeng Yang3Guolei Sun4Chao Zhao5Guangshuai Liu6Honghai Zhang7College of Life Science, Qufu Normal University, Qufu 273165, ChinaCollege of Life Science, Qufu Normal University, Qufu 273165, ChinaCollege of Life Science, Qufu Normal University, Qufu 273165, ChinaCollege of Life Science, Qufu Normal University, Qufu 273165, ChinaCollege of Life Science, Qufu Normal University, Qufu 273165, ChinaCollege of Life Science, Qufu Normal University, Qufu 273165, ChinaCollege of Life Science, Qufu Normal University, Qufu 273165, ChinaCollege of Life Science, Qufu Normal University, Qufu 273165, China<i>Aythya marila</i> is a large diving duck belonging to the family Anatidae. However, the phylogenetic relationship among these <i>Aythya</i> species remains unclear due to the presence of extensive interspecific hybridization events within the <i>Aythya</i> genus. Here, we sequenced and annotated the complete mitochondrial genome of <i>A. marila</i>, which contained 22 tRNAs, 13 protein-coding genes (PCGs), 2 ribosomal RNAs, and 1 D-loop, with a length of 16,617 bp. The sizes of the PCGs ranged from 297 to 1824 bp and were all, except for <i>ND6</i>, located on the heavy chain (H). ATG and TAA were the most common start and termination codons of the 13 PCGs, respectively. The fastest- and slowest-evolving genes were <i>ATP8</i> and <i>COI</i>, respectively. Codon usage analysis indicated that CUA, AUC, GCC, UUC, CUC, and ACC were the six most frequent codons. The nucleotide diversity values indicated a high level of genetic diversity in <i>A. marila</i>. <i>F</i><sub>ST</sub> analysis suggested a widespread gene exchange between <i>A. baeri</i> and <i>A. nyroca</i>. Moreover, phylogenetic reconstructions using the mitochondrial genomes of all available Anatidae species showed that, in addition to <i>A. marila</i>, four major clades among the Anatidae (Dendrocygninae, Oxyurinae, Anserinae, and Anatinae) were closely related to <i>A. fuligula</i>. Overall, this study provides valuable information on the evolution of <i>A. marila</i> and new insights into the phylogeny of Anatidae.https://www.mdpi.com/2073-4425/14/6/1205greater scaupAnatidaephylogenymitochondrial genome |
| spellingShingle | Lei Zhang Tian Xia Xiaodong Gao Xiufeng Yang Guolei Sun Chao Zhao Guangshuai Liu Honghai Zhang Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of <i>Aythya marila</i> Genes greater scaup Anatidae phylogeny mitochondrial genome |
| title | Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of <i>Aythya marila</i> |
| title_full | Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of <i>Aythya marila</i> |
| title_fullStr | Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of <i>Aythya marila</i> |
| title_full_unstemmed | Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of <i>Aythya marila</i> |
| title_short | Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of <i>Aythya marila</i> |
| title_sort | characterization and phylogenetic analysis of the complete mitochondrial genome of i aythya marila i |
| topic | greater scaup Anatidae phylogeny mitochondrial genome |
| url | https://www.mdpi.com/2073-4425/14/6/1205 |
| work_keys_str_mv | AT leizhang characterizationandphylogeneticanalysisofthecompletemitochondrialgenomeofiaythyamarilai AT tianxia characterizationandphylogeneticanalysisofthecompletemitochondrialgenomeofiaythyamarilai AT xiaodonggao characterizationandphylogeneticanalysisofthecompletemitochondrialgenomeofiaythyamarilai AT xiufengyang characterizationandphylogeneticanalysisofthecompletemitochondrialgenomeofiaythyamarilai AT guoleisun characterizationandphylogeneticanalysisofthecompletemitochondrialgenomeofiaythyamarilai AT chaozhao characterizationandphylogeneticanalysisofthecompletemitochondrialgenomeofiaythyamarilai AT guangshuailiu characterizationandphylogeneticanalysisofthecompletemitochondrialgenomeofiaythyamarilai AT honghaizhang characterizationandphylogeneticanalysisofthecompletemitochondrialgenomeofiaythyamarilai |