Characterization of the Complete Mitochondrial Genome of <i>Agelas nakamurai</i> from the South China Sea
The <i>Agelas</i> genus sponges are widely distributed and provide shelter for organisms that inhabit reefs. However, there is a lack of research on the genetic diversity of the <i>Agelas</i> sponges. Additionally, only one <i>Agelas</i> mitochondrial genome has b...
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MDPI AG
2023-12-01
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| Series: | International Journal of Molecular Sciences |
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| author | Zijian Lu Qiang Lin Huixian Zhang |
| author_facet | Zijian Lu Qiang Lin Huixian Zhang |
| author_sort | Zijian Lu |
| collection | DOAJ |
| description | The <i>Agelas</i> genus sponges are widely distributed and provide shelter for organisms that inhabit reefs. However, there is a lack of research on the genetic diversity of the <i>Agelas</i> sponges. Additionally, only one <i>Agelas</i> mitochondrial genome has been documented, leaving the characteristics of the <i>Agelas</i> genus’s mitogenome in need of further clarification. To address this research gap, we utilized Illumina HiSeq4000 sequencing and de novo assembly to ascertain the complete mitochondrial genome of <i>Agelas</i> sp. specimens, sourced from the South China Sea. Our analysis of the <i>cox1</i> barcoding similarity and phylogenetic relationship reveals that taxonomically, the <i>Agelas</i> sp. corresponds to <i>Agelas nakamurai</i>. The mitogenome of <i>Agelas nakamurai</i> is 20,885 bp in length, encoding 14 protein-coding genes, 24 transfer RNA genes, and 2 ribosomal RNA genes. Through a comparison of the mitochondrial genes, we discovered that both <i>Agelas nakamurai</i> and <i>Agelas schmidti</i> have an identical gene arrangement. Furthermore, we observed a deletion in the <i>trnD</i> gene and duplication and remodeling of the <i>trnL</i> gene in the <i>Agelas nakamurai</i>’s mitogenome. Our evolutionary analysis also identified lineage-specific positive selection sites in the <i>nad3</i> and <i>nad5</i> genes of the <i>Agelas</i> sponges’ mitogenome. These findings shed light on the gene rearrangement events and positive selection sites in the mitogenome of <i>Agelas nakamurai</i>, providing valuable molecular insights into the evolutionary processes of this genus. |
| first_indexed | 2024-03-08T15:05:01Z |
| format | Article |
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| language | English |
| last_indexed | 2024-03-08T15:05:01Z |
| publishDate | 2023-12-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-1a473c3746674697b3308be676b02f652024-01-10T14:59:11ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-12-0125135710.3390/ijms25010357Characterization of the Complete Mitochondrial Genome of <i>Agelas nakamurai</i> from the South China SeaZijian Lu0Qiang Lin1Huixian Zhang2CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510000, ChinaCAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510000, ChinaCAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510000, ChinaThe <i>Agelas</i> genus sponges are widely distributed and provide shelter for organisms that inhabit reefs. However, there is a lack of research on the genetic diversity of the <i>Agelas</i> sponges. Additionally, only one <i>Agelas</i> mitochondrial genome has been documented, leaving the characteristics of the <i>Agelas</i> genus’s mitogenome in need of further clarification. To address this research gap, we utilized Illumina HiSeq4000 sequencing and de novo assembly to ascertain the complete mitochondrial genome of <i>Agelas</i> sp. specimens, sourced from the South China Sea. Our analysis of the <i>cox1</i> barcoding similarity and phylogenetic relationship reveals that taxonomically, the <i>Agelas</i> sp. corresponds to <i>Agelas nakamurai</i>. The mitogenome of <i>Agelas nakamurai</i> is 20,885 bp in length, encoding 14 protein-coding genes, 24 transfer RNA genes, and 2 ribosomal RNA genes. Through a comparison of the mitochondrial genes, we discovered that both <i>Agelas nakamurai</i> and <i>Agelas schmidti</i> have an identical gene arrangement. Furthermore, we observed a deletion in the <i>trnD</i> gene and duplication and remodeling of the <i>trnL</i> gene in the <i>Agelas nakamurai</i>’s mitogenome. Our evolutionary analysis also identified lineage-specific positive selection sites in the <i>nad3</i> and <i>nad5</i> genes of the <i>Agelas</i> sponges’ mitogenome. These findings shed light on the gene rearrangement events and positive selection sites in the mitogenome of <i>Agelas nakamurai</i>, providing valuable molecular insights into the evolutionary processes of this genus.https://www.mdpi.com/1422-0067/25/1/357<i>Agelas</i>mitochondrial genomephylogenypositive selection |
| spellingShingle | Zijian Lu Qiang Lin Huixian Zhang Characterization of the Complete Mitochondrial Genome of <i>Agelas nakamurai</i> from the South China Sea International Journal of Molecular Sciences <i>Agelas</i> mitochondrial genome phylogeny positive selection |
| title | Characterization of the Complete Mitochondrial Genome of <i>Agelas nakamurai</i> from the South China Sea |
| title_full | Characterization of the Complete Mitochondrial Genome of <i>Agelas nakamurai</i> from the South China Sea |
| title_fullStr | Characterization of the Complete Mitochondrial Genome of <i>Agelas nakamurai</i> from the South China Sea |
| title_full_unstemmed | Characterization of the Complete Mitochondrial Genome of <i>Agelas nakamurai</i> from the South China Sea |
| title_short | Characterization of the Complete Mitochondrial Genome of <i>Agelas nakamurai</i> from the South China Sea |
| title_sort | characterization of the complete mitochondrial genome of i agelas nakamurai i from the south china sea |
| topic | <i>Agelas</i> mitochondrial genome phylogeny positive selection |
| url | https://www.mdpi.com/1422-0067/25/1/357 |
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