Characterization of the mitochondrial Huso huso genome and new aspects of its organization in the presence of tandem repeats in 12S rRNA
Abstract Background The sturgeon group has been economically significant worldwide due to caviar production. Sturgeons consist of 27 species in the world. Mitogenome data could be used to infer genetic diversity and investigate the evolutionary history of sturgeons. A limited number of complete mito...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2023-09-01
|
| Series: | BMC Ecology and Evolution |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12862-023-02166-2 |
| _version_ | 1797578529248903168 |
|---|---|
| author | Khadijeh Dadkhah Ghodrat Rahimi Mianji Ali Barzegar Ayoub Farhadi |
| author_facet | Khadijeh Dadkhah Ghodrat Rahimi Mianji Ali Barzegar Ayoub Farhadi |
| author_sort | Khadijeh Dadkhah |
| collection | DOAJ |
| description | Abstract Background The sturgeon group has been economically significant worldwide due to caviar production. Sturgeons consist of 27 species in the world. Mitogenome data could be used to infer genetic diversity and investigate the evolutionary history of sturgeons. A limited number of complete mitogenomes in this family were sequenced. Here, we annotated the mitochondrial Huso huso genome, which revealed new aspects of this species. Results In this species, the mitochondrial genome consisted of 13 genes encoding proteins, 22tRNA and 2rRNA, and two non-coding regions that followed other vertebrates. In addition, H. huso had a pseudo-tRNA-Glu between ND6 and Cytb and a 52-nucleotide tandem repeat with two replications in 12S rRNA. This duplication event is probably related to the slipped strand during replication, which could remain in the strand due to mispairing during replication. Furthermore, an 82 bp repeat sequence with three replications was observed in the D-loop control region, which is usually visible in different species. Regulatory elements were also seen in the control region of the mitochondrial genome, which included termination sequences and conserved regulatory blocks. Genomic compounds showed the highest conservation in rRNA and tRNA, while protein-encoded genes and nonencoded regions had the highest divergence. The mitochondrial genome was phylogenetically assayed using 12 protein-encoding genes. Conclusions In H. huso sequencing, we identified a distinct genome organization relative to other species that have never been reported. In recent years, along with the advancement in sequencing identified more genome rearrangements. However, it is an essential aspect of researching the evolution of the mitochondrial genome that needs to be recognized. |
| first_indexed | 2024-03-10T22:24:03Z |
| format | Article |
| id | doaj.art-50087cd1fe304d3e9508441b6c4b6235 |
| institution | Directory Open Access Journal |
| issn | 2730-7182 |
| language | English |
| last_indexed | 2024-03-10T22:24:03Z |
| publishDate | 2023-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Ecology and Evolution |
| spelling | doaj.art-50087cd1fe304d3e9508441b6c4b62352023-11-19T12:10:52ZengBMCBMC Ecology and Evolution2730-71822023-09-0123111210.1186/s12862-023-02166-2Characterization of the mitochondrial Huso huso genome and new aspects of its organization in the presence of tandem repeats in 12S rRNAKhadijeh Dadkhah0Ghodrat Rahimi Mianji1Ali Barzegar2Ayoub Farhadi3Laboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources UniversityLaboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources UniversityDepartment of Basic Sciences, Sari Agricultural Sciences and Natural Resources UniversityLaboratory for Molecular Genetics and Animal Biotechnology, Faculty of Animal Sciences and Fisheries, Sari Agricultural Sciences and Natural Resources UniversityAbstract Background The sturgeon group has been economically significant worldwide due to caviar production. Sturgeons consist of 27 species in the world. Mitogenome data could be used to infer genetic diversity and investigate the evolutionary history of sturgeons. A limited number of complete mitogenomes in this family were sequenced. Here, we annotated the mitochondrial Huso huso genome, which revealed new aspects of this species. Results In this species, the mitochondrial genome consisted of 13 genes encoding proteins, 22tRNA and 2rRNA, and two non-coding regions that followed other vertebrates. In addition, H. huso had a pseudo-tRNA-Glu between ND6 and Cytb and a 52-nucleotide tandem repeat with two replications in 12S rRNA. This duplication event is probably related to the slipped strand during replication, which could remain in the strand due to mispairing during replication. Furthermore, an 82 bp repeat sequence with three replications was observed in the D-loop control region, which is usually visible in different species. Regulatory elements were also seen in the control region of the mitochondrial genome, which included termination sequences and conserved regulatory blocks. Genomic compounds showed the highest conservation in rRNA and tRNA, while protein-encoded genes and nonencoded regions had the highest divergence. The mitochondrial genome was phylogenetically assayed using 12 protein-encoding genes. Conclusions In H. huso sequencing, we identified a distinct genome organization relative to other species that have never been reported. In recent years, along with the advancement in sequencing identified more genome rearrangements. However, it is an essential aspect of researching the evolution of the mitochondrial genome that needs to be recognized.https://doi.org/10.1186/s12862-023-02166-2Huso husoMitogenomeSturgeonCaspian SeaTandem repeats |
| spellingShingle | Khadijeh Dadkhah Ghodrat Rahimi Mianji Ali Barzegar Ayoub Farhadi Characterization of the mitochondrial Huso huso genome and new aspects of its organization in the presence of tandem repeats in 12S rRNA BMC Ecology and Evolution Huso huso Mitogenome Sturgeon Caspian Sea Tandem repeats |
| title | Characterization of the mitochondrial Huso huso genome and new aspects of its organization in the presence of tandem repeats in 12S rRNA |
| title_full | Characterization of the mitochondrial Huso huso genome and new aspects of its organization in the presence of tandem repeats in 12S rRNA |
| title_fullStr | Characterization of the mitochondrial Huso huso genome and new aspects of its organization in the presence of tandem repeats in 12S rRNA |
| title_full_unstemmed | Characterization of the mitochondrial Huso huso genome and new aspects of its organization in the presence of tandem repeats in 12S rRNA |
| title_short | Characterization of the mitochondrial Huso huso genome and new aspects of its organization in the presence of tandem repeats in 12S rRNA |
| title_sort | characterization of the mitochondrial huso huso genome and new aspects of its organization in the presence of tandem repeats in 12s rrna |
| topic | Huso huso Mitogenome Sturgeon Caspian Sea Tandem repeats |
| url | https://doi.org/10.1186/s12862-023-02166-2 |
| work_keys_str_mv | AT khadijehdadkhah characterizationofthemitochondrialhusohusogenomeandnewaspectsofitsorganizationinthepresenceoftandemrepeatsin12srrna AT ghodratrahimimianji characterizationofthemitochondrialhusohusogenomeandnewaspectsofitsorganizationinthepresenceoftandemrepeatsin12srrna AT alibarzegar characterizationofthemitochondrialhusohusogenomeandnewaspectsofitsorganizationinthepresenceoftandemrepeatsin12srrna AT ayoubfarhadi characterizationofthemitochondrialhusohusogenomeandnewaspectsofitsorganizationinthepresenceoftandemrepeatsin12srrna |