Chromosome-level genome provides insights into environmental adaptability and innate immunity in the common dolphin (delphinus delphis)
Abstract The common dolphin (Delphinus delphis) is widely distributed worldwide and well adapted to various habitats. Animal genomes store clues about their pasts, and can reveal the genes underlying their evolutionary success. Here, we report the first high-quality chromosome-level genome of D. del...
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| Format: | Article |
| Language: | English |
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BMC
2024-04-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-024-10268-4 |
| _version_ | 1797199589450711040 |
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| author | Kui Ding Qinzeng Xu Liyuan Zhao Yixuan Li Zhong Li Wenge Shi Qianhui Zeng Xianyan Wang Xuelei Zhang |
| author_facet | Kui Ding Qinzeng Xu Liyuan Zhao Yixuan Li Zhong Li Wenge Shi Qianhui Zeng Xianyan Wang Xuelei Zhang |
| author_sort | Kui Ding |
| collection | DOAJ |
| description | Abstract The common dolphin (Delphinus delphis) is widely distributed worldwide and well adapted to various habitats. Animal genomes store clues about their pasts, and can reveal the genes underlying their evolutionary success. Here, we report the first high-quality chromosome-level genome of D. delphis. The assembled genome size was 2.56 Gb with a contig N50 of 63.85 Mb. Phylogenetically, D. delphis was close to Tursiops truncatus and T. aduncus. The genome of D. delphis exhibited 428 expanded and 1,885 contracted gene families, and 120 genes were identified as positively selected. The expansion of the HSP70 gene family suggested that D. delphis has a powerful system for buffering stress, which might be associated with its broad adaptability, longevity, and detoxification capacity. The expanded IFN-α and IFN-ω gene families, as well as the positively selected genes encoding tripartite motif-containing protein 25, peptidyl-prolyl cis-trans isomerase NIMA-interacting 1, and p38 MAP kinase, were all involved in pathways for antiviral, anti-inflammatory, and antineoplastic mechanisms. The genome data also revealed dramatic fluctuations in the effective population size during the Pleistocene. Overall, the high-quality genome assembly and annotation represent significant molecular resources for ecological and evolutionary studies of Delphinus and help support their sustainable treatment and conservation. |
| first_indexed | 2024-04-24T07:18:09Z |
| format | Article |
| id | doaj.art-1388c4c9f45c460d90cb70cafd2b3b88 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-24T07:18:09Z |
| publishDate | 2024-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-1388c4c9f45c460d90cb70cafd2b3b882024-04-21T11:10:07ZengBMCBMC Genomics1471-21642024-04-0125111510.1186/s12864-024-10268-4Chromosome-level genome provides insights into environmental adaptability and innate immunity in the common dolphin (delphinus delphis)Kui Ding0Qinzeng Xu1Liyuan Zhao2Yixuan Li3Zhong Li4Wenge Shi5Qianhui Zeng6Xianyan Wang7Xuelei Zhang8Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural ResourcesKey Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural ResourcesKey Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural ResourcesKey Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural ResourcesKey Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural ResourcesKey Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural ResourcesKey Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural ResourcesKey Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural ResourcesKey Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural ResourcesAbstract The common dolphin (Delphinus delphis) is widely distributed worldwide and well adapted to various habitats. Animal genomes store clues about their pasts, and can reveal the genes underlying their evolutionary success. Here, we report the first high-quality chromosome-level genome of D. delphis. The assembled genome size was 2.56 Gb with a contig N50 of 63.85 Mb. Phylogenetically, D. delphis was close to Tursiops truncatus and T. aduncus. The genome of D. delphis exhibited 428 expanded and 1,885 contracted gene families, and 120 genes were identified as positively selected. The expansion of the HSP70 gene family suggested that D. delphis has a powerful system for buffering stress, which might be associated with its broad adaptability, longevity, and detoxification capacity. The expanded IFN-α and IFN-ω gene families, as well as the positively selected genes encoding tripartite motif-containing protein 25, peptidyl-prolyl cis-trans isomerase NIMA-interacting 1, and p38 MAP kinase, were all involved in pathways for antiviral, anti-inflammatory, and antineoplastic mechanisms. The genome data also revealed dramatic fluctuations in the effective population size during the Pleistocene. Overall, the high-quality genome assembly and annotation represent significant molecular resources for ecological and evolutionary studies of Delphinus and help support their sustainable treatment and conservation.https://doi.org/10.1186/s12864-024-10268-4Delphinus delphisGenome sequencingChromosome assemblyComparative genomicsDemographic history |
| spellingShingle | Kui Ding Qinzeng Xu Liyuan Zhao Yixuan Li Zhong Li Wenge Shi Qianhui Zeng Xianyan Wang Xuelei Zhang Chromosome-level genome provides insights into environmental adaptability and innate immunity in the common dolphin (delphinus delphis) BMC Genomics Delphinus delphis Genome sequencing Chromosome assembly Comparative genomics Demographic history |
| title | Chromosome-level genome provides insights into environmental adaptability and innate immunity in the common dolphin (delphinus delphis) |
| title_full | Chromosome-level genome provides insights into environmental adaptability and innate immunity in the common dolphin (delphinus delphis) |
| title_fullStr | Chromosome-level genome provides insights into environmental adaptability and innate immunity in the common dolphin (delphinus delphis) |
| title_full_unstemmed | Chromosome-level genome provides insights into environmental adaptability and innate immunity in the common dolphin (delphinus delphis) |
| title_short | Chromosome-level genome provides insights into environmental adaptability and innate immunity in the common dolphin (delphinus delphis) |
| title_sort | chromosome level genome provides insights into environmental adaptability and innate immunity in the common dolphin delphinus delphis |
| topic | Delphinus delphis Genome sequencing Chromosome assembly Comparative genomics Demographic history |
| url | https://doi.org/10.1186/s12864-024-10268-4 |
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