Chromosome-scale genome assembly of three-spotted seahorse (Hippocampus trimaculatus) with a unique karyotype
Abstract Three-spotted seahorse (Hippocampi trimaculata) is a unique fish with important economic and medicinal values, and its total chromosome number is potentially quite different from other seahorse species. Herein, we constructed a chromosome-level genome assembly for this special seahorse by i...
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Nature Portfolio
2025-01-01
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| Online Access: | https://doi.org/10.1038/s41597-024-04349-y |
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| author | Ning Li Xinhui Zhang Xin Liu Xueqiang Lin Cancan Hu Jieming Chen Shengchao Wang Dong Zhang Shuguang Wei Qiong Shi |
| author_facet | Ning Li Xinhui Zhang Xin Liu Xueqiang Lin Cancan Hu Jieming Chen Shengchao Wang Dong Zhang Shuguang Wei Qiong Shi |
| author_sort | Ning Li |
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| description | Abstract Three-spotted seahorse (Hippocampi trimaculata) is a unique fish with important economic and medicinal values, and its total chromosome number is potentially quite different from other seahorse species. Herein, we constructed a chromosome-level genome assembly for this special seahorse by integration of MGI short-read, PacBio HiFi long-read and Hi-C sequencing techniques. A 416.57-Mb haplotypic genome assembly was obtained. Subsequently, 99.38% of its scaffold sequences were anchored onto 18 chromosomes, with identification of 29.1% repeat sequences in the assembled genome. Additional karyotype analysis validated the diploid chromosomes of 2n = 36, which are remarkably different from other seahorses’ 2n = 42 or 44. The genome completeness (BUSCO score: 96.5%, CEGMA score: 97.87%) confirmed that this chromosome-scale assembly is indeed of high quality. Moreover, a total of 18,712 protein-coding genes were annotated, of which 96.36% could be predicted with functions. Based on construction of a phylogenetic tree, we estimated that Hippocampus and Syngnathoides diverged approximately 50.1 million years ago (Mya). Taken together, our genome data presented in this study provide a valuable genetic resource for numerical chromosome changes and in-depth evolutionary and functional investigations, as well as conservation and molecular breeding of this endangered teleost. |
| format | Article |
| id | doaj-art-ca83dbccf03941acaf43e16e2288e62c |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
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| spelling | doaj-art-ca83dbccf03941acaf43e16e2288e62c2025-01-12T12:07:50ZengNature PortfolioScientific Data2052-44632025-01-011211810.1038/s41597-024-04349-yChromosome-scale genome assembly of three-spotted seahorse (Hippocampus trimaculatus) with a unique karyotypeNing Li0Xinhui Zhang1Xin Liu2Xueqiang Lin3Cancan Hu4Jieming Chen5Shengchao Wang6Dong Zhang7Shuguang Wei8Qiong Shi9College of Forensic Science, Xi’an Jiaotong UniversityLaboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen UniversityEast China Sea Fisheries Research Institute, Chinese Academy of Fisheries SciencesHainan BGI Marine Sci & Tech Co. LtdShenzhen Institute, Ocean University of ChinaShenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine SciencesHainan BGI Marine Sci & Tech Co. LtdEast China Sea Fisheries Research Institute, Chinese Academy of Fisheries SciencesCollege of Forensic Science, Xi’an Jiaotong UniversityLaboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen UniversityAbstract Three-spotted seahorse (Hippocampi trimaculata) is a unique fish with important economic and medicinal values, and its total chromosome number is potentially quite different from other seahorse species. Herein, we constructed a chromosome-level genome assembly for this special seahorse by integration of MGI short-read, PacBio HiFi long-read and Hi-C sequencing techniques. A 416.57-Mb haplotypic genome assembly was obtained. Subsequently, 99.38% of its scaffold sequences were anchored onto 18 chromosomes, with identification of 29.1% repeat sequences in the assembled genome. Additional karyotype analysis validated the diploid chromosomes of 2n = 36, which are remarkably different from other seahorses’ 2n = 42 or 44. The genome completeness (BUSCO score: 96.5%, CEGMA score: 97.87%) confirmed that this chromosome-scale assembly is indeed of high quality. Moreover, a total of 18,712 protein-coding genes were annotated, of which 96.36% could be predicted with functions. Based on construction of a phylogenetic tree, we estimated that Hippocampus and Syngnathoides diverged approximately 50.1 million years ago (Mya). Taken together, our genome data presented in this study provide a valuable genetic resource for numerical chromosome changes and in-depth evolutionary and functional investigations, as well as conservation and molecular breeding of this endangered teleost.https://doi.org/10.1038/s41597-024-04349-y |
| spellingShingle | Ning Li Xinhui Zhang Xin Liu Xueqiang Lin Cancan Hu Jieming Chen Shengchao Wang Dong Zhang Shuguang Wei Qiong Shi Chromosome-scale genome assembly of three-spotted seahorse (Hippocampus trimaculatus) with a unique karyotype Scientific Data |
| title | Chromosome-scale genome assembly of three-spotted seahorse (Hippocampus trimaculatus) with a unique karyotype |
| title_full | Chromosome-scale genome assembly of three-spotted seahorse (Hippocampus trimaculatus) with a unique karyotype |
| title_fullStr | Chromosome-scale genome assembly of three-spotted seahorse (Hippocampus trimaculatus) with a unique karyotype |
| title_full_unstemmed | Chromosome-scale genome assembly of three-spotted seahorse (Hippocampus trimaculatus) with a unique karyotype |
| title_short | Chromosome-scale genome assembly of three-spotted seahorse (Hippocampus trimaculatus) with a unique karyotype |
| title_sort | chromosome scale genome assembly of three spotted seahorse hippocampus trimaculatus with a unique karyotype |
| url | https://doi.org/10.1038/s41597-024-04349-y |
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