A chromosome-scale reference genome assembly for Triplophysa lixianensis
Abstract In this study, we constructed a chromosome-scale reference genome assembly for Lixian plateau loach, Triplophysa lixianensis, by integration of MGI short-read, PacBio HiFi long-read and Hi-C sequencing technologies. A 668-Mb haplotypic genome assembly was obtained for a female T. lixianensi...
| الحاوية / القاعدة: | Scientific Data |
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| المؤلفون الرئيسيون: | , , , , |
| التنسيق: | مقال |
| اللغة: | الإنجليزية |
| منشور في: |
Nature Portfolio
2024-12-01
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| الوصول للمادة أونلاين: | https://doi.org/10.1038/s41597-024-04268-y |
| _version_ | 1849551025577394176 |
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| author | Chunlin He Xinhui Zhang Zhengyong Wen Qiong Shi Zhaobin Song |
| author_facet | Chunlin He Xinhui Zhang Zhengyong Wen Qiong Shi Zhaobin Song |
| author_sort | Chunlin He |
| collection | DOAJ |
| container_title | Scientific Data |
| description | Abstract In this study, we constructed a chromosome-scale reference genome assembly for Lixian plateau loach, Triplophysa lixianensis, by integration of MGI short-read, PacBio HiFi long-read and Hi-C sequencing technologies. A 668-Mb haplotypic genome assembly was obtained for a female T. lixianensis, and 98.91% of the assembled sequences were anchored into 25 chromosomes. This assembly owned a moderate repeat content (35.63%) and an annotation of 23,774 protein-coding genes, among them 94.15% were predicted with functions. The assembled genome of T. lixianensis shared a good syntenic relationship with previously published data of its relative T. dalaica. Taken together, our genome data presented here provide a valuable genetic resource for in-depth evolutionary and functional studies, as well as molecular breeding and conservation of this valuable fish species to elevate its ecological and economical values. |
| format | Article |
| id | doaj-art-e69eede7c0e04265a6345fbe88160878 |
| institution | Directory of Open Access Journals |
| issn | 2052-4463 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| spelling | doaj-art-e69eede7c0e04265a6345fbe881608782025-08-20T02:39:38ZengNature PortfolioScientific Data2052-44632024-12-011111710.1038/s41597-024-04268-yA chromosome-scale reference genome assembly for Triplophysa lixianensisChunlin He0Xinhui Zhang1Zhengyong Wen2Qiong Shi3Zhaobin Song4Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan UniversityLaboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen UniversityKey Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Neijiang Normal UniversityLaboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen UniversityKey Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan UniversityAbstract In this study, we constructed a chromosome-scale reference genome assembly for Lixian plateau loach, Triplophysa lixianensis, by integration of MGI short-read, PacBio HiFi long-read and Hi-C sequencing technologies. A 668-Mb haplotypic genome assembly was obtained for a female T. lixianensis, and 98.91% of the assembled sequences were anchored into 25 chromosomes. This assembly owned a moderate repeat content (35.63%) and an annotation of 23,774 protein-coding genes, among them 94.15% were predicted with functions. The assembled genome of T. lixianensis shared a good syntenic relationship with previously published data of its relative T. dalaica. Taken together, our genome data presented here provide a valuable genetic resource for in-depth evolutionary and functional studies, as well as molecular breeding and conservation of this valuable fish species to elevate its ecological and economical values.https://doi.org/10.1038/s41597-024-04268-y |
| spellingShingle | Chunlin He Xinhui Zhang Zhengyong Wen Qiong Shi Zhaobin Song A chromosome-scale reference genome assembly for Triplophysa lixianensis |
| title | A chromosome-scale reference genome assembly for Triplophysa lixianensis |
| title_full | A chromosome-scale reference genome assembly for Triplophysa lixianensis |
| title_fullStr | A chromosome-scale reference genome assembly for Triplophysa lixianensis |
| title_full_unstemmed | A chromosome-scale reference genome assembly for Triplophysa lixianensis |
| title_short | A chromosome-scale reference genome assembly for Triplophysa lixianensis |
| title_sort | chromosome scale reference genome assembly for triplophysa lixianensis |
| url | https://doi.org/10.1038/s41597-024-04268-y |
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