Chromosome-level genome assembly of rock carp (Procypris rabaudi)
Abstract Rock carp (Procypris rabaudi) is an endemic fish species distributed in upper reaches of the Yangtze River. Due to anthropogenic influences, such as hydropower development, over-fishing and habitat destruction, the wild populations of the species have dramatically declined in recent decades...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-05-01
|
| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-05248-6 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850242836902969344 |
|---|---|
| author | Zhongyi Wang Miling Ran Xiaoshuai Liu Chuang Zhou Zhaobin Song |
| author_facet | Zhongyi Wang Miling Ran Xiaoshuai Liu Chuang Zhou Zhaobin Song |
| author_sort | Zhongyi Wang |
| collection | DOAJ |
| description | Abstract Rock carp (Procypris rabaudi) is an endemic fish species distributed in upper reaches of the Yangtze River. Due to anthropogenic influences, such as hydropower development, over-fishing and habitat destruction, the wild populations of the species have dramatically declined in recent decades. To inform effective conservation strategies, it is essential to elucidate the species’ adaptive mechanisms through genomic analyses. The present study reported a high-quality genome assembly at the chromosome level of P. rabaudi. The final genome assembly was 1.66 Gb in length, with a contig N50 of 24.95 Mb and a scaffold N50 of 32.60 Mb, and was anchored to 50 chromosomes. The assembled genome achieved a BUSCO completeness score of 97.8%, with 45,784 protein-coding genes identified, of which 94.78% were functionally annotated in at least one protein database. Additionally, 1,305 gene families were found to be expanded, while 14,463 gene families showed contraction. The high-quality reference genome of P. rabaudi served as a valuable genetic resource, providing a foundation for the conservation of wild populations and the exploration of evolutionary mechanisms. |
| format | Article |
| id | doaj-art-8f0cc0ae88f048c29b15bf4ee0bdff78 |
| institution | OA Journals |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-8f0cc0ae88f048c29b15bf4ee0bdff782025-08-20T02:00:12ZengNature PortfolioScientific Data2052-44632025-05-011211810.1038/s41597-025-05248-6Chromosome-level genome assembly of rock carp (Procypris rabaudi)Zhongyi Wang0Miling Ran1Xiaoshuai Liu2Chuang Zhou3Zhaobin Song4Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan UniversityKey Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan UniversityYalong River Hydropower Development Company, Ltd.Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan UniversityKey Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan UniversityAbstract Rock carp (Procypris rabaudi) is an endemic fish species distributed in upper reaches of the Yangtze River. Due to anthropogenic influences, such as hydropower development, over-fishing and habitat destruction, the wild populations of the species have dramatically declined in recent decades. To inform effective conservation strategies, it is essential to elucidate the species’ adaptive mechanisms through genomic analyses. The present study reported a high-quality genome assembly at the chromosome level of P. rabaudi. The final genome assembly was 1.66 Gb in length, with a contig N50 of 24.95 Mb and a scaffold N50 of 32.60 Mb, and was anchored to 50 chromosomes. The assembled genome achieved a BUSCO completeness score of 97.8%, with 45,784 protein-coding genes identified, of which 94.78% were functionally annotated in at least one protein database. Additionally, 1,305 gene families were found to be expanded, while 14,463 gene families showed contraction. The high-quality reference genome of P. rabaudi served as a valuable genetic resource, providing a foundation for the conservation of wild populations and the exploration of evolutionary mechanisms.https://doi.org/10.1038/s41597-025-05248-6 |
| spellingShingle | Zhongyi Wang Miling Ran Xiaoshuai Liu Chuang Zhou Zhaobin Song Chromosome-level genome assembly of rock carp (Procypris rabaudi) Scientific Data |
| title | Chromosome-level genome assembly of rock carp (Procypris rabaudi) |
| title_full | Chromosome-level genome assembly of rock carp (Procypris rabaudi) |
| title_fullStr | Chromosome-level genome assembly of rock carp (Procypris rabaudi) |
| title_full_unstemmed | Chromosome-level genome assembly of rock carp (Procypris rabaudi) |
| title_short | Chromosome-level genome assembly of rock carp (Procypris rabaudi) |
| title_sort | chromosome level genome assembly of rock carp procypris rabaudi |
| url | https://doi.org/10.1038/s41597-025-05248-6 |
| work_keys_str_mv | AT zhongyiwang chromosomelevelgenomeassemblyofrockcarpprocyprisrabaudi AT milingran chromosomelevelgenomeassemblyofrockcarpprocyprisrabaudi AT xiaoshuailiu chromosomelevelgenomeassemblyofrockcarpprocyprisrabaudi AT chuangzhou chromosomelevelgenomeassemblyofrockcarpprocyprisrabaudi AT zhaobinsong chromosomelevelgenomeassemblyofrockcarpprocyprisrabaudi |