Chromosome-level genome assembly of grass carp (Ctenopharyngodon idella) provides insights into its genome evolution
Abstract Background The grass carp has great economic value and occupies an important evolutionary position. Genomic information regarding this species could help better understand its rapid growth rate as well as its unique body plan and environmental adaptation. Results We assembled the chromosome...
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BMC
2022-04-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-022-08503-x |
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| author | Chang-Song Wu Zi-You Ma Guo-Dong Zheng Shu-Ming Zou Xu-Jie Zhang Yong-An Zhang |
| author_facet | Chang-Song Wu Zi-You Ma Guo-Dong Zheng Shu-Ming Zou Xu-Jie Zhang Yong-An Zhang |
| author_sort | Chang-Song Wu |
| collection | DOAJ |
| description | Abstract Background The grass carp has great economic value and occupies an important evolutionary position. Genomic information regarding this species could help better understand its rapid growth rate as well as its unique body plan and environmental adaptation. Results We assembled the chromosome-level grass carp genome using the PacBio sequencing and chromosome structure capture technique. The final genome assembly has a total length of 893.2 Mb with a contig N50 of 19.3 Mb and a scaffold N50 of 35.7 Mb. About 99.85% of the assembled contigs were anchored into 24 chromosomes. Based on the prediction, this genome contained 30,342 protein-coding genes and 43.26% repetitive sequences. Furthermore, we determined that the large genome size can be attributed to the DNA-mediated transposable elements which accounted for 58.9% of the repetitive sequences in grass carp. We identified that the grass carp has only 24 pairs of chromosomes due to the fusion of two ancestral chromosomes. Enrichment analyses of significantly expanded and positively selected genes reflected evolutionary adaptation of grass carp to the feeding habits. We also detected the loss of conserved non-coding regulatory elements associated with the development of the immune system, nervous system, and digestive system, which may be critical for grass carp herbivorous traits. Conclusions The high-quality reference genome reported here provides a valuable resource for the genetic improvement and molecular-guided breeding of the grass carp. |
| first_indexed | 2024-12-21T14:41:10Z |
| format | Article |
| id | doaj.art-282d2356f5f449a1ad35769da6ca7389 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-21T14:41:10Z |
| publishDate | 2022-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-282d2356f5f449a1ad35769da6ca73892022-12-21T19:00:10ZengBMCBMC Genomics1471-21642022-04-0123111410.1186/s12864-022-08503-xChromosome-level genome assembly of grass carp (Ctenopharyngodon idella) provides insights into its genome evolutionChang-Song Wu0Zi-You Ma1Guo-Dong Zheng2Shu-Ming Zou3Xu-Jie Zhang4Yong-An Zhang5State Key Laboratory of Agricultural Microbiology, College of Fisheries, Huazhong Agricultural UniversityState Key Laboratory of Agricultural Microbiology, College of Fisheries, Huazhong Agricultural UniversityGenetics and Breeding Center for Blunt Snout Bream, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean UniversityGenetics and Breeding Center for Blunt Snout Bream, Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean UniversityState Key Laboratory of Agricultural Microbiology, College of Fisheries, Huazhong Agricultural UniversityState Key Laboratory of Agricultural Microbiology, College of Fisheries, Huazhong Agricultural UniversityAbstract Background The grass carp has great economic value and occupies an important evolutionary position. Genomic information regarding this species could help better understand its rapid growth rate as well as its unique body plan and environmental adaptation. Results We assembled the chromosome-level grass carp genome using the PacBio sequencing and chromosome structure capture technique. The final genome assembly has a total length of 893.2 Mb with a contig N50 of 19.3 Mb and a scaffold N50 of 35.7 Mb. About 99.85% of the assembled contigs were anchored into 24 chromosomes. Based on the prediction, this genome contained 30,342 protein-coding genes and 43.26% repetitive sequences. Furthermore, we determined that the large genome size can be attributed to the DNA-mediated transposable elements which accounted for 58.9% of the repetitive sequences in grass carp. We identified that the grass carp has only 24 pairs of chromosomes due to the fusion of two ancestral chromosomes. Enrichment analyses of significantly expanded and positively selected genes reflected evolutionary adaptation of grass carp to the feeding habits. We also detected the loss of conserved non-coding regulatory elements associated with the development of the immune system, nervous system, and digestive system, which may be critical for grass carp herbivorous traits. Conclusions The high-quality reference genome reported here provides a valuable resource for the genetic improvement and molecular-guided breeding of the grass carp.https://doi.org/10.1186/s12864-022-08503-xGrass carpCyprinid fishChromosome-level genomeComparative genomicsAdaptive evolution |
| spellingShingle | Chang-Song Wu Zi-You Ma Guo-Dong Zheng Shu-Ming Zou Xu-Jie Zhang Yong-An Zhang Chromosome-level genome assembly of grass carp (Ctenopharyngodon idella) provides insights into its genome evolution BMC Genomics Grass carp Cyprinid fish Chromosome-level genome Comparative genomics Adaptive evolution |
| title | Chromosome-level genome assembly of grass carp (Ctenopharyngodon idella) provides insights into its genome evolution |
| title_full | Chromosome-level genome assembly of grass carp (Ctenopharyngodon idella) provides insights into its genome evolution |
| title_fullStr | Chromosome-level genome assembly of grass carp (Ctenopharyngodon idella) provides insights into its genome evolution |
| title_full_unstemmed | Chromosome-level genome assembly of grass carp (Ctenopharyngodon idella) provides insights into its genome evolution |
| title_short | Chromosome-level genome assembly of grass carp (Ctenopharyngodon idella) provides insights into its genome evolution |
| title_sort | chromosome level genome assembly of grass carp ctenopharyngodon idella provides insights into its genome evolution |
| topic | Grass carp Cyprinid fish Chromosome-level genome Comparative genomics Adaptive evolution |
| url | https://doi.org/10.1186/s12864-022-08503-x |
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