Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea)
Abstract The Asian Clam (Corbicula fluminea) is a valuable commercial and medicinal bivalve, which is widely distributed in East and Southeast Asia. As a natural nutrient source, the clam is rich in protein, amino acids, and microelements. The genome of C. fluminea has not yet been characterized; th...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2021-07-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-021-94545-2 |
| _version_ | 1818342745586008064 |
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| author | Tongqing Zhang Jiawen Yin Shengkai Tang Daming Li Xiankun Gu Shengyu Zhang Weiguo Suo Xiaowei Liu Yanshan Liu Qicheng Jiang Muzi Zhao Yue Yin Jianlin Pan |
| author_facet | Tongqing Zhang Jiawen Yin Shengkai Tang Daming Li Xiankun Gu Shengyu Zhang Weiguo Suo Xiaowei Liu Yanshan Liu Qicheng Jiang Muzi Zhao Yue Yin Jianlin Pan |
| author_sort | Tongqing Zhang |
| collection | DOAJ |
| description | Abstract The Asian Clam (Corbicula fluminea) is a valuable commercial and medicinal bivalve, which is widely distributed in East and Southeast Asia. As a natural nutrient source, the clam is rich in protein, amino acids, and microelements. The genome of C. fluminea has not yet been characterized; therefore, genome-assisted breeding and improvements cannot yet be implemented. In this work, we present a de novo chromosome-scale genome assembly of C. fluminea using PacBio and Hi-C sequencing technologies. The assembled genome comprised 4728 contigs, with a contig N50 of 521.06 Kb, and 1,215 scaffolds with a scaffold N50 of 70.62 Mb. More than 1.51 Gb (99.17%) of genomic sequences were anchored to 18 chromosomes, of which 1.40 Gb (92.81%) of genomic sequences were ordered and oriented. The genome contains 38,841 coding genes, 32,591 (83.91%) of which were annotated in at least one functional database. Compared with related species, C. fluminea had 851 expanded gene families and 191 contracted gene families. The phylogenetic tree showed that C. fluminea diverged from Ruditapes philippinarum, ~ 228.89 million years ago (Mya), and the genomes of C. fluminea and R. philippinarum shared 244 syntenic blocks. Additionally, we identified 2 MITF members and 99 NLRP members in C. fluminea genome. The high-quality and chromosomal Asian Clam genome will be a valuable resource for a range of development and breeding studies of C. fluminea in future research. |
| first_indexed | 2024-12-13T16:19:34Z |
| format | Article |
| id | doaj.art-241921e46fb84beebfa1053da6a3adb5 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-13T16:19:34Z |
| publishDate | 2021-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-241921e46fb84beebfa1053da6a3adb52022-12-21T23:38:45ZengNature PortfolioScientific Reports2045-23222021-07-0111111310.1038/s41598-021-94545-2Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea)Tongqing Zhang0Jiawen Yin1Shengkai Tang2Daming Li3Xiankun Gu4Shengyu Zhang5Weiguo Suo6Xiaowei Liu7Yanshan Liu8Qicheng Jiang9Muzi Zhao10Yue Yin11Jianlin Pan12Freshwater Fisheries Research Institute of Jiangsu ProvinceFreshwater Fisheries Research Institute of Jiangsu ProvinceFreshwater Fisheries Research Institute of Jiangsu ProvinceFreshwater Fisheries Research Institute of Jiangsu ProvinceFreshwater Fisheries Research Institute of Jiangsu ProvinceHongze Lake Fisheries Administration Committee Office of Jiangsu ProvinceFisheries Management Commission of Gehu LakeFreshwater Fisheries Research Institute of Jiangsu ProvinceFreshwater Fisheries Research Institute of Jiangsu ProvinceFreshwater Fisheries Research Institute of Jiangsu ProvinceFreshwater Fisheries Research Institute of Jiangsu ProvinceFreshwater Fisheries Research Institute of Jiangsu ProvinceFreshwater Fisheries Research Institute of Jiangsu ProvinceAbstract The Asian Clam (Corbicula fluminea) is a valuable commercial and medicinal bivalve, which is widely distributed in East and Southeast Asia. As a natural nutrient source, the clam is rich in protein, amino acids, and microelements. The genome of C. fluminea has not yet been characterized; therefore, genome-assisted breeding and improvements cannot yet be implemented. In this work, we present a de novo chromosome-scale genome assembly of C. fluminea using PacBio and Hi-C sequencing technologies. The assembled genome comprised 4728 contigs, with a contig N50 of 521.06 Kb, and 1,215 scaffolds with a scaffold N50 of 70.62 Mb. More than 1.51 Gb (99.17%) of genomic sequences were anchored to 18 chromosomes, of which 1.40 Gb (92.81%) of genomic sequences were ordered and oriented. The genome contains 38,841 coding genes, 32,591 (83.91%) of which were annotated in at least one functional database. Compared with related species, C. fluminea had 851 expanded gene families and 191 contracted gene families. The phylogenetic tree showed that C. fluminea diverged from Ruditapes philippinarum, ~ 228.89 million years ago (Mya), and the genomes of C. fluminea and R. philippinarum shared 244 syntenic blocks. Additionally, we identified 2 MITF members and 99 NLRP members in C. fluminea genome. The high-quality and chromosomal Asian Clam genome will be a valuable resource for a range of development and breeding studies of C. fluminea in future research.https://doi.org/10.1038/s41598-021-94545-2 |
| spellingShingle | Tongqing Zhang Jiawen Yin Shengkai Tang Daming Li Xiankun Gu Shengyu Zhang Weiguo Suo Xiaowei Liu Yanshan Liu Qicheng Jiang Muzi Zhao Yue Yin Jianlin Pan Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea) Scientific Reports |
| title | Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea) |
| title_full | Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea) |
| title_fullStr | Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea) |
| title_full_unstemmed | Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea) |
| title_short | Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea) |
| title_sort | dissecting the chromosome level genome of the asian clam corbicula fluminea |
| url | https://doi.org/10.1038/s41598-021-94545-2 |
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