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Li J, Ma H, Qin Y, Zhao Z, Niu Y, Lian J, Li J, Noor Z, Guo S, Yu Z, Zhang Y. Chromosome-level genome assembly and annotation of rare and endangered tropical bivalve, Tridacna crocea. Sci Data 2024; 11:186. [PMID: 38341475 PMCID: PMC10858879 DOI: 10.1038/s41597-024-03014-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Tridacna crocea is an ecologically important marine bivalve inhabiting tropical coral reef waters. High quality and available genomic resources will help us understand the population structure and genetic diversity of giant clams. This study reports a high-quality chromosome-scale T. crocea genome sequence of 1.30 Gb, with a scaffold N50 and contig N50 of 56.38 Mb and 1.29 Mb, respectively, which was assembled by combining PacBio long reads and Hi-C sequencing data. Repetitive sequences cover 71.60% of the total length, and a total of 25,440 protein-coding genes were annotated. A total of 1,963 non-coding RNA (ncRNA) were determined in the T. crocea genome, including 62 micro RNA (miRNA), 58 small nuclear RNA (snRNA), 83 ribosomal RNA (rRNA), and 1,760 transfer RNA (tRNA). Phylogenetic analysis revealed that giant clams diverged from oyster about 505.7 Mya during the evolution of bivalves. The genome assembly presented here provides valuable genomic resources to enhance our understanding of the genetic diversity and population structure of giant clams.
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Affiliation(s)
- Jun Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Hainan Sanya Marine Ecosystem National Observation and Research Station, Sanya, 572024, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518124, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519015, China
| | - Haitao Ma
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Hainan Sanya Marine Ecosystem National Observation and Research Station, Sanya, 572024, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518124, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519015, China
| | - Yanpin Qin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Hainan Sanya Marine Ecosystem National Observation and Research Station, Sanya, 572024, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518124, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519015, China
| | - Zhen Zhao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Hainan Sanya Marine Ecosystem National Observation and Research Station, Sanya, 572024, China
| | | | | | - Jiang Li
- Biozeron Shenzhen, Inc, Shenzhen, 518000, China
| | - Zohaib Noor
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
- Hainan Key Laboratory of Tropical Marine Biotechnology, Hainan Sanya Marine Ecosystem National Observation and Research Station, Sanya, 572024, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuming Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ziniu Yu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China.
- Hainan Key Laboratory of Tropical Marine Biotechnology, Hainan Sanya Marine Ecosystem National Observation and Research Station, Sanya, 572024, China.
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518124, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519015, China.
| | - Yuehuan Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China.
- Hainan Key Laboratory of Tropical Marine Biotechnology, Hainan Sanya Marine Ecosystem National Observation and Research Station, Sanya, 572024, China.
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, 518124, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519015, China.
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