期刊
G3-GENES GENOMES GENETICS
卷 11, 期 9, 页码 -出版社
OXFORD UNIV PRESS INC
DOI: 10.1093/g3journal/jkab212
关键词
genome assembly; chromosome; synteny; Brachyura; Portunidae; Callinectes sapidus
资金
- Vetlesen Foundation
- Edward St. John Foundation
- Sea Grant College of Maryland, National Science Foundation [1146774]
- National Science Foundation BioOce Grant [1658466]
- Direct For Biological Sciences
- Division Of Integrative Organismal Systems [1146774] Funding Source: National Science Foundation
- Directorate For Geosciences
- Division Of Ocean Sciences [1658466] Funding Source: National Science Foundation
The assembly of the blue crab genome involved multiple sequencing technologies and tools, resulting in a 985 Mb assembly and prediction of 25,249 protein-coding genes. This serves as an important reference for research on the blue crab.
The blue crab, Callinectes sapidus (Rathbun, 1896) is an economically, culturally, and ecologically important species found across the temperate and tropical North and South American Atlantic coast. A reference genome will enable research for this high-value species. Initial assembly combined 200x coverage Illumina paired-end reads, a 60x 8 kb mate-paired library, and 50x PacBio data using the MaSuRCA assembler resulting in a 985 Mb assembly with a scaffold N50 of 153 kb. Dovetail Chicago and HiC sequencing with the 3d DNA assembler and Juicebox assembly tools were then used for chromosome scaffolding. The 50 largest scaffolds span 810 Mb are 1.5-37 Mb long and have a repeat content of 36%. The 190 Mb unplaced sequence is in 3921 sequences over 10 kb with a repeat content of 68%. The final assembly N50 is 18.9Mb for scaffolds and 9317 bases for contigs. Of arthropod BUSCO, similar to 88% (888/1013) were complete and single copies. Using 309 million RNAseq read pairs from 12 different tissues and developmental stages, 25,249 protein-coding genes were predicted. Between C. sapidus and Portunus trituberculatus genomes, 41 of 50 large scaffolds had high nucleotide identity and protein-coding synteny, but 9 scaffolds in both assemblies were not clear matches. The protein-coding genes included 9423 one-to-one putative orthologs, of which 7165 were syntenic between the two crab species. Overall, the two crab genome assemblies show strong similarities at the nucleotide, protein, and chromosome level and verify the blue crab genome as an excellent reference for this important seafood species.
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