Supporting data for "Chromosome-level genome assembly reveals the unique genome evolution of swimming crab (Portunus trituberculatus)"

Dataset type: Genomic, Transcriptomic
Data released on December 02, 2019

Tang B; Zhang D; Li H; Jiang S; Zhang H; Xuan F; Ge B; Wang Z; Liu Y; Sha Z; Cheng Y; Jiang W; Jiang H; Wang Z; Wang K; Li C; Sun Y; She S; Qiu Q; Wang W; Li X; Li Y; Liu Q; Ren Y (2019): Supporting data for "Chromosome-level genome assembly reveals the unique genome evolution of swimming crab (Portunus trituberculatus)" GigaScience Database. http://dx.doi.org/10.5524/100678

DOI10.5524/100678

The swimming crab, Portunus trituberculatus, is an important commercial species in China and is widely distributed in the coastal waters of Asia-Pacific countries. Despite increasing interest in swimming crab research, a high quality chromosome-level genome is still missing.
Here, we assembled the first chromosome-level reference genome of P. trituberculatus by combining the short reads, Nanopore long reads, and Hi-C data. The genome assembly size was 1.00 Gb with a contig N50 length of 4.12 Mb. In addition, BUSCO assessment indicated that 94.7% of core eukaryotic genes were present in the genome assembly. Approximately 54.52% of the genome was identified as repetitive sequences, with a total of 16,796 annotated protein-coding genes. In addition, we anchored contigs into chromosomes and identified 50 chromosomes with a N50 length of 21.80 Mb by Hi-C technology.
We anticipate that this chromosome-level assembly of the P. trituberculatus genome will not only promote study of basic development and evolution but also provide important resources for swimming crab reproduction.

Additional details

Read the peer-reviewed publication(s):


Accessions (data generated as part of this study):

BioProject: PRJNA555262





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN12306490_DNA210409  Portunus trituberculatus Description:DNA extracted from the muscle of a mal...
Alternative accession-BioProject:PRJNA555262
Alternative accession-BioSample:SAMN12306490
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SAMN12306490_RNA210409  Portunus trituberculatus Description:RNA extracted from the muscle of a mal...
Alternative accession-BioProject:PRJNA555262
Alternative accession-BioSample:SAMN12306490
...
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Displaying 1-2 of 2 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
otherTSV60.37 KB2019-11-28
Phylogenetic treeUNKNOWN0.29 KB2019-11-28
Coding SequenceFASTA10.58 MB2019-11-28
annotationGFF2.09 MB2019-11-28
protein sequenceFASTA7.02 MB2019-11-28
Sequence assemblyFASTA239.83 MB2019-11-28
Repeat sequenceGFF115.83 MB2019-11-28
readme.txtTEXT3.24 KB2019-12-02
otherTEXT0.87 KB2019-11-28
AlignmentsFASTA3.02 MB2019-11-28
Displaying 1-10 of 10 File(s).
Funding body Awardee Award ID Comments
National Natural Science Foundation of China B Tang 31672267
National Natural Science Foundation of China Q Lui 31640074
Jiangsu Agriculture Science and Technology Innovation Fund B Tang CX(18)3027
Jiangsu Agriculture Science and Technology Innovation Fund B Tang CX(18)2027
Natural Science Foundation of Jiangsu Province D Zhang BK20171276
Natural Science Foundation of Jiangsu Province D Zhang BK20160444
Qinglan Project of Jiangsu Province of China D Zhang 2018M642105
Date Action
December 2, 2019 Dataset publish
December 30, 2019 Manuscript Link added : 10.1093/gigascience/giz161
January 8, 2021 Link updated : BioProject:PRJNA555262