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Gigascience. 2016 Jan 28;5:5. doi: 10.1186/s13742-016-0112-y. eCollection 2016.

Draft genome of the Chinese mitten crab, Eriocheir sinensis.

Author information

1
Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 China ; College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023 China.
2
Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, 518083 China.
3
Guangxi Academy of Fisher Sciences, Nanning, 530021 China.
4
Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 China.
5
BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, 212000 China.
6
Zhenjiang Agriculture Committee, Zhenjiang, 212000 China.
7
Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 China.
8
BGI-Hong Kong, Hong Kong, 999077 China.
9
Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, 518083 China ; BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, 212000 China.

Abstract

BACKGROUND:

The Chinese mitten crab, Eriocheir sinensis, is one of the most studied and economically important crustaceans in China. Its transition from a swimming to a crawling method of movement during early development, anadromous migration during growth, and catadromous migration during breeding have been attractive features for research. However, knowledge of the underlying molecular mechanisms that regulate these processes is still very limited.

FINDINGS:

A total of 258.8 gigabases (Gb) of raw reads from whole-genome sequencing of the crab were generated by the Illumina HiSeq2000 platform. The final genome assembly (1.12 Gb), about 67.5 % of the estimated genome size (1.66 Gb), is composed of 17,553 scaffolds (>2 kb) with an N50 of 224 kb. We identified 14,436 genes using AUGUSTUS, of which 7,549 were shown to have significant supporting evidence using the GLEAN pipeline. This gene number is much greater than that of the horseshoe crab, and the annotation completeness, as evaluated by CEGMA, reached 66.9 %.

CONCLUSIONS:

We report the first genome sequencing, assembly, and annotation of the Chinese mitten crab. The assembled draft genome will provide a valuable resource for the study of essential developmental processes and genetic determination of important traits of the Chinese mitten crab, and also for investigating crustacean evolution.

KEYWORDS:

Annotation; Assembly; Crab genome; Genomics

PMID:
26823974
PMCID:
PMC4730596
DOI:
10.1186/s13742-016-0112-y
[Indexed for MEDLINE]
Free PMC Article

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