title: Draft genome of the Chinese mitten crab, Eriocheir sinensis.
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.
  
  
  RESULTS
  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.
authors.affiliation: 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.
authors.forename: Linsheng
authors.initials: L
authors.lastname: Song
authors.affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, 518083 China.
authors.forename: Chao
authors.initials: C
authors.lastname: Bian
authors.affiliation: Guangxi Academy of Fisher Sciences, Nanning, 530021 China.
authors.forename: Yongju
authors.initials: Y
authors.lastname: Luo
authors.affiliation: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 China.
authors.forename: Lingling
authors.initials: L
authors.lastname: Wang
authors.affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, 518083 China.
authors.forename: Xinxin
authors.initials: X
authors.lastname: You
authors.affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, 518083 China.
authors.forename: Jia
authors.initials: J
authors.lastname: Li
authors.affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, 518083 China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Qiu
authors.affiliation: BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, 212000 China.
authors.forename: Xingyu
authors.initials: X
authors.lastname: Ma
authors.affiliation: BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, 212000 China.
authors.forename: Zhifei
authors.initials: Z
authors.lastname: Zhu
authors.affiliation: Zhenjiang Agriculture Committee, Zhenjiang, 212000 China.
authors.forename: Liang
authors.initials: L
authors.lastname: Ma
authors.affiliation: Zhenjiang Agriculture Committee, Zhenjiang, 212000 China.
authors.forename: Zhaogen
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Zhenjiang Agriculture Committee, Zhenjiang, 212000 China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Lei
authors.affiliation: Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 China.
authors.forename: Jun
authors.initials: J
authors.lastname: Qiang
authors.affiliation: Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 China.
authors.forename: Hongxia
authors.initials: H
authors.lastname: Li
authors.affiliation: Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 China.
authors.forename: Juhua
authors.initials: J
authors.lastname: Yu
authors.affiliation: BGI-Hong Kong, Hong Kong, 999077 China.
authors.forename: Alex
authors.initials: A
authors.lastname: Wong
authors.affiliation: 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.
authors.forename: Junmin
authors.initials: J
authors.lastname: Xu
authors.affiliation: 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.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Shi
authors.affiliation: Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081 China.
authors.forename: Pao
authors.initials: P
authors.lastname: Xu
mesh_terms: D000818:Animals; D003386:Brachyura / Q000235:genetics*; D002681:China; D019143:Evolution, Molecular; D005260:Female; D016678:Genome / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D058977:Molecular Sequence Annotation / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*
keywords: Annotation; Assembly; Crab genome; Genomics
references.citation: Gigascience. 2016 Jan 28;5:5
references.pmid: 26823974
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W435-9
references.pmid: 16845043
references.citation: Curr Protoc Bioinformatics. 2004 May;Chapter 4:Unit 4.10
references.pmid: 18428725
references.citation: Nat Biotechnol. 2010 May;28(5):511-5
references.pmid: 20436464
references.citation: Cytogenet Genome Res. 2005;110(1-4):462-7
references.pmid: 16093699
references.citation: Genome Res. 2004 May;14(5):988-95
references.pmid: 15123596
references.citation: Nucleic Acids Res. 1999 Jan 15;27(2):573-80
references.pmid: 9862982
references.citation: Nature. 2010 Jan 21;463(7279):311-7
references.pmid: 20010809
references.citation: Bioinformatics. 2009 May 1;25(9):1105-11
references.pmid: 19289445
references.citation: Gigascience. 2014 May 14;3:9
references.pmid: 24987520
references.citation: J Mol Biol. 1997 Apr 25;268(1):78-94
references.pmid: 9149143
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W265-8
references.pmid: 17485477
references.citation: Genome Res. 2014 Aug;24(8):1384-95
references.pmid: 24755901
references.citation: Genome Biol. 2007;8(1):R13
references.pmid: 17241472
references.citation: Sci Rep. 2015 Sep 15;5:14015
references.pmid: 26369734
references.citation: Bioinformatics. 2007 May 1;23(9):1061-7
references.pmid: 17332020