Draft genome of the Chinese mitten crab, Eriocheir sinensis

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• 作者：Linsheng Song ; Chao Bian ; Yongju Luo ; Lingling Wang ; Xinxin You ; Jia Li…
• 关键词：Crab genome ; Genomics ; Assembly ; Annotation
• 刊名：GigaScience
• 出版年：2016
• 出版时间：December 2016
• 年：2016
• 卷：5
• 期：1
• 全文大小：392 KB
• 参考文献：1.Li R, Fan W, Tian G, Zhu H, He L, Cai J, et al. The sequence and de novo assembly of the giant panda genome. Nature. 2010;463:311–7.PubMed PubMedCentral CrossRef
  2.Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y, Okuno M, et al. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res. 2014;24:1384–95.PubMed PubMedCentral CrossRef
  3.Xu Z, Wang H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 2007;35:W265–8.PubMed PubMedCentral CrossRef
  4.Chen N. Using RepeatMasker to identify repetitive elements in genomic sequences. Current protocols in bioinformatics/editoral board, Andreas D Baxevanis [et al.] 2004; Chapter 4:Unit 4 10.
  5.Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005;110:462–7.PubMed CrossRef
  6.Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573–80.PubMed PubMedCentral CrossRef
  7.Birney E, Clamp M, Durbin R. GeneWise and Genomewise. Genome Res. 2004;14:988–95.PubMed PubMedCentral CrossRef
  8.Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 2006;34:W435–9.PubMed PubMedCentral CrossRef
  9.Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. Journal Mol Bio. 1997;268:78–94.CrossRef
  10.Huang S, Wang J, Yue W, Chen J, Gaughan S, Lu W. Transcriptomic variation of hepatopancreas reveals the energy metabolism and biological processes associated with molting in Chinese mitten crab, Eriocheir sinensis.
  11.Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25:1105–11.PubMed PubMedCentral CrossRef
  12.Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotech. 2010;28:511–5.CrossRef
  13.Elsik CG, Mackey AJ, Reese JT, Milshina NV, Roos DS, Weinstock GM. Creating a honey bee consensus gene set. Genome Biol 2007;8:R13.
  14.Nossa CW, Havlak P, Yue JX, Lv J, Vincent KY, Brockmann HJ, et. al. Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication. GigaScience 2014;3:9.
  15.Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 2007;23:1061-7.
  16.Song L, Bian C, Luo Y, Wang L, You X, Li J, Qiu Y, Ma X, Zhu Z, Ma L, Wang Z, Lei Y, Qiang J, Li H, Yu J, Wong A, Xu J, Shi Q, Xu P. Supporting data for the “Draft genome of the Chinese mitten crab, Eriocheir sinensis”. GigaScience Database. 2016. http://​dx.​doi.​org/​10.​5524/​100186 .
  
• 作者单位：Linsheng Song (1) (2)
  Chao Bian (3)
  Yongju Luo (4)
  Lingling Wang (5)
  Xinxin You (3)
  Jia Li (3)
  Ying Qiu (3)
  Xingyu Ma (6)
  Zhifei Zhu (6)
  Liang Ma (7)
  Zhaogen Wang (7)
  Ying Lei (7)
  Jun Qiang (1)
  Hongxia Li (1)
  Juhua Yu (1)
  Alex Wong (8)
  Junmin Xu (3) (6)
  Qiong Shi (3) (6)
  Pao Xu (1)
  
  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
  2. College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
  3. Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen, 518083, China
  4. Guangxi Academy of Fisher Sciences, Nanning, 530021, China
  5. Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
  6. BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, 212000, China
  7. Zhenjiang Agriculture Committee, Zhenjiang, 212000, China
  8. BGI-Hong Kong, Hong Kong, 999077, China
  
• 刊物主题：Bioinformatics; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Proteomics; Data Mining and Knowledge Discovery;
• 出版者：BioMed Central
• ISSN：2047-217X

文摘

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.