The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation

Nature Genetics

Volumn 47, Issue 6, 2015, Pages 625-631

  Wang, Yaping ^a   Lu, Ying ^b   Zhang, Yong ^c   Ning, Zemin ^d   Li, Yan ^b   Zhao, Qiang ^b   Lu, Hengyun ^b   Huang, Rong ^a   Xia, Xiaoqin ^a   Feng, Qi ^b   Liang, Xufang ^e   Liu, Kunyan ^b   Zhang, Lei ^b   Lu, Tingting ^b   Huang, Tao ^b   Fan, Danlin ^b   Weng, Qijun ^b   Zhu, Chuanrang ^b   Lu, Yiqi ^b   Li, Wenjun ^b   Wen, Ziruo ^b   Zhou, Congcong ^b   Tian, Qilin ^b   Kang, Xiaojun ^a,f   Shi, Mijuan ^a   Zhang, Wanting ^a   Jang, Songhun ^a,g   Du, Fukuan ^a   He, Shan ^e   Liao, Lanjie ^a   Li, Yongming ^a   Gui, Bin ^a   He, Huihui ^a   Ning, Zhen ^a   Yang, Cheng ^a,f   He, Libo ^a   Luo, Lifei ^a   Yang, Rui ^h   Luo, Qiong ^h   Liu, Xiaochun ^c   Li, Shuisheng ^c   Huang, Wen ^c   Xiao, Ling ^c   Lin, Haoran ^c   Han, Bin ^b   Zhu, Zuoyan ^a   more..

^a INSTITUTE OF HYDROBIOLOGY   (China)

^b INSTITUTE OF PLANT PHYSIOLOGY AND ECOLOGY   (China)

^c SUN YAT SEN UNIVERSITY   (China)

^d WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^e HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^f CHINA UNIVERSITY OF GEOSCIENCES   (China)

^g KIM IL SUNG UNIVERSITY   (North Korea)

^h YUNNAN AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MEVALONIC ACID; TRANSCRIPTOME; FISH PROTEIN;

ADAPTATION; ADULT; ARTICLE; CHROMOSOME; CONTROLLED STUDY; EVOLUTION; FEEDING BEHAVIOR; FEMALE; GENETIC LINKAGE; GENETIC VARIABILITY; GENOME; GRASS CARP; LIVER; MALE; NONHUMAN; PRIORITY JOURNAL; SEX DETERMINATION; STEROIDOGENESIS; TRANSCRIPTION INITIATION; VEGETARIAN DIET; X CHROMOSOME; Y CHROMOSOME; ZEBRA FISH; ANIMAL; CARP; DNA SEQUENCE; GENETICS; HERBIVORY; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS;

CTENOPHARYNGODON; CTENOPHARYNGODON IDELLA; DANIO RERIO;

ADAPTATION, BIOLOGICAL; ANIMALS; CARPS; EVOLUTION, MOLECULAR; FEMALE; FISH PROTEINS; GENOME; HERBIVORY; MALE; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA; TRANSCRIPTOME;

EID: 84930083595     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3280     Document Type: Article

References (54)

1. Chilton, E.W. & Muoneke, M.I. Biology and management of grass carp (Ctenopharyngodon idella, Cyprinidae) for vegetation control: a North American perspective. Rev. Fish Biol. Fish. 2, 283-320 (1992).
2. Statistics and Information Service, Fisheries and Aquaculture Department, Food and Agriculture Organization of the United Nations. FAO Yearbook of Fishery and Aquaculture Statistics 2011 (Food and Agriculture Organization of the United Nations, 2013).
3. Howe, K. et al. The zebrafsh reference genome sequence and its relationship to the human genome. Nature 496, 498-503 (2013).
4. Xia, J.H. et al. A consensus linkage map of the grass carp (Ctenopharyngodon idella) based on microsatellites and SNPs. BMC Genomics 11, 135 (2010).
5. Chen, J. et al. Transcriptome analysis of head kidney in grass carp and discovery of immune-related genes. BMC Vet. Res. 8, 108 (2012).
6. Xu, B. et al. Generation and analysis of ESTs from the grass carp, Ctenopharyngodon idellus. Anim. Biotechnol. 21, 217-225 (2010).
7. 3 ) gene from grass carp (Ctenopharyngodon idellus). Fish Shellfsh Immunol. 35, 1624-1634 (2013).
8. Wang, T.T. et al. Molecular characterization, expression analysis, and biological effects of interleukin-8 in grass carp Ctenopharyngodon idellus. Fish Shellfsh Immunol. 35, 1421-1432 (2013).
9. Chen, Y., Pandit, N.P., Fu, J., Li, D. & Li, J. Identifcation, characterization and feeding response of peptide YYb (PYYb) gene in grass carp (Ctenopharyngodon idellus). Fish Physiol. Biochem. 40, 45-55 (2014).
10. Feng, K., Zhang, G.R., Wei, K.J. & Xiong, B.X. Molecular cloning, tissue distribution, and ontogenetic expression of ghrelin and regulation of expression by fasting and refeeding in the grass carp (Ctenopharyngodon idellus). J. Exp. Zool. A Ecol. Genet. Physiol. 319, 202-212 (2013).
11. Yu, E.M. et al. Molecular cloning of type I collagen cDNA and nutritional regulation of type I collagen mRNA expression in grass carp. J. Anim. Physiol. Anim. Nutr. (Berl.) 98, 755-765 (2014).
12. Zhong, S.S., Jiang, X.Y., Sun, C.F. & Zou, S.M. Identifcation of a second follistatin gene in grass carp (Ctenopharyngodon idellus) and its regulatory function in myogenesis during embryogenesis. Gen. Comp. Endocrinol. 185, 19-27 (2013).
13. Star, B. et al. The genome sequence of Atlantic cod reveals a unique immune system. Nature 477, 207-210 (2011).
14. Aparicio, S. et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297, 1301-1310 (2002).
15. Kasahara, M. et al. The medaka draft genome and insights into vertebrate genome evolution. Nature 447, 714-719 (2007).
16. Jaillon, O. et al. Genome duplication in the teleost fsh Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431, 946-957 (2004).
17. Jones, F.C. et al. The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484, 55-61 (2012).
18. Nocusa, S. A comparative study of the chromosomes in the fshes with particular consideration on taxonomy and evolution. Mem. Hyogo Univ. Agric. 3, 1-62 (1960).
19. Stanley, J.G. Female homogamety in grass carp (Ctenopharyngodon idella) determined by gynogenesis. J. Fish. Res. Board Can. 33, 1372-1374 (1976).
20. Peng, Z. et al. The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla). Nat. Genet. 45, 456-461 (2013).
21. Jang, S. et al. Construction and characterization of two bacterial artifcial chromosome libraries of grass carp. Mar. Biotechnol. (NY) 12, 261-266 (2010).
22. Kumar, S. & Hedges, S.B. TimeTree2: species divergence times on the iPhone. Bioinformatics 27, 2023-2024 (2011).
23. Li, H. et al. TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res. 34, D572-D580 (2006).
24. Crow, K.D., Stadler, P.F., Lynch, V.J., Amemiya, C. & Wagner, G.P. The "fsh-specifc" Hox cluster duplication is coincident with the origin of teleosts. Mol. Biol. Evol. 23, 121-136 (2006).
25. Kurosawa, G. et al. Organization and structure of hox gene loci in medaka genome and comparison with those of pufferfsh and zebrafsh genomes. Gene 370, 75-82 (2006).
26. Wegner, M. All purpose Sox: the many roles of Sox proteins in gene expression. Int. J. Biochem. Cell Biol. 42, 381-390 (2010).
27. Akira, S., Yamamoto, M. & Takeda, K. Role of adapters in Toll-like receptor signalling. Biochem. Soc. Trans. 31, 637-642 (2003).
28. Braasch, I. & Postlethwait, J.H. in. Polyploidy and Genome Evolution (eds. Soltis, P.S. and Soltis, D.E.) 341-383 (Springer, 2012).
29. Kanehisa, M. et al. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42, D199-D205 (2014).
30. Petit, V. & Thiery, J.P. Focal adhesions: structure and dynamics. Biol. Cell 92, 477-494 (2000).
31. Danen, E.H. & Yamada, K.M. Fibronectin, integrins, and growth control. J. Cell. Physiol. 189, 1-13 (2001).
32. Palacín, M. et al. The genetics of heteromeric amino acid transporters. Physiology (Bethesda) 20, 112-124 (2005).
33. Goodman, B.E. Insights into digestion and absorption of major nutrients in humans. Adv. Physiol. Educ. 34, 44-53 (2010).
34. Zhao, B., Tumaneng, K. & Guan, K.L. The Hippo pathway in organ size control, tissue regeneration and stem cell self-renewal. Nat. Cell Biol. 13, 877-883 (2011).
35. Zhao, B., Lei, Q.Y. & Guan, K.L. The Hippo-YAP pathway: new connections between regulation of organ size and cancer. Curr. Opin. Cell Biol. 20, 638-646 (2008).
36. Traut, W. & Winking, H. Meiotic chromosomes and stages of sex chromosome evolution in fsh: zebrafsh, platyfsh and guppy. Chromosome Res. 9, 659-672 (2001).
37. Cui, Y., Chen, S., Wang, S. & Liu, X. Laboratory observations on the circadian feeding patterns in the grass carp (Ctenopharyngodon idella Val.) fed three different diets. Aquaculture 113, 57-64 (1993).
38. Huang, W., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nat. Protoc. 4, 44-57 (2009).
39. Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc., B 57, 289-300 (1995).
40. Dempsey, M.E. Regulation of steroid biosynthesis. Annu. Rev. Biochem. 43, 967-990 (1974).
41. Lange, B.M., Rujan, T., Martin, W. & Croteau, R. Isoprenoid biosynthesis: the evolution of two ancient and distinct pathways across genomes. Proc. Natl. Acad. Sci. USA 97, 13172-13177 (2000).
42. Flores, M.V. et al. The zebrafsh retinoid-related orphan receptor (ror) gene family. Gene Expr. Patterns 7, 535-543 (2007).
43. Tan, Y., DeBruyne, J., Cahill, G.M. & Wells, D.E. Identifcation of a mutation in the Clock1 gene affecting zebrafsh circadian rhythms. J. Neurogenet. 22, 149-166 (2008).
44. Zhou, Y. et al. Enhancement of growth and intestinal fora in grass carp: the effect of exogenous cellulase. Aquaculture 416-417, 1-7 (2013).
45. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat. Methods 5, 621-628 (2008).
46. Kozarewa, I. et al. Amplifcation-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat. Methods 6, 291-295 (2009).
47. Simpson, J.T. et al. ABySS: a parallel assembler for short read sequence data. Genome Res. 19, 1117-1123 (2009).
48. Li, H. Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics 28, 1838-1844 (2012).
49. Li, R. et al. SOAP: short oligonucleotide alignment program. Bioinformatics 24, 713-714 (2008).
50. Bonfeld, J.K. & Whitwham, A. Gap5-editing the billion fragment sequence assembly. Bioinformatics 26, 1699-1703 (2010).
51. Wu, T.D. & Watanabe, C.K. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21, 1859-1875 (2005).
52. Birney, E., Clamp, M. & Durbin, R. GeneWise and Genomewise. Genome Res. 14, 988-995 (2004).
53. Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004).
54. Wang, L., Feng, Z., Wang, X., Wang, X. & Zhang, X. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26, 136-138 (2010).