The genome of the miiuy croaker reveals well-developed innate immune and sensory systems

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Xu, Tianjun ^a   Xu, Guoliang ^a   Che, Rongbo ^a   Wang, Rixin ^a   Wang, Yanjin ^a   Li, Jinrui ^a   Wang, Shanchen ^a   Shu, Chang ^a   Sun, Yuena ^a   Liu, Tianxing ^a   Liu, Jiang ^a   Wang, Aishuai ^a   Han, Jingjing ^a   Chu, Qing ^a   Yang, Qiong ^a  

^a ZHEJIANG OCEAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AQUATIC ENVIRONMENT; GENOME; INNATE IMMUNITY; MODEL; MULTIGENE FAMILY; NATURAL SELECTION; SENSORY SYSTEM; SPECIES; VISION; ADAPTATION; ANIMAL; CLASSIFICATION; EVOLUTION; FEMALE; GENE EXPRESSION; GENE ONTOLOGY; GENETIC SELECTION; GENETICS; IMMUNOLOGY; METABOLISM; MOLECULAR GENETICS; ODOR; OLFACTORY RECEPTOR; PERCIFORMES; PHYLOGENY; TASTE BUD;

FISH PROTEIN; G PROTEIN COUPLED RECEPTOR; OLFACTORY RECEPTOR;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; BIOLOGICAL EVOLUTION; FEMALE; FISH PROTEINS; GENE EXPRESSION; GENE ONTOLOGY; GENOME; IMMUNITY, INNATE; MOLECULAR SEQUENCE ANNOTATION; PERCIFORMES; PHYLOGENY; RECEPTORS, G-PROTEIN-COUPLED; RECEPTORS, ODORANT; SELECTION, GENETIC; SMELL; TASTE BUDS; VISION, OCULAR;

EID: 84959143101     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep21902     Document Type: Article

References (60)

1. Johnson, G. D. & Gill, A. C. Encyclopedia of Fishes. (eds Paxton, J. R. & Eschmeyer, W. N.) 182, (San Diego Academic Press, 1998).
2. Masuda, H., Amaoka, K. & Araga, C. The fishes of the Japanese Archipelago. Tokyo: Tokai University Press (1984).
3. Xu, T. J., Meng, F. X., Sun, Y. N., Shi, G. & Wang, R. X. Identification of immune genes of the miiuy croaker (Miichthys miiuy) by sequencing and bioinformatic analysis of ESTs. Fish Shellfish Immunol. 29, 1099-1105 (2010).
4. Che, R. B., Sun, Y. Y., Sun, D. Q. & Xu, T. J. Characterization of the miiuy croaker (Miichthys miiuy) transcriptome and development of immune-relevant genes and molecular markers. PloS ONE 9, e94046 (2014).
5. Zhu, Z. H., Wang, R. X., Ren, L. P. & Xu, T. J. Characterization of the CCR3 and CCR9 genes in miiuy croaker and different selection pressures imposed on different domains between mammals and teleosts. Dev. Comp. Immunol. 41, 631-643 (2013).
6. Xu, T. J., Meng, F. X., Zhu, Z. H. & Wang, R. X. Characterization and comprehensive analysis of the miiuy croaker TLR2 reveals a direct evidence for intron insert and loss. Fish Shellfish Immunol. 34, 119-128 (2013).
7. Xu, T. J., Sun, Y. N., Shi, G., Cheng, Y. Z. & Wang, R. X. Characterization of the major histocompatibility complex class II genes in miiuy croaker. PloS ONE 6, e23823 (2011).
8. Zhu, L. Y., Nie, L., Zhu, G., Xiang, L. X. & Shao, J. Z. Advances in research of fish immune-relevant genes: a comparative overview of innate and adaptive immunity in teleosts. Dev. Comp. Immunol. 39, 39-62 (2013).
9. Gnerre, S. et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc. Natl Acad. Sci. USA 108, 1513-1518 (2011).
10. Li, R., Li, Y., Kristiansen, K. & Wang, J. SOAP: short oligonucleotide alignment program. Bioinformatics 24, 713-714 (2008).
11. Kent, W. J. BLAT-The BLAST-like alignment tool. Genome Res. 12, 656-664 (2002).
12. Price, A. L., Jones, N. C. & Pevzner, P. A. De novo identification of repeat families in large genomes. Bioinformatics 21, i351-i358 (2005).
13. Jurka, J. et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462-467 (2005).
14. Kasahara, M. et al. The medaka draft genome and insights into vertebrate genome evolution. Nature 447, 714-719 (2007).
15. Jones, F. C. et al. The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484, 55-61 (2012).
16. Star, B. et al. The genome sequence of Atlantic cod reveals a unique immune system. Nature 477, 207-210 (2011).
17. Elsik, C. G. et al. Creating a honey bee consensus gene set. Genome Biol. 8, R13 (2007).
18. Jirimutu, et al. Genome sequences of wild and domestic bactrian camels. Nat. Commun. 3, 1202 (2012).
19. The Gene Ontology Consortium. The gene ontology: enhancements for 2011. Nucleic Acids Res. 40, D559-D564 (2012).
20. Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. & Tanabe, M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 40, D109-D114 (2012).
21. Near, T. J. et al. Resolution of ray-finned fish phylogeny and timing of diversification. Proc. Natl Acad. Sci. USA 109, 13698-13703 (2012).
22. Wainwright, P. C. et al. The evolution of pharyngognathy: a phylogenetic and functional appraisal of the pharyngeal jaw key innovation in labroid fishes and beyond. Systematic Biol. 61, 1001-1027 (2012).
23. Rochman, Y., Spolski, R. & Leonard, W. J. New insights into the regulation of T cells by gamma (c) family cytokines. Nat. Rev. Immunol. 9, 480-490 (2009).
24. Chu, W. M. Tumor necrosis factor. Cancer Lett. 328, 222-225 (2013).
25. Laing, K. J., Purcell, M. K., Winton, J. R. & Hansen, J. D. A genomic view of the NOD-like receptor family in teleost fish: identification of a novel NLR subfamily in zebrafish. BMC Evol. Biol. 8, 42 (2008).
26. Spady, T. C. et al. Adaptive molecular evolution in the opsin genes of rapidly speciating cichlid species. Mol. Biol. Evol. 22, 1412-1422 (2005).
27. Yokoyama, S., Yang, H. & Starmer, W. T. Molecular basis of spectral tuning in the red- and green-sensitive (M/LWS) pigments in vertebrates. Genetics 179, 2037-2043 (2008).
28. Bowmaker, J. K. & Hunt, D. M. Evolution of vertebrate visual pigments. Vision Res. 16, R484-R489 (2006).
29. Nakamura,Y. et al. Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna. Proc. Natl Acad. Sci. USA 110, 11061-11066 (2013).
30. Oike, H. et al. Characterization of ligands for fish taste receptors. The Journal of neuroscience 27, 5584-5592 (2007).
31. Nei, M., Niimura, Y. & Nozawa, M. The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity. Nat. Rev. Genet. 9, 951-963 (2008).
32. Hashiguchi, Y. et al. Diversification and adaptive evolution of putative sweet taste receptors in three spine stickleback. Gene 396, 170-179 (2007).
33. Boetzer, M., Henkel, C. V., Jansen, H. J., Butler, D. & Pirovano, W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27, 578-579 (2011).
34. Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265-272 (2010).
35. Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573-580 (1999).
36. Tarailo-Graovac, M. & Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinformatics Chapter 4, Unit 4.10 (2009).
37. Lowe, T. M. & Eddy, S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955-964 (1997).
38. Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997).
39. Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188-7196 (2007).
40. Griffiths-Jones, S., Saini, H. K., Van Dongen, S. & Enright, A. J. miRBase: tools for microRNA genomics. Nucleic Acids Res. 36, D154-D158 (2008).
41. Birney, E., Clamp, M. & Durbin, R. Genewise and genomewise. Genome Res. 14, 988-995 (2004).
42. Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
43. Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. biotechnol. 28, 511-515 (2010).
44. Stanke, M. & Waack, S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19, ii215-ii225 (2003).
45. Majoros, W. H., Pertea, M. & Salzberg, S. L. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20, 2878-2879 (2004).
46. Korf, I. Gene finding in novel genomes. BMC Bioinformatics 5, 59 (2004).
47. Zdobnov, E. M. & Apweiler, R. InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17, 847-848 (2001).
48. Conesa, A. et al. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674-3676 (2005).
49. Ye, J. et al. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. 34 (suppl 2), W293-W297 (2006).
50. Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A. C. & Kanehisa, M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182-W185 (2007).
51. Li, L., Stoeckert, C. J. & Roos, D. S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178-2189 (2003).
52. Han, M. V. et al. Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. Mol. Biol. Evol. 30, 1987-1997 (2013).
53. Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772-780 (2013).
54. Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540-552 (2000).
55. Darriba, D. et al. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27, 1164-1165 (2011).
56. Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690 (2006).
57. Ronquist, F. & Huelsenbeck, J. P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574 (2003).
58. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591 (2007).
59. Louis, A., Muffato, M. & Crollius, H. R. Genomicus: five genome browsers for comparative genomics in eukaryota. Nucleic Acids Res. 41, 700-705 (2013).
60. Sawyer, S. A. Statistical tests for detecting gene conversion. Mol. Biol. Evol. 6, 526-538 (1989).