Transcriptome assembly, gene annotation and tissue gene expression atlas of the rainbow trout

PLoS ONE

Volumn 10, Issue 3, 2015, Pages

  Salem, Mohamed ^a   Paneru, Bam ^a   Al Tobasei, Rafet ^a   Abdouni, Fatima ^a   Thorgaard, Gary H ^b   Rexroad, Caird E ^c   Yao, Jianbo ^d  

^a MIDDLE TENNESSEE STATE UNIVERSITY   (United States)

^b WASHINGTON STATE UNIVERSITY   (United States)

^c NATIONAL CENTER FOR COOL AND COLD WATER AQUACULTURE   (United States)

^d WEST VIRGINIA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG; MESSENGER RNA; TRANSCRIPTOME; COMPLEMENTARY DNA;

ANIMAL TISSUE; ARTICLE; BASE PAIRING; BRAIN; CONTROLLED STUDY; DNA LIBRARY; FAST MUSCLE; FUNCTIONAL GENOMICS; GENE ANNOTATION; GENE EXPRESSION; GENE MAPPING; GENE NUMBER; GENE SEQUENCE; HAPLOIDY; HOUSEKEEPING GENE; INTESTINE; MOLECULAR GENETICS; NONHUMAN; PROTEIN DATABASE; RAINBOW TROUT; RNA SEQUENCE; SEQUENCE HOMOLOGY; STOMACH; TESTIS; ALTERNATIVE RNA SPLICING; ANIMAL; ANTIBODY SPECIFICITY; CICHLID; CLASSIFICATION; CONTIG MAPPING; ESSENTIAL GENE; GENE EXPRESSION PROFILING; GENE LIBRARY; GENE ONTOLOGY; GENETICS; GENOME; HIGH THROUGHPUT SEQUENCING; METABOLISM; NUCLEOTIDE SEQUENCE; ONCORHYNCHUS MYKISS;

ONCORHYNCHUS MYKISS;

ALTERNATIVE SPLICING; ANIMALS; BASE SEQUENCE; CICHLIDS; CONTIG MAPPING; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; GENE LIBRARY; GENE ONTOLOGY; GENES, ESSENTIAL; GENOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE ANNOTATION; ONCORHYNCHUS MYKISS; ORGAN SPECIFICITY; RNA, MESSENGER; TRANSCRIPTOME;

EID: 84925600188     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0121778     Document Type: Article

References (95)

1. Behenke RJ (1992) Native trout of western North America. American Fisheries Society Monograph: 0362-1715.
2. Papanastasiou AD, Georgaka E, Zarkadis IK (2007) Cloning of a CD59-like gene in rainbow trout. Expression and phylogenetic analysis of two isoforms. Mol Immunol 44: 1300-1306. PMID: 16876248
3. Williams DE (2012) The rainbow trout liver cancer model: response to environmental chemicals and studies on promotion and chemoprevention. Comp Biochem Physiol C Toxicol Pharmacol 155: 121-127. doi: 10.1016/j.cbpc.2011.05.013 PMID: 21704190
4. Giaquinto PC, Hara TJ (2008) Discrimination of bile acids by the rainbow trout olfactory system: evidence as potential pheromone. Biol Res 41: 33-42. doi: 10.4067/S0716-97602008000100005 PMID: 18769761
5. Mc LB, O'Donnell DJ, Elvehjem CA (1947) Nutrition of rainbow trout. Fed Proc 6: 413. PMID: 20343876
6. Patel M, Rogers JT, Pane EF, Wood CM (2006) Renal responses to acute lead waterborne exposure in the freshwater rainbow trout (Oncorhynchus mykiss). Aquat Toxicol 80: 362-371. PMID: 17125852
7. Welsh PG, Lipton J, Mebane CA, Marr JC (2008) Influence of flow-through and renewal exposures on the toxicity of copper to rainbow trout. Ecotoxicol Environ Saf 69: 199-208. PMID: 17517436
8. Speare D, Arsenault G, Buote M (1998) Evaluation of Rainbow Trout as a Model for use in Studies on Pathogenesis of the Branchial Microsporidian Loma salmonae. Contemp Top Lab Anim Sci 37: 55-58. PMID: 12456170
9. Davidson WS (2012) Adaptation genomics: next generation sequencing reveals a shared haplotype for rapid early development in geographically and genetically distant populations of rainbow trout. Mol Ecol 21: 219-222. PMID: 22329016
10. Ncbi National Center for Biotechnology Information; Bethesda (MD).
11. Salem M, Kenney PB, Rexroad CE Iii, Yao J (2008) Development of a 37 k high-density oligonucleotide microarray: a new tool for functional genome research in rainbow trout. Journal of Fish Biology 72: 2187-2206.
12. Genet C, Dehais P, Palti Y, Gao G, Gavory F, Wincker P, et al. (2011) Analysis of BAC-end sequences in rainbow trout: content characterization and assessment of synteny between trout and other fish genomes. BMC Genomics 12: 314. doi: 10.1186/1471-2164-12-314 PMID: 21672188
13. rd (2004) Characterization of a new BAC library for rainbow trout: evidence for multi-locus duplication. Anim Genet 35: 130-133. PMID: 15025574
14. Berthelot C, Brunet F, Chalopin D, Juanchich A, Bernard M, Noel B, et al. (2014) The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat Commun 5: 3657. doi: 10.1038/ncomms4657 PMID: 24755649
15. Miller M, Palti Y, Luo M, Miller J, Brunelli J, Wheeler P, et al. (2011) Rapid and Accurate Sequencing of the Rainbow Trout Physical Map using Illumina Technology. San Diego, California.
16. Palti Y, Luo MC, Hu Y, Genet C, You FM, Vallejo RL, et al. (2009) A first generation BAC-based physical map of the rainbow trout genome. BMC Genomics 10: 462. doi: 10.1186/1471-2164-10-462 PMID: 19814815
17. Palti Y (2010) Production of a Draft Reference Genome Sequence for Rainbow Trout. Leetown, West Virginia: USDA-ARS.
18. Palti Y, Genet C, Luo MC, Charlet A, Gao G, Hu Y, et al. (2011) A first generation integrated map of the rainbow trout genome. BMC Genomics 12: 180-180. doi: 10.1186/1471-2164-12-180 PMID: 21473775
19. Palti Y, Rexroad Iii CE, Luo MC, Thorgaard GH, Doe CQ, Salem M, et al. (2011) Generation of a high density SNP chip for genomic analysis in rainbow trout. USDA/NIFA grant number WVAR-2010-04523 http://cris.nifa.usda.gov/.
20. Palti Y, Genet C, Gao G, Hu Y, You FM, Boussaha M, et al. (2012) A second generation integrated map of the rainbow trout (Oncorhynchus mykiss) genome: analysis of conserved synteny with model fish genomes. Mar Biotechnol (NY) 14: 343-357. doi: 10.1007/s10126-011-9418-z PMID: 22101344
21. Palti Y, Gao G, Miller MR, Vallejo RL, Wheeler PA, Quillet Yao JE, et al. (2013) Single nucleotide polymorphism (SNP) discovery in rainbow trout using restriction site associated DNA (RAD) sequencing of doubled haploids and assessment of polymorphism in a population survey. San Diego, California.
22. Palti Y, Gao G, Miller MR, Vallejo RL, Wheeler PA, Quillet E, et al. (2014) A resource of single-nucleotide polymorphisms for rainbow trout generated by restriction-site associated DNA sequencing of doubled haploids. Mol Ecol Resour 14: 588-596. doi: 10.1111/1755-0998.12204 PMID: 24251403
23. Palti Y, Gao G, Liu S, Kent MP, Lien S, Miller MR, et al. (2014) The development and characterization of a 57K single nucleotide polymorphism array for rainbow trout. Mol Ecol Resour.
24. Salem M, Vallejo RL, Leeds TD, Palti Y, Liu S, Sabbagh A, et al. (2012) RNA-Seq identifies SNP markers for growth traits in rainbow trout. PLoS One 7: e36264. doi: 10.1371/journal.pone.0036264 PMID: 22574143
25. Salgado LR, Koop DM, Pinheiro DG, Rivallan R, Le Guen V, Nicolas MF, et al. (2014) De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers. BMC Genomics 15: 236. doi: 10.1186/1471-2164-15-236 PMID: 24670056
26. Devisetty UK, Covington MF, Tat AV, Lekkala S, Maloof JN (2014) Polymorphism Identification and Improved Genome Annotation of Brassica rapa Through Deep RNA Sequencing. G3 (Bethesda) 4: 2065-2078. doi: 10.1534/g3.114.012526 PMID: 25122667
27. Marancik D, Gao G, Paneru B, Ma H, Hernandez AG, Salem M, et al. (2014) Whole-body transcriptome of selectively bred, resistant-, control-, and susceptible-line rainbow trout following experimental challenge with Flavobacterium psychrophilum. Front Genet 5: 453. doi: 10.3389/fgene.2014.00453 PMID: 25620978
28. Liu S, Vallejo RL, Gao G, Palti Y, Weber GM, Hernandez A, et al. (2015) Identification of Single-Nucleotide Polymorphism Markers Associated with Cortisol Response to Crowding in Rainbow Trout. Mar Biotechnol (NY).
29. Salem M, Rexroad CE, Wang J, Thorgaard GH, Yao J (2010) Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches. BMC Genomics 11: 564. doi: 10.1186/1471-2164-11-564 PMID: 20942956
30. rd (2011) Generation of a reference transcriptome for evaluating rainbow trout responses to various stressors. BMC Genomics 12: 626. doi: 10.1186/1471-2164-12-626 PMID: 22188770
31. Fox SE, Christie MR, Marine M, Priest HD, Mockler TC, Blouin MS (2014) Sequencing and characterization of the anadromous steelhead (Oncorhynchus mykiss) transcriptome. Mar Genomics 15: 13-15. doi: 10.1016/j.margen.2013.12.001 PMID: 24440488
32. Miller M (2013) Rainbow trout genome assembly draft. USDA/NAGRP.
33. Alkan C, Sajjadian S, Eichler EE (2011) Limitations of next-generation genome sequence assembly. Nat Methods 8: 61-65. doi: 10.1038/nmeth.1527 PMID: 21102452
34. Bailey GS, Poulter RTM, Stockwell PA (1978) Gene Duplication in Tetraploid Fish - Model for Gene Silencing at Unlinked Duplicated Loci. Proceedings of the National Academy of Sciences of the United States of America 75: 5575-5579. PMID: 281706
35. Ryynanen HJ, Primmer CR (2006) Single nucleotide polymorphism (SNP) discovery in duplicated genomes: intron-primed exon-crossing (IPEC) as a strategy for avoiding amplification of duplicated loci in Atlantic salmon (Salmo salar) and other salmonid fishes. BMC Genomics 7: 192-192. PMID: 16872523
36. Smith CT, Elfstrom CM, Seeb LW, Seeb JE (2005) Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon. Mol Ecol 14: 4193-4203. PMID: 16262869
37. Sanchez CC, Smith TP, Wiedmann RT, Vallejo RL, Salem M, Yao J, et al. (2009) Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library. BMC Genomics 10: 559-559. doi: 10.1186/1471-2164-10-559 PMID: 19939274
38. Christensen KA, Brunelli JP, Lambert MJ, DeKoning J, Phillips RB, Thorgaard GH (2013) Identification of single nucleotide polymorphisms from the transcriptome of an organism with a whole genome duplication. BMC Bioinformatics 14: 325. doi: 10.1186/1471-2105-14-325 PMID: 24237905
39. Robison BD, Wheeler PA, Thorgaard GH (1999) Variation in development rate among clonal lines of rainbow trout (Oncorhynchus mykiss). Aquaculture 173: 131-141.
40. Young WP, Wheeler PA, Fields RD, Thorgaard GH (1996) DNA fingerprinting confirms isogenicity of androgenetically derived rainbow trout lines. J Hered 87: 77-80. PMID: 8742822
41. Palti Y, Genet C, Gao G, Hu Y, You FM, Boussaha M, et al. (2011) A second Generation Integrated Map of the Rainbow Trout (Oncorhynchus mykiss) Genome: Analysis of Conserved Synteny with Model Fish Genomes. Mar Biotechnol (NY) 10.1007/s1.
42. Zhang H, Tan E, Suzuki Y, Hirose Y, Kinoshita S, Okano H, et al. (2014) Dramatic improvement in genome assembly achieved using doubled-haploid genomes. Sci Rep 4: 6780. doi: 10.1038/srep06780 PMID: 25345569
43. Watson JD HN, Roberts JW, Steitz JA, Weiner AM (1987) The functioning of higher eukaryotic genes. In: Gene MBot, editor. Molecular Biology of the Gene. Molecular Biology of the Gene.
44. Butte AJ, Dzau VJ, Glueck SB (2001) Further defining housekeeping, or "maintenance," genes Focus on "A compendium of gene expression in normal human tissues". Physiol Genomics 7: 95-96. PMID: 11773595
45. Xiao SJ, Zhang C, Zou Q, Ji ZL (2010) TiSGeD: a database for tissue-specific genes. Bioinformatics 26: 1273-1275. doi: 10.1093/bioinformatics/btq109 PMID: 20223836
46. Fowlkes CC, Hendriks CL, Keranen SV, Weber GH, Rubel O, Huang MY, et al. (2008) A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell 133: 364-374. doi: 10.1016/j.cell.2008.01.053 PMID: 18423206
47. Tomancak P, Berman BP, Beaton A, Weiszmann R, Kwan E, Hartenstein V, et al. (2007) Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol 8: R145. PMID: 17645804
48. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 101: 6062-6067. PMID: 15075390
49. Lein ES, Hawrylycz MJ, Ao N, Ayres M, Bensinger A, Bernard A, et al. (2007) Genome-wide atlas of gene expression in the adult mouse brain. Nature 445: 168-176. PMID: 17151600
50. Bamps S, Hope IA (2008) Large-scale gene expression pattern analysis, in situ, in Caenorhabditis elegans. Brief Funct Genomic Proteomic 7: 175-183. doi: 10.1093/bfgp/eln013 PMID: 18332038
51. Chikina MD, Huttenhower C, Murphy CT, Troyanskaya OG (2009) Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans. PLoS Comput Biol 5: e1000417. doi: 10.1371/journal.pcbi.1000417 PMID: 19543383
52. Kudoh T, Tsang M, Hukriede NA, Chen X, Dedekian M, Clarke CJ, et al. (2001) A gene expression screen in zebrafish embryogenesis. Genome Res 11: 1979-1987. PMID: 11731487
53. Henrich T, Ramialison M, Wittbrodt B, Assouline B, Bourrat F, Berger A, et al. (2005) MEPD: a resource for medaka gene expression patterns. Bioinformatics 21: 3195-3197. PMID: 15879458
54. Allendorf FW, Thorgaard GH (1984) Tetraploidy and the evolution of salmonid fishes. In: Bj T, editor: Plenum Press, New York. pp. 1-53.
55. Scheerer PD, Thorgaard GH, Allendorf FW (1991) Genetic analysis of androgenetic rainbow trout. J Exp Zool 260: 382-390. PMID: 1744618
56. Scheerer PDTG, Allendorf FW, Knudsen KL (1986) Androgenetic rainbow trout produced from inbred and outbred sperm show similar survival. Aquaculture 57: 289-298.
57. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29: 644-652. doi: 10.1038/nbt.1883 PMID: 21572440
58. Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol: 138-148. PMID: 10786296
59. Lottaz C, Iseli C, Jongeneel CV, Bucher P (2003) Modeling sequencing errors by combining Hidden Markov models. Bioinformatics 19 Suppl 2: ii103-112. PMID: 14534179
60. Gotz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, et al. (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36: 3420-3435. doi: 10.1093/nar/gkn176 PMID: 18445632
61. Gene Ontology C (2008) The Gene Ontology project in 2008. Nucleic Acids Res 36: D440-444. PMID: 17984083
62. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29. PMID: 10802651
63. Jongeneel CV, Delorenzi M, Iseli C, Zhou D, Haudenschild CD, Khrebtukova I, et al. (2005) An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Res 15: 1007-1014. PMID: 15998913
64. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7: 562-578. doi: 10.1038/nprot.2012.016 PMID: 22383036
65. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357-359. doi: 10.1038/nmeth.1923 PMID: 22388286
66. Min XJ, Butler G, Storms R, Tsang A (2005) OrfPredictor: predicting protein-coding regions in EST-derived sequences. Nucleic Acids Res Web Server Issue W677-W680.
67. Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Res 12: 656-664. PMID: 11932250
68. Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12: 671-682. doi: 10.1038/nrg3068 PMID: 21897427
69. Zhao QY, Wang Y, Kong YM, Luo D, Li X, Hao P (2011) Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics 12 Suppl 14: S2. doi: 10.1186/1471-2105-12-S14-S2 PMID: 22373417
70. Rexroad CE 3rd, Lee Y, Keele JW, Karamycheva S, Brown G, Koop B, et al. (2003) Sequence analysis of a rainbow trout cDNA library and creation of a gene index. Cytogenet Genome Res 102: 347-354. PMID: 14970727
71. Wang S, Peatman E, Abernathy J, Waldbieser G, Lindquist E, Richardson P, et al. (2010) Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biol 11: R8. doi: 10.1186/gb-2010-11-1-r8 PMID: 20096101
72. Shin SC, Kim SJ, Lee JK, Ahn do H, Kim MG, Lee H, et al. (2012) Transcriptomics and comparative analysis of three antarctic notothenioid fishes. PLoS One 7: e43762. doi: 10.1371/journal.pone.0043762 PMID: 22916302
73. Lee AP, Kerk SY, Tan YY, Brenner S, Venkatesh B (2011) Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes. Mol Biol Evol 28: 1205-1215. doi: 10.1093/molbev/msq304 PMID: 21081479
74. Ravi V, Venkatesh B (2008) Rapidly evolving fish genomes and teleost diversity. Curr Opin Genet Dev 18: 544-550. doi: 10.1016/j.gde.2008.11.001 PMID: 19095434
75. Koop BF, von Schalburg KR, Leong J, Walker N, Lieph R, Cooper GA, et al. (2008) A salmonid EST genomic study: genes, duplications, phylogeny and microarrays. BMC Genomics 9: 545. doi: 10.1186/1471-2164-9-545 PMID: 19014685
76. Ji P, Liu G, Xu J, Wang X, Li J, Zhao Z, et al. (2012) Characterization of common carp transcriptome: sequencing, de novo assembly, annotation and comparative genomics. PLoS One 7: e35152. doi: 10.1371/journal.pone.0035152 PMID: 22514716
77. Ramskold D, Wang ET, Burge CB, Sandberg R (2009) An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol 5: e1000598. doi: 10.1371/journal.pcbi.1000598 PMID: 20011106
78. Conn PJJP. P Physiology and pharmacology of metabotropic glutamate receptors. Annual review of pharmacology and toxicology 37: 205-237. PMID: 9131252
79. Spooren WP, Gasparini F, Salt TE, Kuhn R (2001) Novel allosteric antagonists shed light on mglu(5) receptors and CNS disorders. Trends Pharmacol Sci 22: 331-337. PMID: 11431019
80. Lamp K, Humeny A, Nikolic Z, Imai K, Adamski J, Schiebel K, et al. (2001) The murine GABA(B) receptor 1: cDNA cloning, tissue distribution, structure of the Gabbr1 gene, and mapping to chromosome 17. Cytogenet Cell Genet 92: 116-121. PMID: 11306808
81. Suzuki Y, Tasumi S, Tsutsui S, Okamoto M, Suetake H (2003) Molecular diversity of skin mucus lectins in fish. Comp Biochem Physiol B Biochem Mol Biol 136: 723-730. PMID: 14662297
82. Tsutsui S, Tasumi S, Suetake H, Suzuki Y (2003) Lectins homologous to those of monocotyledonous plants in the skin mucus and intestine of pufferfish, Fugu rubripes. J Biol Chem 278: 20882-20889. PMID: 12654913
83. Hastie ND, Bishop JO (1976) The expression of three abundance classes of messenger RNA in mouse tissues. Cell 9: 761-774. PMID: 1017013
84. Axel R, Feigelson P, Schutz G (1976) Analysis of the complexity and diversity of mRNA from chicken liver and oviduct. Cell 7: 247-254. PMID: 954082
85. Bishop JO, Morton JG, Rosbash M, Richardson M (1974) Three abundance classes in HeLa cell messenger RNA. Nature 250: 199-204. PMID: 4855195
86. Chan ET, Quon GT, Chua G, Babak T, Trochesset M, Zirngibl RA, et al. (2009) Conservation of core gene expression in vertebrate tissues. J Biol 8: 33. doi: 10.1186/jbiol130 PMID: 19371447
87. Ali A, Rexroad CE, Thorgaard GH, Yao J, Salem M (2014) Characterization of the rainbow trout spleen transcriptome and identification of immune-related genes. Front Genet 5: 348. doi: 10.3389/fgene.2014.00348 PMID: 25352861
88. Modrek B, Lee C (2002) A genomic view of alternative splicing. Nat Genet 30: 13-19. PMID: 11753382
89. Taylor JS, Braasch I, Frickey T, Meyer A, Van de Peer Y (2003) Genome duplication, a trait shared by 22000 species of ray-finned fish. Genome Res 13: 382-390. PMID: 12618368
90. Steinke D, Salzburger W, Braasch I, Meyer A (2006) Many genes in fish have species-specific asymmetric rates of molecular evolution. BMC Genomics 7: 20. PMID: 16466575
91. Hoegg S, Brinkmann H, Taylor JS, Meyer A (2004) Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish. J Mol Evol 59: 190-203. PMID: 15486693
92. Yu WP, Brenner S, Venkatesh B (2003) Duplication, degeneration and subfunctionalization of the nested synapsin-Timp genes in Fugu. Trends Genet 19: 180-183. PMID: 12683968
93. Altschmied J, Delfgaauw J, Wilde B, Duschl J, Bouneau L, Volff JN, et al. (2002) Subfunctionalization of duplicate mitf genes associated with differential degeneration of alternative exons in fish. Genetics 161: 259-267. PMID: 12019239
94. Xing Y, Lee C (2006) Alternative splicing and RNA selection pressure - evolutionary consequences for eukaryotic genomes. Nat Rev Genet 7: 499-509. PMID: 16770337
95. Lu J, Peatman E, Wang W, Yang Q, Abernathy J, Wang S, et al. (2010) Alternative splicing in teleost fish genomes: same-species and cross-species analysis and comparisons. Mol Genet Genomics 283: 531-539. doi: 10.1007/s00438-010-0538-3 PMID: 20383527