Transcriptome Analysis of Artificial Hybrid Pufferfish Jiyan-1 and Its Parental Species: Implications for Pufferfish Heterosis

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Gao, Yang ^a,b   Zhang, Huan ^a   Gao, Qiang ^a   Wang, Lingling ^a   Zhang, Fuchong ^c   Siva, Vinu S ^a,b   Zhou, Zhi ^a   Song, Linsheng ^a   Zhang, Shicui ^d  

^a INSTITUTE OF OCEANOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c Fisheries Research Institute of Hebei Province   (China)

^d OCEAN UNIVERSITY OF CHINA   (China)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; PHOSPHOTRANSFERASE; RNA ISOFORM; TRANSCRIPTOME;

ANIMAL TISSUE; ARTICLE; CATALYSIS; CODOMINANCE; COMPARATIVE STUDY; GENE ACTIVITY; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC MODEL; GENETIC VARIABILITY; HETEROSIS; INTERACTIONS WITH NUCLEIC ACID; JIYAN 1; METABOLISM; NONHUMAN; NUCLEOTIDE BINDING; PUFFER FISH; RNA ANALYSIS; RNA SEQUENCE; TAKIFUGU FLAVIDUS; TAKIFUGU RUBRIPES;

ANIMALS; CHIMERA; GENE EXPRESSION REGULATION; HYBRID VIGOR; TETRAODONTIFORMES; TRANSCRIPTION, GENETIC;

EID: 84874776730     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0058453     Document Type: Article

References (64)

1. Song L, Liu B, Xiang J, Qian PY, (2001) Molecular phylogeny and species identification of pufferfish of the genus Takifugu (Tetraodontiformes, Tetraodontidae). Marine Biotechnology 3: 398-406.
2. Aparicio S, Chapman J, Stupka E, Putnam N, Chia J-m, et al. (2002) Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes. Science 297: 1301-1310.
3. Zhang G, Shi Y, Zhu Y, Liu J, Zang W, (2010) Effects of salinity on embryos and larvae of tawny puffer Takifugu flavidus. Aquaculture 302: 71-75.
4. Fan W, Liu H, Zhao W, Zhang F, (2011) Research of morphological characteristics and growth comparison of Fugu flavidus, Fugu rubripes and the hybridization (Fugu flavidus♀× Fugu rubripes♂) in early growth stages. Journal of Fisheries of China 7: 1065-1071.
5. Shull GH (1908) The composition of a field of maize. Journal of Heredity: 296-301.
6. Hua J, Xing Y, Wu W, Xu C, Sun X, et al. (2003) Single-locus heterotic effects and dominance by dominance interactions can adequately explain the genetic basis of heterosis in an elite rice hybrid. PNAS 100: 2574-2579.
7. Birchler JA, Auger DL, Riddle NC, (2003) In Search of the Molecular Basis of Heterosis. The Plant Cell 15: 2236-2239.
8. Rahmana MA, Ueharaa T, Lawrence JM, (2005) Growth and heterosis of hybrids of two closely related species of Pacific sea urchins (Genus Echinometra) in Okinawa. Aquaculture 245: 121-133.
9. Troyer AF, (2006) Adaptedness and Heterosis in Corn and Mule Hybrids. Crop Science 46: 528-543.
10. Yamashita H, (1968) Electrophoretic patterns of serum proteins in the blood of four species of puff-fish, genus Fugu, and their F 1 hybrids. Marine Biology 1: 277-281.
11. CB D, (1908) Degeneration, albinism and inbreeding. Science 28: 455.
12. Vuylsteke M, Van Eeuwijk F, Van Hummelen P, Kuiper M, Zabeau M, (2005) Genetic analysis of variation in gene expression in Arabidopsis thaliana. Genetics 171: 1267-1275.
13. Yao Y, Ni Z, Zhang Y, Chen Y, Ding Y, et al. (2005) Identification of differentially expressed genes in leaf and root between wheat hybrid and its parental inbreds using PCR-based cDNA subtraction. Plant molecular biology 58: 367-384.
14. Wei G, Tao Y, Liu G, Chen C, Luo R, et al. (2009) A transcriptomic analysis of superhybrid rice LYP9 and its parents. PNAS 106: 7695-7701.
15. Metzker ML, (2009) Sequencing technologies-the next generation. Nature Reviews Genetics 11: 31-46.
16. Morozova O, Marra MA, (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92: 255-264.
17. Mardis ER, (2008) The impact of next-generation sequencing technology on genetics. TRENDS in Genetics 24: 133-141.
18. Brenner S, G.Elgar, Sandford R, Macrae A, Venkatesh B, et al. (1993) Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome. Nature 366: 265-268.
19. Jaillon O, Aury J-M, Brunet Fdr, Petit J-L, Stange-Thomann N, et al. (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431: 946-957.
20. Cloonan N, Forrest ARR, Kolle G, Gardiner BBA, Faulkner GJ, et al. (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nature Methods 5: 613-619.
21. Ni Z, Kim ED, Ha M, Lackey E, Liu J, et al. (2008) Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 457: 327-331.
22. Lariepe A, Mangin B, Jasson S, Combes V, Dumas F, et al. (2012) The Genetic Basis of Heterosis: Multiparental Quantitative Trait Loci Mapping Reveals Contrasted Levels of Apparent Overdominance Among Traits of Agronomical Interest in Maize (Zea mays L.). Genetics 190: 795-811.
23. Springer NM, Stupar RM, (2007) Allelic variation and heterosis in maize: How do two halves make more than a whole? Genome research 17: 264-275.
24. Matera AG, Terns RM, Terns MP, (2007) Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nature reviews Molecular cell biology 8: 209-220.
25. Swanson-Wagner RA, Jia Y, DeCook R, Borsuk LA, Nettleton D, et al. (2006) All possible modes of gene action are observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents. PNAS 103: 6805-6810.
26. Luo QJ, Samanta MP, Köksal F, Janda J, Galbraith DW, et al. (2009) Evidence for antisense transcription associated with microRNA target mRNAs in Arabidopsis. PLoS genetics 5: e1000457.
27. Xiao J, Li J, Yuan L, Tanksley SD, (1995) Dominance is the major genetic basis of heterosis in rice as revealed by QTL analysis using molecular markers. Genetics 140: 745-754.
28. Sun Q, Wu L, Ni Z, Meng F, Wang Z, et al. (2004) Differential gene expression patterns in leaves between hybrids and their parental inbreds are correlated with heterosis in a wheat diallel cross. Plant Science: 651-657.
29. Li L, Lu K, Chen Z, Mu T, Hu Z, et al. (2008) Dominance, overdominance and epistasis condition the heterosis in two heterotic rice hybrids. Genetics 180: 1725-1742.
30. Zhu JY, Zhao N, Yang B, (2012) Global Transcriptome Profiling of the Pine Shoot Beetle, Tomicus yunnanensis (Coleoptera: Scolytinae). PLoS One 7: e32291.
31. Bai X, Mamidala P, Rajarapu SP, Jones SC, Mittapalli O, (2011) Transcriptomics of the Bed Bug (Cimex lectularius). PLoS One 6: e16336.
32. Li H, Dong Y, Yang J, Liu X, Wang Y, et al. (2012) De novo transcriptome of safflower and the identification of putative genes for oleosin and the biosynthesis of flavonoids. PLoS One 7: e30987.
33. Huan P, Wang H, Liu B, (2011) Transcriptomic analysis of the clam Meretrix meretrix on different larval stages. Marine Biotechnology 14: 1-10.
34. Meyer RC, Witucka-Wall H, Becher M, Blacha A, Boudichevskaia A, et al. (2012) Heterosis manifestation during early Arabidopsis seedling development is characterized by intermediate gene expression and enhanced metabolic activity in the hybrids. The Plant Journal 71: 669-683.
35. Nuhse TS, Peck SC, Hirt H, Boller T, (2000) Microbial elicitors induce activation and dual phosphorylation of the Arabidopsis thaliana MAPK 6. Science's STKE 275: 7521.
36. Han J, Jiang Y, Li Z, Kravchenko V, Ulevitch R, (1997) Activation of the transcription factor MEF2C by the MAP kinase p38 in inflammation. Nature 386: 296-299.
37. Liu X, Serova L, Kvetňanský R, Sabban EL, (2008) Identifying the stress transcriptome in the adrenal medulla following acute and repeated immobilization. Annals of the New York Academy of Sciences 1148: 1-28.
38. Li S, Rédei G, (1969) Direct evidence for models of heterosis provided by mutants of Arabidopsis blocked in the thiamine pathway. TAG Theoretical and Applied Genetics 39: 68-72.
39. Li X, Schuler MA, Berenbaum MR, (2007) Molecular mechanisms of metabolic resistance to synthetic and natural xenobiotics. Annu Rev Entomol 52: 231-253.
40. Scott JG, (1999) Cytochromes P450 and insecticide resistance. Insect Biochemistry and Molecular Biology 29: 757-777.
41. Marichal P, Koymans L, Willemsens S, Bellens D, Verhasselt P, et al. (1999) Contribution of mutations in the cytochrome P450 14α-demethylase (Erg11p, Cyp51p) to azole resistance in Candida albicans. Microbiology 145: 2701-2713.
42. Scott JG, Liu N, Wen Z, (1998) Insect cytochromes P450: diversity, insecticide resistance and tolerance to plant toxins1. Comparative Biochemistry and Physiology Part C: Pharmacology, Toxicology and Endocrinology 121: 147-155.
43. Lau WC, Gurbel PA, Watkins PB, Neer CJ, Hopp AS, et al. (2004) Contribution of hepatic cytochrome P450 3A4 metabolic activity to the phenomenon of clopidogrel resistance. Circulation 109: 166-171.
44. Daborn P, Yen J, Bogwitz M, Le Goff G, Feil E, et al. (2002) A single P450 allele associated with insecticide resistance in Drosophila. Science 297: 2253-2256.
45. McDaniel RG, Sarkissian IV, (1968) Mitochondrial heterosis in maize. Genetics 59: 465-475.
46. McDaniel RG, (1969) Relationships of seed weight, seedling vigor and mitochondrial metabolism in barley. Crop Science 9: 823-827.
47. Korn M, Gärtner T, Erban A, Kopka J, Selbig J, et al. (2010) Predicting Arabidopsis freezing tolerance and heterosis in freezing tolerance from metabolite composition. Molecular plant 3: 224-235.
48. Malau-Aduli A, Siebert B, Bottema C, Pitchford W, (2000) Heterosis, sex and breed differences in the fatty acid composition of muscle phospholipids in beef cattle. Journal of Animal Physiology and Animal Nutrition 83: 113-120.
49. Ebato H, Seyfried T, Yu R, (1983) Biochemical study of heterosis for brain myelin content in mice. Journal of neurochemistry 40: 440-446.
50. Huang Y, Zhang L, Zhang J, Yuan D, Xu C, et al. (2006) Heterosis and polymorphisms of gene expression in an elite rice hybrid as revealed by a microarray analysis of 9198 unique ESTs. Plant molecular biology 62: 579-591.
51. Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, et al. (2004) Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Research 14: 331-342.
52. Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, et al. (2008) Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453: 1239-1243.
53. Attisano L, Wrana JL, Cheifetz S, Massague J, (1992) Novel activin receptors: distinct genes and alternative mRNA splicing generate a repertoire of serine/threonine kinase receptors. Cell 68: 97-108.
54. Hsu T, Gogos JA, Kirsh SA, Kafatos FC, (1992) Multiple zinc finger forms resulting from developmentally regulated alternative splicing of a transcription factor gene. Science 257: 1946.
55. Pihlajamäki J, Lerin C, Itkonen P, Boes T, Floss T, et al. (2011) Expression of the splicing factor gene SFRS10 is reduced in human obesity and contributes to enhanced lipogenesis. Cell Metabolism 14: 208-218.
56. Mutter GL, Zahrieh D, Liu C, Neuberg D, Finkelstein D, et al. (2004) Comparison of frozen and RNALater solid tissue storage methods for use in RNA expression microarrays. BMC Genomics 5: 88.
57. Flicek P, Amode MR, Barrell D, Beal K, Brent S, et al. (2012) Ensembl 2012. Nucleic Acids Research 40: D84-D90.
58. Quinlan AR, Hall IM, (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
59. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 28: 511-515.
60. Smedley D, Haider S, Ballester B, Holland R, London D, et al. (2009) BioMart - biological queries made easy. BMC Genomics 10: 22.
61. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, et al. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.
62. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36: D480-D484.
63. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10: 421.
64. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, et al. (2009) InterPro: the integrative protein signature database. Nucleic Acids Research 37: D211-D215.