Differential transcriptome analysis between Paulownia fortunei and its synthesized autopolyploid

International Journal of Molecular Sciences

Volumn 15, Issue 3, 2014, Pages 5079-5093

  Zhang, Xiaoshen ^a   Deng, Minjie ^a   Fan, Guoqiang ^a  

^a HENAN AGRICULTURAL UNIVERSITY   (China)

Author keywords

De novo assembly; Next generation sequencing; Paulownia fortunei; Polyploidy; Transcriptome

Indexed keywords

COLCHICINE; MESSENGER RNA; TRANSCRIPTOME;

ARTICLE; DIPLOIDY; DNA LIBRARY; DNA SEQUENCE; ENERGY METABOLISM; EPIGENETICS; GENE EXPRESSION; GENE ONTOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; ORTHOLOGY; PAULOWNIA FORTUNEI; PLANT GENE; PLANT GENOME; PLANT LEAF; PLANT TISSUE CULTURE; POLYPLOIDY; PROTEIN ASSEMBLY; PROTEIN DATABASE; PROTEIN EXPRESSION; REAL TIME POLYMERASE CHAIN REACTION; RNA ISOLATION; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; TETRAPLOIDY; TREE; ANGIOSPERM; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETICS; MOLECULAR GENETICS; PROCEDURES; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

ANGIOSPERMS; DIPLOIDY; GENE EXPRESSION PROFILING; GENE LIBRARY; GENE ONTOLOGY; MOLECULAR SEQUENCE ANNOTATION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; TETRAPLOIDY; TRANSCRIPTOME; TREES;

EID: 84897398835     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms15035079     Document Type: Article

References (55)

1. Caparrósa, S.; Díaza, M.J.; Arizaa, J.; Lópeza, F.; Jiménezb, L. New perspectives for Paulownia fortunei L. valorisation of the autohydrolysis and pulping processes. Bioresour. Technol. 2008, 99, 741-749.
2. Rai, A.K.; Singh, S.P.; Luxmi, C.; Savita, G. Paulownia fortunei-A new fiber source for pulp and paper. Indian Pulp Pap. Tech. Assoc. 2000, 12, 51-56.
3. Ipekci, Z.; Gozukirmizi, N. Direct somatic embryogenesis and synthetic seed production from Paulownia elongata. Plant Cell Rep. 2003, 22, 16-24.
4. Tang, R.C.; Carpenter, S.B.; Wittwer, R.F.; Graves, D.H. Paulownia-A crop tree for wood products and reclamation of surface mined land. South J. Appl. For. 1980, 4, 19-24.
5. Melhuish, J.H.; Gentry, C.E.; Beckjord, P.R. Paulownia tomentosa seedling growth at differing levels of ph, nitrogen, and phosphorus. J. Environ. Hort. 1990, 8, 205-207.
6. Comai, L. The advantages and disadvantages of being polyploid. Nat. Rev. Genet. 2005, 6, 836-846.
7. Wood, T.E.; Takebayashi, N.; Barker, M.S.; Mayrose, I.; Greenspoon, P.B.; Rieseberg, L.H. The frequency of polyploid speciation in vascular plants. Proc. Natl. Acad. Sci. USA 2009, 106, 13875-13879.
8. Cifuentes, M.; Grandont, L.; Moore, G.; Chevre, A.M.; Jenczewski, E. Genetic regulation of meiosis in polyploid species: New insights into an old question. New Phytol. 2010, 186, 29-36.
9. Higgins, J.; Magusin, A.; Trick, M.; Fraser, F.; Bancroft, I. Use of mRNA-seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus. BMC Genomics 2012, 13, 247.
10. Kaensaksiri, T.; Soontornchainaksaeng, P.; Soonthornchareonnon, N.; Prathanturarug, S. In vitro induction of polyploidy in Centella asiatica (L.) Urban. Plant Cell Tiss. Organ Cult. 2011, 107, 187-194.
11. Yu, Z.; Haberer, G.; Matthes, M.; Rattei, T.; Mayer, K.F.; Gierl, A.; Torres-Ruiz, R.A. Impact of natural genetic variation on the transcriptome of autotetraploid Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 2010, 107, 17809-17814.
12. Wang, J.; Tian, L.; Madlung, A.; Lee, H.S.; Chen, M.; Lee, J.J.; Watson, B.; Kagochi, T.; Comai, L.; Chen, Z.J. Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 2004, 167, 1961-1973.
13. Harper, A.L.; Trick, M.; Higgins, J.; Fraser, F.; Clissold, L.; Wells, R.; Hattori, C.; Werner, P.; Bancroft, I. Associative transcriptomics of traits in the polyploid crop species Brassica napus. Nat. Biotechnol. 2012, 30, 798-802.
14. Jiang, J.; Shao, Y.; Du, K.; Ran, L.; Fang, X.; Wang, Y. Use of digital gene expression to discriminate gene expression differences in early generations of resynthesized Brassica napus and its diploid progenitors. BMC Genomics 2013, 14, 72.
15. Hovav, R.; Udall, J.A.; Chaudhary, B.; Hovav, E.; Flagel, L.; Hu, G.; Wendel, J.F. The evolution of spinnable cotton fiber entailed prolonged development and a novel metabolism. PLoS Genet. 2008, 4, e25.
16. Salmon, A.; Ainouche, M.L.; Wendel, J.F. Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol. Ecol. 2005, 14, 1163-1175.
17. Buggs, R.J.; Doust, A.N.; Tate, J.A.; Koh, J.; Soltis, K.; Feltus, F.A.; Paterson, A.H.; Soltis, P.S.; Soltis, D.E. Gene loss and silencing in Tragopogon miscellus (Asteraceae): Comparison of natural and synthetic allotetraploids. Heredity (Edinb.) 2009, 103, 73-81.
18. Udall, J.A.; Wendel, J.F. Polyploidy and crop improvement. Crop Sci. 2006, 46, S3-S14.
19. Fan, G.Q.; Cao, Y.C.; Zhao, Z.L.; Yang, Z.Q. Induction of autotetraploid of Paulownia fortunei. Sci. Silv. Sin. 2007, 43, 31-35.
20. Collins, L.J.; Biggs, P.J.; Voelckel, C.; Joly, S. An approach to transcriptome analysis of non-model organisms using short-read sequences. Genome Inform. 2008, 21, 3-14.
21. Grabherr, M.G.; Haas, B.J.; Yassour, M.; Levin, J.Z.; Thompson, D.A.; Amit, I.; Adiconis, X.; Fan, L.; Raychowdhury, R.; Zeng, Q. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 2011, 29, 644-652.
22. Zhai, X.Q.; Zhang, X.S.; Zhao, Z.L.; Deng, M.J.; Fan, G.Q. Study on wood physical properties of tetraploid Paulownia fortunei. J. Henan Agric. Univ. 2012, 46, 651-654.
23. Mardis, E.R. The impact of next-generation sequencing technology on genetics. Trends Genet. 2008, 24, 133-141.
24. Morozova, O.; Marra, M.A. Applications of next-generation sequencing technologies in functional genomics. Genomics 2008, 92, 255-264.
25. Liu, R.; Dong, Y.; Fan, G.; Zhao, Z.; Deng, M.; Cao, X.; Niu, S. Discovery of genes related to witches' broom disease in Paulownia tomentosa × Paulownia fortunei by a de novo assembled transcriptome. PLoS One 2013, 8, e80238.
26. Garg, R.; Patel, R.K.; Jhanwar, S.; Priya, P.; Bhattacharjee, A.; Yadav, G.; Bhatia, S.; Chattopadhyay, D.; Tyagi, A.K.; Jain, M. Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development. Plant Physiol. 2011, 156, 1661-1678.
27. Wang, Y.; Zeng, X.; Iyer, N.J.; Bryant, D.W.; Mockler, T.C.; Mahalingam, R. Exploring the switchgrass transcriptome using second-generation sequencing technology. PLoS One 2012, 7, e34225.
28. Liu, S.; Chen, C.; Chen, G.; Cao, B.; Chen, Q.; Lei, J. RNA-sequencing tag profiling of the placenta and pericarp of pungent pepper provides robust candidates contributing to capsaicinoid biosynthesis. Plant Cell Tissue Organ. Cult. 2012, 110, 111-121.
29. Hsiao, Y.Y.; Chen, Y.W.; Huang, S.C.; Pan, Z.J.; Fu, C.H.; Chen, W.H.; Tsai, W.C.; Chen, H.H. Gene discovery using next-generation pyrosequencing to develop ESTs for Phalaenopsis orchids. BMC Genomics 2011, 12, 360.
30. Parchman, T.L.; Geist, K.S.; Grahnen, J.A.; Benkman, C.W.; Buerkle, C.A. Transcriptome sequencing in an ecologically important tree species: Assembly, annotation, and marker discovery. BMC Genomics 2010, 11, 180.
31. Huang, L.L.; Yang, X.; Sun, P.; Tong, W.; Hu, S.Q. The first Illumina-based de novo transcriptome sequencing and analysis of safflower flowers. PLoS One 2012, 7, e38653.
32. Barash, Y.; Calarco, J.A.; Gao, W.; Pan, Q.; Wang, X.; Shai, O.; Blencowe, B.J.; Frey, B.J. Deciphering the splicing code. Nature 2010, 465, 53-59.
33. Barrero, R.A.; Chapman, B.; Yang, Y.; Moolhuijzen, P.; Keeble-Gagnere, G.; Zhang, N.; Tang, Q.; Bellgard, M.I.; Qiu, D. De novo assembly of Euphorbia fischeriana root transcriptome identifies prostratin pathway related genes. BMC Genomics 2011, 12, 600.
34. Zhou, Y.; Gao, F.; Liu, R.; Feng, J.; Li, H. De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus. BMC Genomics 2012, 13, 266.
35. Harhay, G.P.; Sonstegard, T.S.; Keele, J.W.; Heaton, M.P.; Clawson, M.L.; Snelling, W.M.; Wiedmann, R.T.; van Tassell, C.P.; Smith, T.P. Characterization of 954 bovine full-CDS cDNA sequences. BMC Genomics 2005, 6, 166.
36. Chen, F.; Lee, Y.; Jiang, Y.; Wang, S.; Peatman, E.; Abernathy, J.; Liu, H.; Liu, S.; Kucuktas, H.; Ke, C et al. Identification and characterization of full-length cDNAs in channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus). PLoS One 2010, 5, e11546.
37. Andreassen, R.; Lunner, S.; Hoyheim, B. Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (Salmo salar). BMC Genomics 2009, 10, 502.
38. Jackson, S.; Chen, Z.J. Genomic and expression plasticity of polyploidy. Curr. Opin. Plant Biol. 2010, 13, 153-159.
39. Anssour, S.; Krugel, T.; Sharbel, T.F.; Saluz, H.P.; Bonaventure, G.; Baldwin, I.T. Phenotypic, genetic and genomic consequences of natural and synthetic polyploidization of Nicotiana attenuata and Nicotiana obtusifolia. Ann. Bot. 2009, 103, 1207-1217.
40. Stupar, R.M.; Bhaskar, P.B.; Yandell, B.S.; Rensink, W.A.; Hart, A.L.; Ouyang, S.; Veilleux, R.E.; Busse, J.S.; Erhardt, R.J.; Buell, C.R.; et al. Phenotypic and transcriptomic changes associated with potato autopolyploidization. Genetics 2007, 176, 2055-2067.
41. Albertin, W.; Brabant, P.; Catrice, O.; Eber, F.; Jenczewski, E.; Chevre, A.M.; Thiellement, H. Autopolyploidy in cabbage (Brassica oleracea L.) does not alter significantly the proteomes of green tissues. Proteomics 2005, 5, 2131-2139.
42. Cervigni, G.D.; Paniego, N.; Pessino, S.; Selva, J.P.; Diaz, M.; Spangenberg, G.; Echenique, V. Gene expression in diplosporous and sexual Eragrostis curvula genotypes with differing ploidy levels. Plant Mol. Biol. 2008, 67, 11-23.
43. Wang, J.; Tian, L.; Lee, H.S.; Wei, N.E.; Jiang, H.; Watson, B.; Madlung, A.; Osborn, T.C.; Doerge, R.W.; Comai, L.; et al. Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 2006, 172, 507-517.
44. Lu, B.; Pan, X.; Zhang, L.; Huang, B.; Sun, L.; Li, B.; Yi, B.; Zheng, S.; Yu, X.; Ding, R.; et al. A genome-wide comparison of genes responsive to autopolyploidy in Isatis indigotica using Arabidopsis thaliana Affymetrix genechips. Plant Mol. Biol. Rep. 2006, 24, 197-204.
45. Fu, W.; Ma, X.; Tang, Q.; Mo, C. Karyotype analysis and genetic variation of a mutant in Siraitia grosvenorii. Mol. Biol. Rep. 2012, 39, 1247-1252.
46. Salmon, A.; Ainouche, M.L. Polyploidy and DNA methylation: New tools available. Mol. Ecol. 2010, 19, 213-215.
47. Ha, M.; Lu, J.; Tian, L.; Ramachandran, V.; Kasschau, K.D.; Chapman, E.J.; Carrington, J.C.; Chen, X.; Wang, X.J.; Chen, Z.J. Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids. Proc. Natl. Acad. Sci. USA 2009, 106, 17835-17840.
48. Cox, M.P.; Peterson, D.A.; Biggs, P.J. SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinform. 2010, 11, 485.
49. Kanehisa, M.; Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28, 27-30.
50. Altschul, S.F.; Madden, T.L.; Schaffer, A.A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D.J. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 1997, 25, 3389-3402.
51. Conesa, A.; Gotz, S.; Garcia-Gomez, J.M.; Terol, J.; Talon, M.; Robles, M. Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21, 3674-3676.
52. Ashburner, M.; Ball, C.A.; Blake, J.A.; Botstein, D.; Butler, H.; Cherry, J.M.; Davis, A.P.; Dolinski, K.; Dwight, S.S.; Eppig, J.T.; et al. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25, 25-29.
53. Ye, J.; Fang, L.; Zheng, H.; Zhang, Y.; Chen, J.; Zhang, Z.; Wang, J.; Li, S.; Li, R.; Bolund, L.; et al. WEGO: A web tool for plotting GO annotations. Nucleic Acids Res. 2006, 34, W293-W297.
54. Langmead, B.; Trapnell, C.; Pop, M.; Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10, R25.
55. Li, B.; Dewey, C.N. RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinforma. 2011, 12, 323.