Phân tích toàn diện các thẻ trình tự biểu hiện từ củ cải (Raphanus spp.) nuôi trồng và hoang dã
Tóm tắt
Củ cải (
Trong nghiên cứu này, khoảng 315.000 ESTs được lấy từ 22 thư viện cDNA của giống
Từ khóa
#Củ cải #Raphanus #thẻ trình tự biểu hiện #SSR #SNP #phát sinh chủng loại #tiến hóa bộ genTài liệu tham khảo
Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF: Complementary DNA sequencing: expressed sequence tags and human genome project. Science. 1992, 252: 1651-1656.
Yang H, Kaur N, Kiriakopolos S, McCormick S: EST generation and analyses towards identifying female gametophyte-specific genes in Zea mays L. Planta. 2006, 224: 1004-1014. 10.1007/s00425-006-0283-3.
Eswaran N, Parameswaran S, Anantharaman B, Kumar GR, Sathram B, Johnson TS: Generation of an expressed sequence tag (EST) library from salt-stressed roots of Jatrophacurcas for identification of abiotic stress-responsive genes. Plant Biol. 2012, 14: 428-437. 10.1111/j.1438-8677.2011.00529.x.
Shi T, Huang H, Barker MS: Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related Ericales. Ann Bot. 2010, 106: 497-504. 10.1093/aob/mcq129.
Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS: Ancestral polyploidy in seed plants and angiosperms. Nature. 2011, 473: 97-100. 10.1038/nature09916.
Chatzopoulou FM, Makris AM, Argiriou A, Degenhardt J, Kanellis AK: EST analysis and annotation of transcripts derived from a trichome-specific cDNA library from Salvia fruticosa. Plant Cell Rep. 2010, 29: 523-534. 10.1007/s00299-010-0841-9.
Büchel K, McDowell E, Nelson W, Descour A, Gershenzon J, Hilker M, Soderlund C, Gang DR, Fenning T, Meiners T: An elm EST database for identifying leaf beetle egg-induced defense genes. BMC Genomics. 2012, 13: 242-10.1186/1471-2164-13-242.
Budahn H, Peterka H, Mousa MA, Ding Y, Zhang S, Li J: Molecular mapping in oil radish (Raphanus sativus L.) and QTL analysis of resistance against beet cyst nematode (Heterodera schachtii). Theor Appl Genet. 2009, 118: 775-782. 10.1007/s00122-008-0937-6.
Xu L, Wang L, Gong Y, Dai W, Wang Y, Zhu X, Wen T, Liu L: Genetic linkage map construction and QTL mapping of cadmium accumulation in radish (Raphanus sativus L.). Theor Appl Genet. 2012, 125: 659-670. 10.1007/s00122-012-1858-y.
Shirasawa K, Shiokai S, Yamaguchi M, Kishitani S, Nishio T: Dot-blot-SNP analysis for practical plant breeding and cultivar identification in rice. Theor Appl Genet. 2006, 113: 147-155. 10.1007/s00122-006-0281-7.
Li F, Hasegawa Y, Saito M, Shirasawa S, Fukushima A, Ito T, Fujii H, Kishitani S, Kitashiba H, Nishio T: Extensive chromosome homoeology among Brassiceae species were revealed by comparative genetic mapping with high-density EST-based SNP markers in radish (Raphanus sativus L.). DNA Res. 2011, 18: 401-411. 10.1093/dnares/dsr027.
Bourret V, Kent MP, Primmer CR, Vasemägi A, Karlsson S, Hindar K, McGinnity P, Verspoor E, Bernatchez L, Lien S: SNP-array reveals genome-wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmosalar). Mol Ecol. 2012, 22: 532-551.
Wang S, Wang X, He Q, Liu X, Xu W, Li L, Gao J, Wang F: Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish. Plant Cell Rep. 2012, 31: 1437-1447. 10.1007/s00299-012-1259-3.
Anithakumari AM, Tang J, Van Eck HJ, Visser RG, Leunissen JA, Vosman B, van der Linden CG: A pipeline for high throughput detection and mapping of SNPs from EST databases. Mol Breed. 2010, 26: 65-75. 10.1007/s11032-009-9377-5.
Ersoz ES, Wright MH, Pangilinan JL, Sheehan MJ, Tobias C, Casler MD, Buckler ES, Costich DE: SNP discovery with EST and NextGen sequencing in switchgrass (Panicum virgatum L.). PLoS One. 2012, 7: e44112-10.1371/journal.pone.0044112.
Herbst ST: Barron’s Cooking Guide. The new food lover’s companion: comprehensive definitions of nearly 6,000 food, drink, and culinary terms. 2001, Hauppauge, NY: Barron’s Educational Series
Zohary D, Hopf M: Domestication of plants in the old world. 2000, Oxford: University Press, 3
Lewis-Jones LJ, Thorpe JP, Wallis GP: Genetic divergence in four species of the genus Raphanus: implications for the ancestry of the domestic radish R. sativus. Biol J Linn Soc. 1982, 18: 35-48. 10.1111/j.1095-8312.1982.tb02032.x.
Kitamura S: Cultivars of radish and their change. Japanese radish. Edited by: Nishiyama I. 1958, Tokyo: Japan Society for the Promotion of Science, 1-19.
Kaneko Y, Kimizuka-Takagi C, Bang SW, Matsuzawa Y: Radish. Genome mapping and molecular breeding in plants. Edited by: Kole C. 2007, New York: Springer, 141-160.
Wang Y, Xu L, Chen Y, Shen H, Gong Y, Limera C, Liu L: Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to lead (Pb) stress with next generation sequencing. PLoS One. 2013, 8: e66539-10.1371/journal.pone.0066539.
NCBI dbEST database.http://www.ncbi.nlm.nih.gov/dbEST/,
iTAK program.http://bioinfo.bti.cornell.edu/tool/itak,
Rood SB, Mandel R, Pharis RP: Endogenous gibberellins and shoot growth and development in Brassica napus. Plant Physiol. 1989, 89: 269-273. 10.1104/pp.89.1.269.
Rieu I, Ruiz-Rivero O, Fernandez-Garcia N, Griffiths J, Powers SJ, Gong F, Linhartova T, Eriksson S, Nilsson O, Thomas SG: The gibberellin biosynthetic genes AtGA20ox1 and AtGA20ox2 act, partially redundantly, to promote growth and development throughout the Arabidopsis life cycle. Plant J. 2008, 53: 488-504.
Tzen JTC, Huang AHC: Surface structure and properties of plant seed oil bodies. J Cell Biol. 1992, 117: 327-335. 10.1083/jcb.117.2.327.
He YQ, Wu Y: Oil body biogenesis during Brassica napus embryogenesis. J Integr Plant Biol. 2009, 51: 792-799. 10.1111/j.1744-7909.2009.00851.x.
Wang W, Gong Y, Liu L, Wang Y, Jing Z, Huang D, Wang L: Changes of sugar content and sucrose metabolizing enzyme activities during fleshy taproot development in radish (Raphanus sativus L.). Acta Hortic Sinica. 2007, 34: 1313-1316.
Lee T-H, Tang H, Wang X, Paterson AH: PGDD: a database of gene and genome duplication in plants. Nucleic Acids Res. 2013, 41: D1152-D1158. 10.1093/nar/gks1104.
Yang YW, Lai KN, Tai PY, Li WH: Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages. J Mol Evol. 1999, 48: 597-604. 10.1007/PL00006502.
Koch M, Haubold B, Mitchell-Olds T: Molecular systematics of the Brassicaceae: evidence from coding plastidic matK and nuclear Chs sequences. Am J Bot. 2001, 88: 534-544. 10.2307/2657117.
Shirasawa K, Oyama M, Hirakawa H, Sato S, Tabata S, Fujioka T, Kimizuka-Takagi C, Sasamoto S, Watanabe A, Kato M: An EST-SSR linkage map of Raphanus sativus and comparative genomics of the Brassicaceae. DNA Res. 2011, 18: 221-232. 10.1093/dnares/dsr013.
Guo S, Liu J, Zheng Y, Huang M, Zhang H, Gong G, He H, Ren Y, Zhong S, Fei Z: Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles. BMC Genomics. 2011, 12: 454-10.1186/1471-2164-12-454.
Shen D, Sun H, Huang M, Zheng Y, Li X, Fei Z: RadishBase: a database for genomics and genetics of radish. Plant Cell Physiol. 2013, 54: e3-10.1093/pcp/pcs176.
Nei M: Phylogenetic analysis in molecular evolutionary genetics. Annu Rev Genet. 1996, 30: 371-403. 10.1146/annurev.genet.30.1.371.
Tsuro M, Suwabe K, Kubo N, Matsumoto S, Hirai M: Construction of a molecular linkage map of radish (Raphanus sativus L.), based on AFLP and Brassica-SSR markers. Breed Sci. 2005, 55: 107-111. 10.1270/jsbbs.55.107.
Yamagishi H, Terachi T: Multiple origins of cultivated radishes as evidenced by a comparison of the structural variations in mitochondrial DNA of Raphanus. Genome. 2003, 46: 89-94. 10.1139/g02-110.
Yamane K, Lü N, Ohnishi O: Multiple origins and high genetic diversity of cultivated radish inferred from polymorphism in chloroplast simple sequence repeats. Breed Sci. 2009, 59: 55-65. 10.1270/jsbbs.59.55.
Lü N, Yamane K, Ohnishi O: Genetic diversity of cultivated and wild radish and phylogenetic relationships among Raphanus and Brassica species revealed by the analysis of trn K/mat K sequence. Breed Sci. 2008, 58: 15-22. 10.1270/jsbbs.58.15.
NCBI UniVec database.http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html,
SeqClean program.http://sourceforge.net/projects/seqclean/,
Zheng Y, Zhao L, Gao J, Fei Z: iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences. BMC Bioinformatics. 2011, 12: 453-10.1186/1471-2105-12-453.
Plant specific GO slims.http://www.geneontology.org/GO.slims.shtml,
Li L, Stoeckert CJJ, Roos DS: OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003, 13: 2178-2189. 10.1101/gr.1224503.
Venn diagrams.http://bioinformatics.psb.ugent.be/webtools/Venn,
Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G: GO: TermFinder-open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes. Bioinformatics. 2004, 20: 3710-3715. 10.1093/bioinformatics/bth456.
Iseli C, Jongeneel CV, Bucher P: ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol. 1999, 138-148.
Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F: The genome of the mesopolyploid crop species Brassica rapa. Nat Genet. 2011, 43: 1035-1039. 10.1038/ng.919.
Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L: The arabidopsis information resource (TAIR): gene structure and function annotation. Nucleic Acids Res. 2008, 36: D1009-D1014.
Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL: The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 2008, 452: 991-996. 10.1038/nature06856.
Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32: 1792-1797. 10.1093/nar/gkh340.
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T: trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009, 25: 1972-1973. 10.1093/bioinformatics/btp348.
Yang Z: PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007, 24: 1586-1591. 10.1093/molbev/msm088.
Wikström N, Savolainen V, Chase MW: Evolution of the angiosperms: calibrating the family tree. Proc Biol Sci. 2001, 268: 2211-2220. 10.1098/rspb.2001.1782.
Crepet WL, Nixon KC, Gandolfo MA: Fossil evidence and phylogeny: the age of major angiosperm clades based on mesofossil and macrofossil evidence from cretaceous deposits. Am J Bot. 2004, 91: 1666-1682. 10.3732/ajb.91.10.1666.
Salse J, Abrouk M, Bolot S, Guilhot N, Courcelle E, Faraut T, Waugh R, Close TJ, Messing J, Feuillet C: Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. Proc Natl Acad Sci USA. 2009, 106: 14908-14913. 10.1073/pnas.0902350106.
Murat F, Xu JH, Tannier E, Abrouk M, Guilhot N, Pont C, Messing J, Salse J: Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res. 2010, 20: 1545-1557. 10.1101/gr.109744.110.
MISA program.http://pgrc.ipk-gatersleben.de/misa,
Primer3 program.http://frodo.wi.mit.edu,
Clepet C, Joobeur T, Zheng Y, Jublot D, Huang M, Truniger V, Boualem A, Hernandez-Gonzalez ME, Dolcet-Sanjuan R: Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon. BMC Genomics. 2011, 12: 252-10.1186/1471-2164-12-252.
Marth GT, Korf I, Yandell MD, Yeh RT, Gu Z, Zakeri H, Stitziel NO, Hillier L, Kwok PY, Gish WR: A general approach to single-nucleotide polymorphism discovery. Nat Genet. 1999, 23: 452-456. 10.1038/70570.