A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing
Tóm tắt
Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management. We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of ~159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at
http://www.corkoakdb.org
. This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response.
Tài liệu tham khảo
de Gestão Florestal DN: Inventário Florestal Nacional- Portugal Continental. IFN 2005–2006. 2010, Autoridade Florestal Nacional: Lisbon
Brasier MD, Robredo F, Ferraz J: Evidence for Phytophthora cinnamomi involvement in Iberian oak decline. Plant Pathol. 1993, 42: 140-145. 10.1111/j.1365-3059.1993.tb01482.x.
Sanchez ME, Caetano P, Ferraz J, Trapero A: Phytophthora disease of Quercus ilex in south-western Spain. Forest Pathol. 2002, 32: 5-18. 10.1046/j.1439-0329.2002.00261.x.
Moreira AC, Martins J: Influence of site factors on the impact of Phytophthora cinnamomi in cork oak stands in Portugal. Forest Pathol. 2005, 35: 145-162. 10.1111/j.1439-0329.2005.00397.x.
de Sousa E, Santos M, Varela MC, Henriques J: Perda de vigor dos montados de sobro e azinho: Análise da situação e perspectivas. 2007
Bergot M, Cloppet E, Pérarnaud V: Simulation of potential range expansion of oak disease caused by Phytophthora cinnamomi under climate change. Glob Change Biol. 2004, 10: 1539-1552. 10.1111/j.1365-2486.2004.00824.x.
Pereira JS, Kurz-Besson C: Coping with drought. Cork Oak Woodlands on the Edge – Ecology, Adaptive Management and Restoration. 2009, Washington: Island Press, 73-80. 1
Marum L, Miguel A, Ricardo CP, Miguel C: Reference gene selection for quantitative real-time PCR normalization in Quercus suber. PLoS ONE. 2012, 7: e35113-10.1371/journal.pone.0035113.
Coelho AC, Lima MB, Neves D, Cravador A: Genetic diversity of two evergreen oaks (Quercus suber L. and Q (ilex) rotundifolia Lam.) in Portugal using AFLP markers. Silvae Genetica. 2006, 55: 105-118.
Chaves I, Passarinho JAP, Capitão C, Chaves MM, Fevereiro P, Ricardo CPP: Temperature stress effects in Quercus suber leaf metabolism. J Plant Physiol. 2011, 168: 1729-1734. 10.1016/j.jplph.2011.05.013.
Graça J, Santos S: Suberin: a biopolyester of plants’ skin. Macromol Biosci. 2007, 7: 128-135. 10.1002/mabi.200600218.
Soler M, Serra O, Molinas M, Huguet G, Fluch S, Figueras M: A genomic approach to suberin biosynthesis and cork differentiation. Plant Physiol. 2007, 144: 419-431. 10.1104/pp.106.094227.
Vaz M, Pereira JS, Gazarini LC, David TS, David JS, Rodrigues A, Maroco J, Chaves MM: Drought-induced photosynthetic inhibition and autumn recovery in two Mediterranean oak species (Quercus ilex and Quercus suber). Tree Physiol. 2010, 30: 946-956. 10.1093/treephys/tpq044.
Almeida T, Menéndez E, Capote T, Ribeiro T, Santos C, Gonçalves S: Molecular characterization of Quercus suber MYB1, a transcription factor up-regulated in cork tissues. J Plant Physiol. 2013, 170: 172-178. 10.1016/j.jplph.2012.08.023.
Ueno S, Provost GL, Léger V, Klopp C, Noirot C, Frigerio J-M, Salin F, Salse J, Abrouk M, Murat F, Brendel O, Derory J, Abadie P, Léger P, Cabane C, Barré A, de Daruvar A, Couloux A, Wincker P, Reviron M-P, Kremer A, Plomion C: Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. BMC Genomics. 2010, 11: 650-10.1186/1471-2164-11-650.
Tarkka MT, Herrmann S, Wubet T, Feldhahn L, Recht S, Kurth F, Mailänder S, Bönn M, Neef M, Angay O, Bacht M, Graf M, Maboreke H, Fleischmann F, Grams TEE, Ruess L, Schädler M, Brandl R, Scheu S, Schrey SD, Grosse I, Buscot F: OakContigDF159.1, a reference library for studying differential gene expression in Quercus robur during controlled biotic interactions: use for quantitative transcriptomic profiling of oak roots in ectomycorrhizal symbiosis. New Phytol. 2013, 199: 529-540. 10.1111/nph.12317.
Kremer A, Abbott AG, Carlson JE, Manos PS, Plomion C, Sisco P, Staton ME, Ueno S, Vendramin GG: Genomics of Fagaceae. Tree Genetics & Genomes. 2012, 8: 583-610. 10.1007/s11295-012-0498-3.
Rampant PF, Lesur I, Boussardon C, Bitton F, Martin-Magniette M-L, Bodénès C, Le Provost G, Bergès H, Fluch S, Kremer A, Plomion C: Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome. BMC Genomics. 2011, 12: 292-10.1186/1471-2164-12-292.
Durand J, Bodénès C, Chancerel E, Frigerio J-M, Vendramin G, Sebastiani F, Buonamici A, Gailing O, Koelewijn H-P, Villani F, Mattioni C, Cherubini M, Goicoechea PG, Herrán A, Ikaran Z, Cabane C, Ueno S, Alberto F, Dumoulin P-Y, Guichoux E, de Daruvar A, Kremer A, Plomion C: A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study. BMC Genomics. 2010, 11: 570-10.1186/1471-2164-11-570.
Zhulidov PA, Bogdanova EA, Shcheglov AS, Shagina IA, Wagner LL, Khazpekov GL, Kozhemyako VV, Lukyanov SA, Shagin DA: A method for the preparation of normalized cDNA libraries enriched with full-length sequences. Russ J Bioorg Chem. 2005, 31: 170-177. 10.1007/s11171-005-0023-7.
Timme RE, Delwiche CF: Uncovering the evolutionary origin of plant molecular processes: comparison of Coleochaete (Coleochaetales) and Spirogyra (Zygnematales) transcriptomes. BMC Plant Biol. 2010, 10: 96-10.1186/1471-2229-10-96.
Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA: Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics. 2010, 11: 1-16. 10.1186/1471-2164-11-1.
Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, et al: The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray). Science. 2006, 313: 1596-1604. 10.1126/science.1128691.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25: 25-29. 10.1038/75556.
Zhi-Liang H, Bao J: CateGOrizer: a web-based program to batch analyze Gene Ontology Classification Categories. Online J Bioinformatics. 2008, 9 (2): 108-112.
Barakat A, DiLoreto DS, Zhang Y, Smith C, Baier K, Powell W, Wheeler N, Se deroff R, Carlson JE: Comparison of transcriptome from cankers and healthy stems in American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima). BMC Plant Biol. 2009, 9: 51-62. 10.1186/1471-2229-9-51.
Altenhoff AM, Dessimoz C: Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comp Biol. 2009, 5: e1000262-10.1371/journal.pcbi.1000262.
Varela MC: Handbook of the EU Concerted Action on cork oak: FAIR 1 CT 95-0202; European network for the evaluation of genetic resources of cork oak for appropriate use in breeding and gene conservation strategies. 2003, Lisboa (Portugal): INIA
Shcheglov AS, Zhulidov PA, Bogdanova EA, Shagin DA: Nucleic Acids Hybridization Modern Applications. 2007, Dordrecht: Springer Netherlands, 97-124.
Niu B, Fu L, Sun S, Li W: Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics. 2010, 11: 187-10.1186/1471-2105-11-187.
Falgueras J, Lara AJ, Fernandez-Pozo N, Canton FR, Perez-Trabado G, Claros MG: SeqTrim: a high-throughput pipeline for preprocessing any type of sequence reads. BMC Bioinformatics. 2010, 11: 38-10.1186/1471-2105-11-38.
Ouyang S: The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res. 2004, 32: 360D-363D. 10.1093/nar/gkh099.
Chevreux B, Pfisterer T, Wetter T: Assembly of Genomic Sequences Assisted by Automatic Finishing. German Conf Bioinformatics. 1999, 183-184.
Papanicolaou A, Stierli R, ffrench-Constant RH, Heckel DG: Next generation transcriptomes for next generation genomes using est2assembly. BMC Bioinformatics. 2009, 10: 447-10.1186/1471-2105-10-447.
Li W, Godzik A: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006, 22: 1658-1659. 10.1093/bioinformatics/btl158.
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM: The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucl. Acids Res. 37 (suppl 1): D141-D145.
Apweiler R: UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 2004, 32: 115D-119D. 10.1093/nar/gkh131.
Wasmuth JD, Blaxter ML: prot4EST: translating expressed sequence tags from neglected genomes. BMC Bioinformatics. 2004, 5: 187-10.1186/1471-2105-5-187.
Iseli C, Jongeneel C, Bucher P: ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Bio. 1999, 138-148.
Zdobnov EM, Apweiler R: InterProScan–an integration platform for the signature-recognition methods in InterPro. Bioinformatics. 2001, 17: 847-848. 10.1093/bioinformatics/17.9.847.
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, et al: InterPro: the integrative protein signature database. Nucleic Acids Res. 2009, 37 (Database issue): D211-D215.
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005, 21: 3674-3676. 10.1093/bioinformatics/bti610.
Gough J, Chothia C: SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments. Nucleic Acids Res. 2002, 30: 268-272. 10.1093/nar/30.1.268.