- -

De novo assembly of Phlomis purpurea after challenging with Phytophthora cinnamomi

RiuNet: Repositorio Institucional de la Universidad Politécnica de Valencia

Compartir/Enviar a

Citas

Estadísticas

  • Estadisticas de Uso

De novo assembly of Phlomis purpurea after challenging with Phytophthora cinnamomi

Mostrar el registro sencillo del ítem

Ficheros en el ítem

Thumbnail
Nombre: Baldé;Neves;Garcí ...
Tamaño: 1.588Mb
Formato: PDF
Descripción: Versión editorial
Abrir
dc.contributor.author Baldé, A. es_ES
dc.contributor.author Neves, D. es_ES
dc.contributor.author García-Breijo, Francisco-José es_ES
dc.contributor.author Pais, M. S. es_ES
dc.contributor.author Cravador, A. es_ES
dc.date.accessioned 2020-04-06T08:57:29Z
dc.date.available 2020-04-06T08:57:29Z
dc.date.issued 2017 es_ES
dc.identifier.issn 1471-2164 es_ES
dc.identifier.uri http://hdl.handle.net/10251/140246
dc.description.abstract [EN] Background: Phlomis plants are a source of biological active substances with potential applications in the control of phytopathogens. Phlomis purpurea (Lamiaceae) is autochthonous of southern Iberian Peninsula and Morocco and was found to be resistant to Phytophthora cinnamomi. Phlomis purpurea has revealed antagonistic effect in the rhizosphere of Quercus suber and Q. ilex against P. cinnamomi. Phlomis purpurea roots produce bioactive compounds exhibiting antitumor and anti-Phytophthora activities with potential to protect susceptible plants. Although these important capacities of P. purpurea have been demonstrated, there is no transcriptomic or genomic information available in public databases that could bring insights on the genes underlying this anti-oomycete activity. Results: Using Illumina technology we obtained a de novo assembly of P. purpurea transcriptome and differential transcript abundance to identify putative defence related genes in challenged versus non-challenged plants. A total of 1,272,600,000 reads from 18 cDNA libraries were merged and assembled into 215,739 transcript contigs. BLASTX alignment to Nr NCBI database identified 124,386 unique annotated transcripts (57.7%) with significant hits. Functional annotation identified 83,550 out of 124,386 unique transcripts, which were mapped to 141 pathways. 39% of unigenes were assigned GO terms. Their functions cover biological processes, cellular component and molecular functions. Genes associated with response to stimuli, cellular and primary metabolic processes, catalytic and transporter functions were among those identified. Differential transcript abundance analysis using DESeq revealed significant differences among libraries depending on post-challenge times. Comparative cyto-histological studies of P. purpurea roots challenged with P. cinnamomi zoospores and controls revealed specific morphological features (exodermal strips and epi-cuticular layer), that may provide a constitutive efficient barrier against pathogen penetration. Genes involved in cutin biosynthesis and in exodermal Casparian strips formation were up-regulated. Conclusions: The de novo assembly of transcriptome using short reads for a non-model plant, P. purpurea, revealed many unique transcripts useful for further gene expression, biological function, genomics and functional genomics studies. The data presented suggest a combination of a constitutive resistance and an increased transcriptional response from P. purpurea when challenged with the pathogen. This knowledge opens new perspectives for the understanding of defence responses underlying pathogenic oomycete/plant interaction upon challenge with P. cinnamomi. es_ES
dc.description.sponsorship This work was supported by the project PTDC/AGR-CFL/100217/2008 and the grant SFRH/BD/66016/2009, both funded by Fundacao para a Ciencia e Tecnologia (FCT). The APC charge was supported by the project UID/BIA/04325/2013 - MEDTBIO (FCT). The COST Office and the European Council provided financial support to the Short Term Scientific Mission (COST-STSM-FP0801-10084). es_ES
dc.language Inglés es_ES
dc.publisher Springer (Biomed Central Ltd.) es_ES
dc.relation.ispartof BMC Genomics es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Phlomis purpurea es_ES
dc.subject Transcriptomics es_ES
dc.subject Phytophthora cinnamomi es_ES
dc.subject Resistance es_ES
dc.subject Defence response es_ES
dc.subject Time course challenge es_ES
dc.subject Casparian strips es_ES
dc.subject Cutin es_ES
dc.subject.classification BOTANICA es_ES
dc.title De novo assembly of Phlomis purpurea after challenging with Phytophthora cinnamomi es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1186/s12864-017-4042-6 es_ES
dc.relation.projectID info:eu-repo/grantAgreement/COST//FP0801-10084/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/FCT/3599-PPCDT/100217/PT/Production of active compounds against Phytophthora cinnamomi by Phlomis purpurea, Metabolite and transcript profiling/
dc.relation.projectID info:eu-repo/grantAgreement/FCT/SFRH/SFRH%2FBD%2F66016%2F2009/PT/DETERMINATION OF PHLOMIS PURPUREA ROOT METABOLITES WITH ANTI-PHYTOPHTHORA CINNAMOMI ACTIVITY AND OF THEIR IN VIVO PROTECTIVE EFFECT TOWARDS INFESTED QUERCUS SPP./
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Ecosistemas Agroforestales - Departament d'Ecosistemes Agroforestals es_ES
dc.description.bibliographicCitation Baldé, A.; Neves, D.; García-Breijo, F.; Pais, MS.; Cravador, A. (2017). De novo assembly of Phlomis purpurea after challenging with Phytophthora cinnamomi. BMC Genomics. 18(700):1-17. https://doi.org/10.1186/s12864-017-4042-6 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1186/s12864-017-4042-6 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 17 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 18 es_ES
dc.description.issue 700 es_ES
dc.relation.pasarela S\342208 es_ES
dc.contributor.funder Universidade do Algarve es_ES
dc.contributor.funder European Research Council es_ES
dc.contributor.funder Fundação para a Ciência e a Tecnologia, Portugal es_ES
dc.contributor.funder Centro para os Recursos Biológicos e Alimentos Mediterrânicos es_ES
dc.description.references Li M, Shang XF, Jia ZP, Zhang RX. Phytochemical and biological studies of plants from the genus Phlomis. Chem Biodivers. 2010;7:283–301. es_ES
dc.description.references Erwin DC, Ribeiro OK. Phytophthora diseases worldwide. St Paul: American Phytopathological Society Press; 1996. es_ES
dc.description.references Brasier CM, Robredo F, Ferraz JFP. Evidence for Phytophthora cinnamomi involvement in Iberian oak decline. Plant Pathol. 1993;42:140–5. es_ES
dc.description.references Moreira AC, Martins JMS. Influence of site factors on the impact of Phytophthora cinnamomi in cork stands in Portugal. For Pathol. 2005;35:145–62. es_ES
dc.description.references Neves D, Caetano P, Oliveira J, Maia C, Horta M, Sousa N, Salgado M, Dionísio L, Magan N, Cravador A. Anti-Phytophthora cinnamomi activity of Phlomis purpurea plant and root extracts. Eur J Plant Pathol. 2014;138:835–46. es_ES
dc.description.references Neves D: Evaluation of the protective effect of Phlomis purpurea against Phytophthora cinnamomi in Fagaceae and of root metabolites involved. PhD thesis. Universidade do Algarve; 2015. http://sapientia.ualg.pt/handle/10400.1/6862 . es_ES
dc.description.references Mateus MC, Neves D, Dacunha B, Laczko E, Maia C, Teixeira R, Cravador A. Structure, anti-Phytophthora and anti-tumor activities of a nortriterpenoid from the rhizome of Phlomis purpurea (Lamiaceae). Phytochemistry. 2016;131:158–64. es_ES
dc.description.references Amor IL, Boubaker J, Sgaier MB, Skandrani I, Bhouri W, Neffati A, Kilani S, Bouhlel I, Ghedira K, Chekir-Ghedira L. Phytochemistry and biological activities of Phlomis species. J Ethnopharmacol. 2009;125:183–202. es_ES
dc.description.references Dixon AR. Natural products and plant disease resistance. Nature. 2001;411:843–7. es_ES
dc.description.references Naseer S, Lee Y, Lapierre C, Franke R, Nawrath C, Geldner N. Casparian strip diffusion barrier in Arabidopsis is made of a lignin polymer without suberin. Proc Natl Acad Sci U S A. 2012;109:10101–6. es_ES
dc.description.references Caspary R. Bemerkungen über die Schutzscheide und die Bildung des Stammes und der Wurzel. Jahrb wissensc Botanik. 1865;4:101–24. es_ES
dc.description.references Lee Y, Rubio MC, Alassimone J, Geldner N. A mechanism for localized lignin deposition in the endodermis. Cell. 2013;153:402–12. es_ES
dc.description.references Enstone DE, Peterson CA, Ma FS. Root endodermis and exodermis: structure, function, and responses to the environment. J Plant Growth Reg. 2002;21:335–51. es_ES
dc.description.references Geldner N. The endodermis. Annu Rev Plant Biol. 2013;64:531–58. es_ES
dc.description.references Hammerschmidt R, Bonnen AM, Bergstrom GC, Baker KK. Association of epidermal lignification with nonhost resistance of cucurbits to fungi. Can J Bot. 1985;63:2393–8. es_ES
dc.description.references Mysore KS, Ryu C-M. Nonhost resistance: how much do we know? Trends Plant Sci. 2004;9:97–104. es_ES
dc.description.references Baldé A, Cravador A, Neves D, Pais MS:. De Novo Assembly of Phlomis purpurea Transcriptome challenged with Phytophthora cinnamomi. Abstract in 7th IUFRO Working Party 7–02-09 Phytophthora in Forests and Natural Ecosystems, 2014, 73. es_ES
dc.description.references National Center for Biotechnology Information [ http://www.ncbi.nlm.nih.gov ]. Accessed 30 Mar 2015. es_ES
dc.description.references Kyoto Encyclopedia of Genes and Genomes [ http://www.genome.jp/kegg/kegg1.html ]. Accessed 30 Mar 2015. es_ES
dc.description.references Carels N, Hatey P, Jabbari K, Bernardi G. Compositional properties of homologous coding sequences from plants. J Mol Evol. 1998;46:45–53. es_ES
dc.description.references Birol I, Jackman SD, Nielsen CB, Qian JQ, Varhol R, Stazyk G, Morin RD, Zhao Y, Hirst M, Schein JE, Horsman DE, Connors JM, Gascoyne RD, Marra MA, Jones SJM. De novo transcriptome assembly with ABySS. Bioinformatics. 2009;25:2872–7. es_ES
dc.description.references Gibbons JG, Janson EM, Hittinger CT, Johnston M, Abbot P, Rokas A. Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Mol Biol Evol. 2009;26:2731–4274. es_ES
dc.description.references Surget-Groba Y, Montoya-Burgos JI. Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res. 2010;20:1432–40. es_ES
dc.description.references Sudheesh S, Sawbridge TI, Cogan NOI, Kennedy P, Forster JW, Kaur S. De novo assembly and characterisation of the field pea transcriptome using RNA-Seq. BMC Genomics. 2015;16:616. doi: 10.1186/s12864-015-1815-7 . es_ES
dc.description.references Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, 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(7):644–52. es_ES
dc.description.references Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821–9. es_ES
dc.description.references Schulz MH, Zerbino DR, Vingron M, Birney E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics. 2012;28(8):1086–92. es_ES
dc.description.references Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, et al. De novo assembly and analysis of RNA-seq data. Nat Methods. 2010;7(11):909–12. es_ES
dc.description.references Xie Y, Wu G, Tang J, Luo R, Patterson J, Liu S, Huang W, He G, Gu S, Li S, et al. SOAPdenovo-trans: De novo transcriptome assembly with short RNA-Seq reads. Bioinformatics. 2014;30(12):1660–06. es_ES
dc.description.references Chen S, Yang P, Jiang F, Wei Y, Ma Z, Kang L. De novo analysis of transcriptome dynamics in the migratory locust during the development of phase traits. PLoS One. 2010;5:e15633. es_ES
dc.description.references Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, et al. A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines. Nucleic Acids Res. 2011;39:e100. es_ES
dc.description.references Maher CA, Palanisamy N, Brenner JC, Cao X, Kalyana-Sundaram S, Luo S, et al. Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A. 2009;106:12353–8. es_ES
dc.description.references Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP. Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet. 2014;15:121–32. es_ES
dc.description.references Gotz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, et al. High-throughput functionalannotation and data mining with the Blast2GO suite. Nucleic Acids Res. 2008;36:3420–35. es_ES
dc.description.references Pereira-Leal JB, Abreu IA, Alabaça CS, Almeida MH, Almeida P, Almeida T, et al. A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing. BMC Genomics. 2014;15:371. es_ES
dc.description.references Park S, Sugimoto N, Larson MD, Beaudry R, van Nocker S. Identification of genes with potential roles in apple fruit development and biochemistry through large-scale statistical analysis of expressed sequence tags. Plant Physiol. 2006;141:811–24. es_ES
dc.description.references Bombarely A, Merchante C, Csukasi F, Cruz-Rus E, Caballero JL, Medina-Escobar N, et al. Generation and analysis of ESTs from strawberry (Fragaria xananassa) fruits and evaluation of their utility in genetic and molecular studies. BMC Genomics. 2010;11:503–20. es_ES
dc.description.references Cahill D, Legge B, Grant B, Weste G. Cellular and histopathological changes induced by Phytophthora Cinnamomi in a group of plant species ranging from fully susceptible to fully resistant. Phytopathology. 1989;79:417–24. es_ES
dc.description.references Jung T, Colquhoun IJ, Hardy GESJ. New insights into the survival strategy of the invasive soilborne pathogen Phytophthora Cinnamomi in different natural ecosystems in Western Australia. For Pathol. 2013;43:266–88. es_ES
dc.description.references Ashford AE, Allaway WG, Reed ML. A possible role for the thick-walled epidermal cells in the mycorrhizal hair roots of Lysinema ciliatum R.Br. and other Epacridaceae. Ann Bot. 1996;77:375–81. es_ES
dc.description.references Briggs CL, Ashford AE. Structure and composition of the thick wall in hair root epidermal cells of Woollsia pungens. New Phytol. 2001;149:219–32. es_ES
dc.description.references Fava J, Alzamora SM, Castro MA. Structure and nanostructure of the outer tangential epidermal Cell Wall in Vaccinium Corymbosum L. (blueberry) fruits by blanching, freezing-thawing and ultrasound. Food Sci Technol Int. 2006;12:241–51. es_ES
dc.description.references Pollard M, Beisson F, Li Y, Ohlrogge JB. Building lipid barriers: biosynthesis of cutin and suberin. Trends Plant Sci. 2008;13:236–46. es_ES
dc.description.references Fich EA, Segerson NA, Rose JKC. The plant polyester Cutin: biosynthesis, structure, and biological roles. Annu Rev Plant Biol. 2016;67:18.1–18.27. es_ES
dc.description.references Serrano M, Coluccia F, Torres M, L’Haridon F, Métraux J-P. The cuticle and plant defense to pathogens. Front Plant Sci. 2014;5:274. doi: 10.3389/fpls.2014.00274 . es_ES
dc.description.references Yeats TH, Rose JKC. The formation and function of plant cuticles. Plant Physiol. 2013;163:5–20. es_ES
dc.description.references Delude C, Mousson S, Joubès J, Ingram G, Domergue F. Lipids in Plant and Algae Development, Subcell Biochem. In: Nakamura Y, Li-Beisson Y, editors. Plant surface lipids and epidermis development. Subcell. Biochem, vol. 86. Switzerland: Springer – Intern. Publ; 2016. p. 287–313. es_ES
dc.description.references Molina I, Kosma D. Role of HXXXD-motif/BAHD acyltransferases in the biosynthesis of extracellular lipids. Plant Cell Rep. 2015;34:587–601. es_ES
dc.description.references Hen-Avivi S, Lashbrooke J, Costa F, Aharoni A. Scratching the surface: genetic regulation of cuticle assembly in fleshy fruit. J Exp Bot. 2014;65:4653–64. es_ES
dc.description.references Tominaga-Wada R, Wada T. Regulation of root hair cell differentiation by R3 MYB transcription factors in tomato and Arabidopsis. Front Plant Sci. 2014;5:91. doi: 10.3389/fpls.2014.00091 . es_ES
dc.description.references Wang S, Chen JG. Regulation of cell fate determination by single-repeat R3 MYB transcription factors in Arabidopsis. Front Plant Sci. 2014;5:133. doi: 10.3389/fpls.2014.00133 . es_ES
dc.description.references Tominaga-Wada R, Wada T. The ectopic localization of CAPRICE LIKE MYB3 protein in Arabidopsis root epidermis. J Plant Physiol. 2016;199:111–5. es_ES
dc.description.references Raffaele S, Vailleau F, Léger A, Joubès J, Miersch O, Huard C, et al. A MYB transcription factor regulates very-long-chain fatty acid biosynthesis for activation of the hypersensitive cell death response in Arabidopsis. Plant Cell. 2008;20:752–67. es_ES
dc.description.references Bessire M, Borel S, Fabre G, Carraça L, Efremova N, Yephremov A, et al. A member of the PLEIOTROPIC DRUG RESISTANCE family of ATP binding cassette transporters is required for the formation of a functional cuticle in Arabidopsis. Plant Cell. 2011;23:1958–70. es_ES
dc.description.references Chen G, Komatsudab T, Mac JF, Nawrathd C, Pourkheirandishb M, Tagirib A, et al. An ATP-binding cassette subfamily G full transporter is essential for the retention of leaf water in both wild barley and rice. Proc Natl Acad Sci U S A. 2011;108:12354–9. es_ES
dc.description.references Del Bem LEV, Vincentz MGA. Evolution of xyloglucan-related genes in green plants. BMC Evol Biol. 2010;10:341. es_ES
dc.description.references Cho H-T, Kende H. Expression of Expansin genes 1s correlated with growth in Deepwater Rice. Plant Cell. 1997;9:1661–71. es_ES
dc.description.references Ranathunge K, Schreiber L, Franke R. Suberin research in the genomics era—new interest for an old polymer. Plant Sci. 2011;180:399–413. es_ES
dc.description.references Anderson TG, Barberon M, Geldner N. Suberization — the second life of an endodermal cell. Curr Opin Plant Biol. 2015;28:9–15. es_ES
dc.description.references Lacombe E, Hawkins S, Van Doorsselaere J, Piquemal J, Goffner D, Poeydomenge O, et al. Cinnamoyl CoA reductase, the first committed enzyme of the lignin branch biosynthetic pathway: cloning, expression and phylogenetic relationships. Plant J. 1997;11:429–41. es_ES
dc.description.references Ma Q-H. Functional analysis of a cinnamyl alcohol dehydrogenase involved in lignin biosynthesis in wheat. J Exp Bot. 2010;61(10):2735–44. es_ES
dc.description.references Vanholme R, Demedts B, Morreel K, Ralph J, Boerjan W. Lignin biosynthesis and structure. Plant Physiol. 2010;153:895–905. es_ES
dc.description.references Dean JFD, Eriksson K-EL. Laccase and the deposition of lignin in vascular plants. Holzforschung. 1994;48(s1):21–33. es_ES
dc.description.references Berthet S, Demont-Caulet N, Pollet B, Bidzinski P, Cézard L, Le Bris P, et al. Disruption of LACCASE4 and 17 results in tissue-specific alterations to lignification of Arabidopsis thaliana stems. Plant Cell. 2011;23:1124–37. es_ES
dc.description.references Zhao Q, Nakashima J, Chen F, Yin Y, Fu C, Yun J, et al. LACCASE is necessary and nonredundant with PEROXIDASE for lignin polymerization during vascular development in Arabidopsis. Plant Cell. 2013;25:3976–87. es_ES
dc.description.references Roppolo D, De Rybel B, Tendon VD, Pfister A, Alassimone J, Vermeer JEM, et al. A novel protein family mediates Casparian strip formation in the endodermis. Nature. 2011;473:380–3. es_ES
dc.description.references Zhong R, Ye Z-H. Transcriptional regulation of lignin biosynthesis. Plant Signal Behav. 2009;4(11):1028–34. es_ES
dc.description.references Kamiya T, Borghi M, Wang P, Danku JMC, Kalmbach L, Hosmani PS, et al. The MYB36 transcription factor orchestrates Casparian strip formation. Proc Natl Acad Sci U S A. 2015;112(33):10533–8. es_ES
dc.description.references Wang S, Li E, Porth I, Chen J-G, Mansfield SD, Douglas CJ. Regulation of secondary cell wall biosynthesis by poplar R2R3 MYB transcription factor PtrMYB152 in Arabidopsis. Sci Rep. 2014;4:5054. doi: 10.1038/srep05054 . es_ES
dc.description.references Thomas R, Fang X, Ranathunge K, Anderson TR, Peterson CA, Bernards MA. Soybean root Suberin: anatomical distribution, chemical composition, and relationship to partial resistance to Phytophthora sojae. Plant Physiol. 2007;144(1):299–311. es_ES
dc.description.references Ranathunge K, Thomas RH, Fang X, Peterson CA, Gijzen M, Bernards MA. Soybean root Suberin and partial resistance to root rot caused by Phytophthora sojae. Phytopathology. 2008;98:1179–89. es_ES
dc.description.references Riechmann JL, Meyerowitz EM. The AP2/EREBP family of plant transcription factors. Biol Chem. 1998;379:633–46. es_ES
dc.description.references Dietz K-J, Vogel MO. AP2/EREBP transcription factors are part of gene regulatory networks and integrate metabolic, hormonal and environmental signals in stress acclimation and retrograde signaling. Protoplasma. 2010;245:3–14. es_ES
dc.description.references Lee DS, Kim BK, Kwon SJ, Jin HC, Park OK. Arabidopsis GDSL lipase 2 plays a role in pathogen defense via negative regulation of auxin signaling. Biochem Biophys Res Commun. 2009;379:1038–42. es_ES
dc.description.references Vujaklija I, Bielen A, Paradžik T, Biđin S, Goldstein P, Vujaklija D. An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom. BMC Bioinformatics. 2016;17:91. doi: 10.1186/s12859-016-0919-7 . es_ES
dc.description.references Chepyshko H, Lai C-P, Huang L-M, Liu J-H, Shaw J-F. Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica) genome: new insights from bioinformatics analysis. BMC Genomics. 2012;13:309. es_ES
dc.description.references Petersen M. Hydroxycinnamoyltransferases in plant metabolism. Phytochem Rev. 2016;15:699–727. es_ES
dc.description.references Osbourn A, Goss RJM, Field RA. The saponins – polar isoprenoids with important and diverse biological activities. Nat Prod Rep. 2011;28:1261–8. es_ES
dc.description.references Thimmappa R, Geisler K, Louveau T, O’Maille P, Osbourn A. Triterpene biosynthesis in plants. Annu Rev Plant Biol. 2014;65:225–57. es_ES
dc.description.references Goodwin W, Salmon EJ, Ware WM. The action of certain chemical substances on the zoospores of Pseudoperonospora humuli (Miy. Et Takah.) Wils. J Agric Sci. 1929;19:185–200. es_ES
dc.description.references Deacon JW, Mitchell RT. Toxicity of oat roots, oat root extracts, and saponins to zoospores of Pythium spp. and other fungi. Trans Br Mycol Soc. 1985;84:479–87. es_ES
dc.description.references Jones JDG, Dangl JL. The plant immune system. Nature. 2006;444:323–9. es_ES
dc.description.references Marone D, Russo MA, Laidò G, De Leonardis AM, Mastrangelo AM. Plant nucleotide binding site–leucine-rich repeat (NBS-LRR) genes: active guardians in host defense responses. Int J Mol Sci. 2013;14(4):7302–26. es_ES
dc.description.references Almagro L, Bru R, Pugin A, Pedreño MA. Early signaling network in tobacco cells elicited with methyl jasmonate and cyclodextrins. Plant Physiol Biochem. 2012;51:1–9. es_ES
dc.description.references Byrt P, Grant BR. Some conditions governing zoospore production in axenic cultures of Phytophthora cinnamomi Rands. Aust J Bot. 1979;27(2):103–15. es_ES
dc.description.references Lheirminier J, Benhamou N, Larrue J, Milat M-L, Boudon-Padieu E, Nicole M, Blein J-P. Cytological characterization of elicitin-induced protection in tobacco plants infected by Phytophthora parasitica or phytoplasma. Phytopathology. 2003;93:1308–19. es_ES
dc.description.references Gordon H: FASTQ/a short-reads pre-processing tools. 2009. [ http://hannonlab.cshl.edu/fastx_toolkit/ ]. es_ES
dc.description.references Patel RK, Jain M. NGS QC toolkit: a toolkit for quality control of next generation sequencing data. PLoS One. 2012;7(2):e30619. es_ES
dc.description.references Andrews S: FastQC a quality control tool for high throughput sequence data. 2010. [ http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ]. es_ES
dc.description.references Yang SS, Tu ZJ, Cheung F, Xu WW, Lamb JFS, Jung HJG, et al. Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems. BMC Genomics. 2011;12:199. es_ES
dc.description.references Gutierrez-Gonzalez J, Tu ZJ, Garvin DF. Analysis and annotation of the hexaploid oat seed transcriptome. BMC Genomics. 2013;14:471. es_ES
dc.description.references Conesa A, Götz S. Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int J Plant Genom. 2008; doi: 10.1155/2008/619832 . es_ES
dc.description.references Carels N, Bernardi G. Two classes of genes in plants. Genetics. 2000;154:1819–25. es_ES
dc.description.references Vinogradov AE. DNA helix: the importance of being GC-rich. Nucleic Acids Res. 2003;31:1838–44. es_ES
dc.description.references Zhang L, Kasif S, Cantor CR, Broude NE. GC/AT-content spikes as genomic punctuation marks. Proc Natl Acad Sci U S A. 2004;101:16855–60. es_ES
dc.description.references Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011;27:863–4. es_ES
dc.description.references Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40. es_ES
dc.description.references Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics. 2009;25:1754–60. es_ES


Este ítem aparece en la(s) siguiente(s) colección(ones)

Mostrar el registro sencillo del ítem