- -

De novo assembly of Phlomis purpurea after challenging with Phytophthora cinnamomi

RiuNet: Institutional repository of the Polithecnic University of Valencia

Share/Send to

Cited by


De novo assembly of Phlomis purpurea after challenging with Phytophthora cinnamomi

Show full item record

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

Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/140246

Files in this item

Item Metadata

Title: De novo assembly of Phlomis purpurea after challenging with Phytophthora cinnamomi
Author: Baldé, A. Neves, D. García-Breijo, Francisco-José Pais, M. S. Cravador, A.
UPV Unit: Universitat Politècnica de València. Departamento de Ecosistemas Agroforestales - Departament d'Ecosistemes Agroforestals
Issued date:
[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 ...[+]
Subjects: Phlomis purpurea , Transcriptomics , Phytophthora cinnamomi , Resistance , Defence response , Time course challenge , Casparian strips , Cutin
Copyrigths: Reconocimiento (by)
BMC Genomics. (issn: 1471-2164 )
DOI: 10.1186/s12864-017-4042-6
Springer (Biomed Central Ltd.)
Publisher version: https://doi.org/10.1186/s12864-017-4042-6
Project ID:
info:eu-repo/grantAgreement/FCT/3599-PPCDT/100217/PT/Production of active compounds against Phytophthora cinnamomi by Phlomis purpurea, Metabolite and transcript profiling/
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 - ...[+]
Type: Artículo


Li M, Shang XF, Jia ZP, Zhang RX. Phytochemical and biological studies of plants from the genus Phlomis. Chem Biodivers. 2010;7:283–301.

Erwin DC, Ribeiro OK. Phytophthora diseases worldwide. St Paul: American Phytopathological Society Press; 1996.

Brasier CM, Robredo F, Ferraz JFP. Evidence for Phytophthora cinnamomi involvement in Iberian oak decline. Plant Pathol. 1993;42:140–5. [+]
Li M, Shang XF, Jia ZP, Zhang RX. Phytochemical and biological studies of plants from the genus Phlomis. Chem Biodivers. 2010;7:283–301.

Erwin DC, Ribeiro OK. Phytophthora diseases worldwide. St Paul: American Phytopathological Society Press; 1996.

Brasier CM, Robredo F, Ferraz JFP. Evidence for Phytophthora cinnamomi involvement in Iberian oak decline. Plant Pathol. 1993;42:140–5.

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.

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.

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 .

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.

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.

Dixon AR. Natural products and plant disease resistance. Nature. 2001;411:843–7.

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.

Caspary R. Bemerkungen über die Schutzscheide und die Bildung des Stammes und der Wurzel. Jahrb wissensc Botanik. 1865;4:101–24.

Lee Y, Rubio MC, Alassimone J, Geldner N. A mechanism for localized lignin deposition in the endodermis. Cell. 2013;153:402–12.

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.

Geldner N. The endodermis. Annu Rev Plant Biol. 2013;64:531–58.

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.

Mysore KS, Ryu C-M. Nonhost resistance: how much do we know? Trends Plant Sci. 2004;9:97–104.

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.

National Center for Biotechnology Information [ http://www.ncbi.nlm.nih.gov ]. Accessed 30 Mar 2015.

Kyoto Encyclopedia of Genes and Genomes [ http://www.genome.jp/kegg/kegg1.html ]. Accessed 30 Mar 2015.

Carels N, Hatey P, Jabbari K, Bernardi G. Compositional properties of homologous coding sequences from plants. J Mol Evol. 1998;46:45–53.

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.

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.

Surget-Groba Y, Montoya-Burgos JI. Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res. 2010;20:1432–40.

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 .

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.

Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821–9.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Pollard M, Beisson F, Li Y, Ohlrogge JB. Building lipid barriers: biosynthesis of cutin and suberin. Trends Plant Sci. 2008;13:236–46.

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.

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 .

Yeats TH, Rose JKC. The formation and function of plant cuticles. Plant Physiol. 2013;163:5–20.

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.

Molina I, Kosma D. Role of HXXXD-motif/BAHD acyltransferases in the biosynthesis of extracellular lipids. Plant Cell Rep. 2015;34:587–601.

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.

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 .

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 .

Tominaga-Wada R, Wada T. The ectopic localization of CAPRICE LIKE MYB3 protein in Arabidopsis root epidermis. J Plant Physiol. 2016;199:111–5.

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.

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.

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.

Del Bem LEV, Vincentz MGA. Evolution of xyloglucan-related genes in green plants. BMC Evol Biol. 2010;10:341.

Cho H-T, Kende H. Expression of Expansin genes 1s correlated with growth in Deepwater Rice. Plant Cell. 1997;9:1661–71.

Ranathunge K, Schreiber L, Franke R. Suberin research in the genomics era—new interest for an old polymer. Plant Sci. 2011;180:399–413.

Anderson TG, Barberon M, Geldner N. Suberization — the second life of an endodermal cell. Curr Opin Plant Biol. 2015;28:9–15.

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.

Ma Q-H. Functional analysis of a cinnamyl alcohol dehydrogenase involved in lignin biosynthesis in wheat. J Exp Bot. 2010;61(10):2735–44.

Vanholme R, Demedts B, Morreel K, Ralph J, Boerjan W. Lignin biosynthesis and structure. Plant Physiol. 2010;153:895–905.

Dean JFD, Eriksson K-EL. Laccase and the deposition of lignin in vascular plants. Holzforschung. 1994;48(s1):21–33.

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.

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.

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.

Zhong R, Ye Z-H. Transcriptional regulation of lignin biosynthesis. Plant Signal Behav. 2009;4(11):1028–34.

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.

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 .

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.

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.

Riechmann JL, Meyerowitz EM. The AP2/EREBP family of plant transcription factors. Biol Chem. 1998;379:633–46.

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.

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.

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 .

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.

Petersen M. Hydroxycinnamoyltransferases in plant metabolism. Phytochem Rev. 2016;15:699–727.

Osbourn A, Goss RJM, Field RA. The saponins – polar isoprenoids with important and diverse biological activities. Nat Prod Rep. 2011;28:1261–8.

Thimmappa R, Geisler K, Louveau T, O’Maille P, Osbourn A. Triterpene biosynthesis in plants. Annu Rev Plant Biol. 2014;65:225–57.

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.

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.

Jones JDG, Dangl JL. The plant immune system. Nature. 2006;444:323–9.

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.

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.

Byrt P, Grant BR. Some conditions governing zoospore production in axenic cultures of Phytophthora cinnamomi Rands. Aust J Bot. 1979;27(2):103–15.

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.

Gordon H: FASTQ/a short-reads pre-processing tools. 2009. [ http://hannonlab.cshl.edu/fastx_toolkit/ ].

Patel RK, Jain M. NGS QC toolkit: a toolkit for quality control of next generation sequencing data. PLoS One. 2012;7(2):e30619.

Andrews S: FastQC a quality control tool for high throughput sequence data. 2010. [ http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ].

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.

Gutierrez-Gonzalez J, Tu ZJ, Garvin DF. Analysis and annotation of the hexaploid oat seed transcriptome. BMC Genomics. 2013;14:471.

Conesa A, Götz S. Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int J Plant Genom. 2008; doi: 10.1155/2008/619832 .

Carels N, Bernardi G. Two classes of genes in plants. Genetics. 2000;154:1819–25.

Vinogradov AE. DNA helix: the importance of being GC-rich. Nucleic Acids Res. 2003;31:1838–44.

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.

Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011;27:863–4.

Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.

Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics. 2009;25:1754–60.




This item appears in the following Collection(s)

Show full item record