De Novo Assembly And Transcriptome Analysis Of The Rubber Tree (hevea Brasiliensis) And Snp Markers Development For Rubber Biosynthesis Pathways

dc.creatorMantello C.C.
dc.creatorCardoso-Silva C.B.
dc.creatorDa Silva C.C.
dc.creatorDe Souza L.M.
dc.creatorScaloppi Jr. E.J.
dc.creatorde Goncalves P.S.
dc.creatorVicentini R.
dc.creatorDe Souza A.P.
dc.date2014
dc.date2015-06-25T17:55:06Z
dc.date2015-11-26T14:36:59Z
dc.date2015-06-25T17:55:06Z
dc.date2015-11-26T14:36:59Z
dc.date.accessioned2018-03-28T21:41:07Z
dc.date.available2018-03-28T21:41:07Z
dc.identifier
dc.identifierPlos One. Public Library Of Science, v. 9, n. 7, p. - , 2014.
dc.identifier19326203
dc.identifier10.1371/journal.pone.0102665
dc.identifierhttp://www.scopus.com/inward/record.url?eid=2-s2.0-84904614926&partnerID=40&md5=38896d38e11e0d4a53e19186b64eceb3
dc.identifierhttp://www.repositorio.unicamp.br/handle/REPOSIP/86773
dc.identifierhttp://repositorio.unicamp.br/jspui/handle/REPOSIP/86773
dc.identifier2-s2.0-84904614926
dc.identifier.urihttp://repositorioslatinoamericanos.uchile.cl/handle/2250/1248961
dc.descriptionHevea brasiliensis (Willd. Ex Adr. Juss.) Muell.-Arg. is the primary source of natural rubber that is native to the Amazon rainforest. The singular properties of natural rubber make it superior to and competitive with synthetic rubber for use in several applications. Here, we performed RNA sequencing (RNA-seq) of H. brasiliensis bark on the Illumina GAIIx platform, which generated 179,326,804 raw reads on the Illumina GAIIx platform. A total of 50,384 contigs that were over 400 bp in size were obtained and subjected to further analyses. A similarity search against the non-redundant (nr) protein database returned 32,018 (63%) positive BLASTx hits. The transcriptome analysis was annotated using the clusters of orthologous groups (COG), gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Pfam databases. A search for putative molecular marker was performed to identify simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). In total, 17,927 SSRs and 404,114 SNPs were detected. Finally, we selected sequences that were identified as belonging to the mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways, which are involved in rubber biosynthesis, to validate the SNP markers. A total of 78 SNPs were validated in 36 genotypes of H. brasiliensis. This new dataset represents a powerful information source for rubber tree bark genes and will be an important tool for the development of microsatellites and SNP markers for use in future genetic analyses such as genetic linkage mapping, quantitative trait loci identification, investigations of linkage disequilibrium and marker-assisted selection. © 2014 Mantello et al.
dc.description9
dc.description7
dc.description
dc.description
dc.descriptionSakdapipanich, J.T., Structural characterization of natural rubber based on recent evidence from selective enzymatic treatments (2007) J Biosci Bioeng, 103, pp. 287-292. , doi:10.1263/jbb.103.287
dc.descriptionCornish, K., Similarities and differences in rubber biochemistry among plant species (2001) Phytochemistry, 57, pp. 1123-1134
dc.descriptionGronover, C.S., Wahler, D., Prüfer, D., (2005) Natural Rubber Biosynthesis and Physic- Chemical Studies on Plant Derived Latex
dc.descriptionSaha, T., Priyadarshan, P.M., (2012) Genomics of Tree Crops, , Schnell RJ, Priyadarshan PM, editors New York, NY: Springer New York. doi:10.1007/978-1-4614-0920-5
dc.descriptionPriyadarshan, P.M., Goncalves, P.D.S., (2003) Hevea Gene Pool for Breeding, pp. 101-114
dc.descriptionLeitch, A.R., Lim, K.Y., Leitch, I.J., Neill, M.O., Molecular cytogenetic studies in rubber (1998) Hevea, pp. 464-467
dc.descriptionPires, J.M., Secco, R., Gomes, J.I., (2002) Taxonomia e Filogeografia Das Seringueiras (Hevea Spp) Belem: Embrapa Amazonia Oriental, p. 103
dc.descriptionPushparajah, E., Natural rubber (2001) Tree Crop Ecosystems, , Last, F.T. (ed) Amsterdam, The Netherlands: Elsevier Science
dc.descriptionRaj, S., Das, G., Pothen, J., Dey, S.K., Relationship between latex yield of Hevea brasiliensis and antecedent environmental parameters (2005) International Journal of Biometeorology, 49 (3), pp. 189-196. , DOI 10.1007/s00484-004-0222-6
dc.descriptionLe Guen, V., Garcia, D., Doaré, F., Mattos, C.R.R., Condina, V., A rubber tree's durable resistance to Microcyclus ulei is conferred by a qualitative gene and a major quantitative resistance factor (2011) Tree Genet Genomes, 7, pp. 877-889. , doi:10.1007/s11295-011-0381-7
dc.descriptionMantello, C.C., Suzuki, F.I., Souza, L.M., Gonçalves, P.S., Souza, A.P., Microsatellite marker development for the rubber tree (Hevea brasiliensis): Characterization and cross-amplification in wild Hevea species (2012) BMC Res Notes, 5, p. 329. , doi:10.1186/1756-0500-5-329
dc.descriptionFeng, S.P., Li, W.G., Huang, H.S., Wang, J.Y., Wu, Y.T., Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis) (2008) Mol Breed, 23, pp. 85-97. , doi:10.1007/s11032-008-9216-0
dc.descriptionTriwitayakorn, K., Chatkulkawin, P., Kanjanawattanawong, S., Sraphet, S., Yoocha, T., Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers and construction of a genetic linkage map (2011) DNA Res, 18, pp. 471-482. , doi:10.1093/dnares/dsr034
dc.descriptionLi, D., Deng, Z., Qin, B., Liu, X., Men, Z., De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.) (2012) BMC Genomics, 13, p. 192. , doi:10.1186/1471-2164-13-192
dc.descriptionLespinasse, D., Rodier-Goud, M., Grivet, L., Leconte, A., Legnate, H., Seguin, M., A saturated genetic linkage map of rubber tree (Hevea spp.) based on RFLP, AFLP, microsatellite, and isozyme markers (2000) Theoretical and Applied Genetics, 100 (1), pp. 127-138
dc.descriptionSouza, L.M., Gazaffi, R., Mantello, C.C., Silva, C.C., Garcia, D., QTL mapping of growth-related traits in a full-sib family of rubber tree (Hevea brasiliensis) evaluated in a sub-tropical climate (2013) PLoS One, 8, pp. e61238. , doi:10.1371/journal.pone.0061238
dc.descriptionChow, K.-S., Wan, K.-L., Isa, M.N.M., Bahari, A., Tan, S.-H., Harikrishna, K., Yeang, H.-Y., Insights into rubber biosynthesis from transcriptome analysis of Hevea brasiliensis latex (2007) Journal of Experimental Botany, 58 (10), pp. 2429-2440. , DOI 10.1093/jxb/erm093
dc.descriptionChow, K.-S., Mat-Isa, M.-N., Bahari, A., Ghazali, A.-K., Alias, H., Metabolic routes affecting rubber biosynthesis in Hevea brasiliensis latex (2012) J Exp Bot, 63, pp. 1863-1871. , doi:10.1093/jxb/err363
dc.descriptionRahman, A.Y.A., Usharraj, A.O., Misra, B.B., Thottathil, G.P., Jayasekaran, K., Draft genome sequence of the rubber tree Hevea brasiliensis (2013) BMC Genomics, 14, p. 75. , doi:10.1186/1471-2164-14-75
dc.descriptionWang, Z., Gerstein, M., Snyder, M., RNA-Seq: A revolutionary tool for transcriptomics (2009) Nat Rev Genet, 10, pp. 57-63
dc.descriptionLister, R., O'Malley, R.C., Tonti-Filippini, J., Gregory, B.D., Berry, C.C., Highly integrated single-base resolution maps of the epigenome in Arabidopsis (2008) Cell, 133, pp. 523-536. , doi:10.1016/j.cell.2008.03.029
dc.descriptionLu, T., Lu, G., Fan, D., Zhu, C., Li, W., (2010) Function Annotation of the Rice Transcriptome at Single-nucleotide Resolution by RNA-seq, pp. 1238-1249. , doi:10.1101/gr.106120.110
dc.descriptionHansey, C.N., Vaillancourt, B., Sekhon, R.S., De Leon, N., Kaeppler, S.M., Maize (Zea mays L.) genome diversity as revealed by RNA-sequencing (2012) PLoS One, 7, pp. e33071. , doi:10.1371/journal.pone.0033071
dc.descriptionEgan, A.N., Schlueter, J., Spooner, D.M., Applications of next-generation sequencing in plant biology (2012) Am J Bot, 99, pp. 175-185. , doi:10.3732/ajb.1200020
dc.descriptionXia, Z., Xu, H., Zhai, J., Li, D., Luo, H., RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis (2011) Plant Mol Biol, 77, pp. 299-308. , doi:10.1007/s11103-011-9811-z
dc.descriptionChang, S., Puryear, J., Cairney, J., A simple and efficient method for isolating RNA from pine trees (1993) Plant Mol Biol Report, 11, pp. 113-116. , doi:10.1007/BF02670468
dc.descriptionDoyle, J., Doyle, J., A rapid DNA isolation procedure for small quantities of fresh leaf tissue (1987) Phytochem Bull, 19, pp. 11-15
dc.descriptionConesa, 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 (2005) Bioinformatics, 21 (18), pp. 3674-3676. , DOI 10.1093/bioinformatics/bti610
dc.descriptionYe, J., Fang, L., Zheng, H., Zhang, Y., Chen, J., Zhang, Z., Wang, J., Wang, J., WEGO: A web tool for plotting GO annotations (2006) Nucleic Acids Research, 34 (WEB. SERV. ISS.), pp. W293-W297. , DOI 10.1093/nar/gkl031
dc.descriptionZdobnov, E.M., Apweiler, R., (2001) Signature-recognition Methods in InterPro., 17, pp. 847-848
dc.descriptionSilva, C.C., Mantello, C.C., Campos, T., Souza, L.M., Gonçalves, P.S., Leaf-, panel- and latex-expressed sequenced tags from the rubber tree (Hevea brasiliensis) under cold-stressed and suboptimal growing conditions: The development of gene-targeted functional markers for stress response (2014) Mol Breed, , doi:10.1007/s11032-014-0095-2
dc.descriptionUntergasser, A., Nijveen, H., Rao, X., Bisseling, T., Geurts, R., Primer3Plus, an enhanced web interface to Primer3 (2007) Nucleic Acids Res, 35, pp. W71-W74. , doi:10.1093/nar/gkm306
dc.descriptionMiller, M., 27. Miller MP: Tools for population genetic analysis (TFPGA) 1.3: A Windows program for the analysis of allozyme and molecular population genetic data (1997) Computer Software, , distributed by the author 1997
dc.descriptionTatusov, R.L., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Kiryutin, B., The COG database: An updated version includes eukaryotes (2003) BMC Bioinformatics, 4, p. 41. , doi:10.1186/1471-2105-4-41
dc.descriptionStirnimann, C.U., Petsalaki, E., Russell, R.B., Müller, C.W., WD40 proteins propel cellular networks (2010) Trends Biochem Sci, 35, pp. 565-574. , doi:10.1016/j.tibs.2010.04.003
dc.descriptionRushton, P.J., Somssich, I.E., Ringler, P., Shen, Q.J., WRKY transcription factors (2010) Trends Plant Sci, 15, pp. 247-258. , doi:10.1016/j.tplants.2010.02.006
dc.descriptionCheng, Y., Zhou, Y., Yang, Y., Chi, Y.-J., Zhou, J., Structural and functional analysis of VQ motif-containing proteins in Arabidopsis as interacting proteins of WRKY transcription factors (2012) Plant Physiol, 159, pp. 810-825. , doi:10.1104/pp.112.196816
dc.descriptionKanehisa, M., Goto, S., KEGG: Kyoto Encyclopedia of Genes and Genomes (2000) Nucleic Acids Research, 28 (1), pp. 27-30
dc.descriptionKanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Yamanishi, Y., KEGG for linking genomes to life and the environment (2008) Nucleic Acids Research, 36 (SUPPL. 1), pp. D480-D484. , DOI 10.1093/nar/gkm882
dc.descriptionSando, T., Takeno, S., Watanabe, N., Okumoto, H., Kuzuyama, T., Cloning and Characterization of the 2-C-Methyl-D-erythritol 4-Phosphate (MEP) Pathway Genes of a Natural-Rubber Producing Plant, Hevea brasiliensis (2008) Biosci Biotechnol Biochem, 72, pp. 2903-2917. , doi:10.1271/bbb.80387
dc.descriptionDao, T.T.H., Linthorst, H.J.M., Verpoorte, R., Chalcone synthase and its functions in plant resistance (2011) Phytochem Rev, 10, pp. 397-412. , doi:10.1007/s11101-011-9211-7
dc.descriptionKim, J.Y., Kim, W.Y., Kwak, K.J., Oh, S.H., Han, Y.S., Glycine-rich RNA-binding proteins are functionally conserved in Arabidopsis thaliana and Oryza sativa during cold adaptation process (2010) J Exp Bot, 61, pp. 2317-2325. , doi:10.1093/jxb/erq058
dc.descriptionCaverzan, A., Passaia, G., Rosa, S.B., Ribeiro, C.W., Lazzarotto, F., Plant responses to stresses: Role of ascorbate peroxidase in the antioxidant protection (2012) Genet Mol Biol, 35, pp. 1011-1019
dc.descriptionLam, K.C., Ibrahim, R.K., Behdad, B., Dayanandan, S., (2007) Structure, Function, and Evolution of Plant O -Methyltransferases, 1013, pp. 1001-1013. , doi:10.1139/G07-077
dc.descriptionBadger, M., The roles of carbonic anhydrases in photosynthetic CO(2) concentrating mechanisms (2003) Photosynth Res, 77, pp. 83-94. , doi:10.1023/A:1025821717773
dc.descriptionTanaka, Y., Matsuoka, M., Yamanoto, N., Ohashi, Y., Kano-Murakami, Y., Structure and characterization of a cDNA clone for phenylalanine ammonia-lyase from cut-injured roots of sweet potato (1989) Plant Physiol, 90, pp. 1403-1407
dc.descriptionMorgante, M., Hanafey, M., Powell, W., Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes (2002) Nat Genet, 30, pp. 194-200. , doi:10.1038/ng822
dc.descriptionMarconi, T.G., A, C.E., Miranda, H.R., Mancini, M.C., Cardoso-Silva, C.B., Functional markers for gene mapping and genetic diversity studies in sugarcane (2011) BMC Res Notes, 4, p. 264. , doi:10.1186/1756-0500-4-264
dc.descriptionLa Rota, M., Kantety, R.V., Yu, J.-K., Sorrells, M.E., Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley (2005) BMC Genomics, 6, p. 23. , doi:10.1186/1471-2164-6-23
dc.descriptionWang, Z., Fang, B., Chen, J., Zhang, X., Luo, Z., De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas) (2010) BMC Genomics, 11, p. 726. , doi:10.1186/1471-2164-11-726
dc.descriptionChen, C., Zhou, P., A, C.Y., Huang, S., Gmitter, F.G., Mining and characterizing microsatellites from citrus ESTs (2006) Theor Appl Genet, 112, pp. 1248-1257. , doi:10.1007/s00122-006-0226-1
dc.descriptionWei, W., Qi, X., Wang, L., Zhang, Y., Hua, W., Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers (2011) BMC Genomics, 12, p. 451. , doi:10.1186/1471-2164-12-451
dc.descriptionFraser, L.G., Harvey, C.F., Crowhurst, R.N., De Silva, H.N., EST-derived microsatellites from Actinidia species and their potential for mapping (2004) Theoretical and Applied Genetics, 108 (6), pp. 1010-1016. , DOI 10.1007/s00122-003-1517-4
dc.descriptionAggarwal, R.K., Hendre, P.S., Varshney, R.K., Bhat, P.R., Krishnakumar, V., Singh, L., Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species (2007) Theoretical and Applied Genetics, 114 (2), pp. 359-372. , DOI 10.1007/s00122-006-0440-x
dc.descriptionMeglécz, E., Nève, G., Biffin, E., Gardner, M.G., Breakdown of phylogenetic signal: A survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species (2012) PLoS One, 7, pp. e40861. , doi:10.1371/journal.pone. 0040861
dc.descriptionToth, G., Gaspari, Z., Jurka, J., Microsatellites in different eukaryotic genomes: Surveys and analysis (2000) Genome Research, 10 (7), pp. 967-981. , DOI 10.1101/gr.10.7.967
dc.descriptionKumpatla, S.P., Mukhopadhyay, S., (2005) Mining and Survey of Simple Sequence Repeats in Expressed Sequence Tags of Dicotyledonous Species, 998, pp. 985-998. , doi:10.1139/G05-060
dc.descriptionSplicing, P.R.N.A., Coleman, T.P., Roesser, J.R., Commonwealth, V., Uni, V., (1998) RNA Secondary Structure: An Important Cis -Element in Rat Calcitonin/CGRP, pp. 15941-15950
dc.descriptionNovaes, E., Drost, D.R., Farmerie Jr., W.G., P, G.J., Grattapaglia, D., (2008) High-throughput Gene and SNP Discovery in Eucalyptus Grandis, An Uncharacterized Genome, 14, pp. 1-14. , doi:10.1186/1471-2164-9-312
dc.descriptionChagné, D., Crowhurst, R.N., Troggio, M., Davey, M.W., Gilmore, B., Genome-wide SNP detection, validation, and development of an 8K SNP array for apple (2012) PLoS One, 7, pp. e31745. , doi:10.1371/journal.pone.0031745
dc.descriptionLijavetzky, D., Cabezas, J.A., Ibáñez, A., Rodríguez, V., Martínez-Zapater, J.M., High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology (2007) BMC Genomics, 8, p. 424. , doi:10.1186/1471-2164-8-424
dc.descriptionPootakham, W., Chanprasert, J., Jomchai, N., Sangsrakru, D., Yoocha, T., Single nucleotide polymorphism marker development in the rubber tree, Hevea brasiliensis (Euphorbiaceae) (2011) Am J Bot, 98, pp. e337-e338. , doi:10.3732/ajb.1100228
dc.descriptionSalgado, L.R., Koop, D.M., Pinheiro, D.G., Rivallan, R., Le Guen, V., De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers (2014) BMC Genomics, 15, p. 236. , doi:10.1186/1471-2164-15-236
dc.descriptionAllegre, M., Argout, X., Boccara, M., Fouet, O., Roguet, Y., Discovery and mapping of a new expressed sequence tag-single nucleotide polymorphism and simple sequence repeat panel for large-scale genetic studies and breeding of Theobroma cacao L (2012) DNA Res, 19, pp. 23-35. , doi:10.1093/dnares/dsr039
dc.descriptionNeale, D.B., Kremer, A., Forest tree genomics: Growing resources and applications (2011) Nat Rev Genet, 12, pp. 111-122. , doi:10.1038/nrg2931
dc.descriptionSouza, L.M., Mantello, C.C., Santos, M.O., Goncalves, P.S., Souza, A., Microsatellites from rubber tree (Hevea brasiliensis) for genetic diversity analysis and cross-amplification in six Hevea wild species (2009) Conserv Genet Resour, 1, pp. 75-79
dc.descriptionLe Guen, V., Gay, C., Xiong, T.C., Souza, L.M., Rodier-Goud, M., Seguin, M., Development and characterization of 296 new polymorphic microsatellite markers for rubber tree (Hevea brasiliensis) (2011) Plant Breed, 130, pp. 294-296
dc.descriptionHirakawa, H., Shirasawa, K., Ohyama, A., Fukuoka, H., Aoki, K., Genome-wide SNP genotyping to infer the effects on gene functions in tomato (2013) DNA Res, 20, pp. 221-233. , doi:10.1093/dnares/dst005
dc.languageen
dc.publisherPublic Library of Science
dc.relationPLoS ONE
dc.rightsaberto
dc.sourceScopus
dc.titleDe Novo Assembly And Transcriptome Analysis Of The Rubber Tree (hevea Brasiliensis) And Snp Markers Development For Rubber Biosynthesis Pathways
dc.typeArtículos de revistas


Este ítem pertenece a la siguiente institución