De Novo assembly and transcriptome analysis of the rubber tree (Hevea brasiliensis) and SNP markers development for rubber biosynthesis pathways

PLoS ONE

Volumn 9, Issue 7, 2014, Pages

  Mantello, Camila Campos ^a   Cardoso Silva, Claudio Benicio ^a   Da Silva, Carla Cristina ^a   De Souza, Livia Moura ^a   Scaloppi Jr , Erivaldo José ^b   de Gonçalves, Paulo Souza ^c   Vicentini, Renato ^a   De Souza, Anete Pereira ^a  

^a UNIVERSITY OF CAMPINAS   (Brazil)

^b AGÊNCIA PAULISTA DE TECNOLOGIA DOS AGRONEGÓCIOS   (Brazil)

^c INSTITUTO AGRONÔMICO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

2 C METHYL DEXTRO ERYTHRITOL 4 PHOSPHATE; MEVALONIC ACID; MOLECULAR MARKER; TRANSCRIPTOME; UNCLASSIFIED DRUG; RUBBER; VEGETABLE PROTEIN;

ARTICLE; BASE PAIRING; BIOSYNTHESIS; CONTIG MAPPING; GENE CLUSTER; GENE LINKAGE DISEQUILIBRIUM; GENE ONTOLOGY; GENETIC DATABASE; GENOTYPE; HEVEA BRASILIENSIS; INTER SIMPLE SEQUENCE REPEAT; MICROSATELLITE MARKER; NONHUMAN; PROTEIN DATABASE; PROTEIN DOMAIN; RNA SEQUENCE; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; BARK; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENETICS; HEVEA; METABOLISM; PLANT GENE;

BIOSYNTHETIC PATHWAYS; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE ONTOLOGY; GENES, PLANT; HEVEA; PLANT BARK; PLANT PROTEINS; POLYMORPHISM, SINGLE NUCLEOTIDE; RUBBER;

EID: 84904614926     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0102665     Document Type: Article

References (68)

1. Sakdapipanich JT (2007) Structural characterization of natural rubber based on recent evidence from selective enzymatic treatments. J Biosci Bioeng 103: 287-292. doi:10.1263/jbb.103.287.
2. Cornish K (2001) Similarities and differences in rubber biochemistry among plant species. Phytochemistry 57: 1123-1134.
3. Gronover CS, Wahler D, Prüfer D (2009) Natural Rubber Biosynthesis and Physic- Chemical Studies on Plant Derived Latex. 2005.
4. Saha T, Priyadarshan PM (2012) Genomics of Tree Crops. Schnell RJ, Priyadarshan PM, editors New York, NY: Springer New York. doi:10.1007/978-1- 4614-0920-5.
5. Priyadarshan PM, Goncalves PDS (2003) Hevea gene pool for breeding: 101-114.
6. Leitch AR, Lim KY, Leitch IJ, Neill MO, et al. (1998) Molecular cytogenetic studies in rubber, Hevea: 464-467.
7. Pires JM, Secco R., Gomes JI (2002). Taxonomia e filogeografia das seringueiras (Hevea spp) Belem: Embrapa Amazonia Oriental p.103.
8. Pushparajah E (2001) Natural rubber. In: Last, F.T. (ed) Tree Crop Ecosystems. Amsterdam, The Netherlands: Elsevier Science.
9. Raj S, Das G, Pothen J, Dey SK (2005) Relationship between latex yield of Hevea brasiliensis and antecedent environmental parameters. Int J Biometeorol 49: 189-196. doi:10.1007/s00484-004-0222-6. (Pubitemid 40167455)
10. Le Guen V, Garcia D, Doaré F, Mattos CRR, Condina V, et al. (2011) A rubber tree's durable resistance to Microcyclus ulei is conferred by a qualitative gene and a major quantitative resistance factor. Tree Genet Genomes 7: 877-889. doi:10.1007/s11295-011-0381-7.
11. Mantello CC, Suzuki FI, Souza LM, Gonçalves PS, Souza AP (2012) Microsatellite marker development for the rubber tree (Hevea brasiliensis): characterization and cross-amplification in wild Hevea species. BMC Res Notes 5: 329. doi:10.1186/1756-0500-5-329.
12. Feng SP, Li WG, Huang HS, Wang JY, Wu YT (2008) Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis). Mol Breed 23: 85-97. doi:10.1007/s11032-008- 9216-0.
13. Triwitayakorn K, Chatkulkawin P, Kanjanawattanawong S, Sraphet S, Yoocha T, et al. (2011) Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers and construction of a genetic linkage map. DNA Res 18: 471-482. doi:10.1093/dnares/dsr034.
14. Li D, Deng Z, Qin B, Liu X, Men Z (2012) De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). BMC Genomics 13: 192. doi:10.1186/1471-2164-13-192.
15. Lespinasse D., Rodier-Goud M., Grivet L., Leconte A., Legnate H., & Seguin M (2000) A saturated genetic linkage map of rubber tree (Hevea spp.) based on RFLP, AFLP, microsatellite, and isozyme markers. Theor Appl Genet 100: 127-138. (Pubitemid 30065205)
16. Souza LM, Gazaffi R, Mantello CC, Silva CC, Garcia D, et al. (2013) QTL mapping of growth-related traits in a full-sib family of rubber tree (Hevea brasiliensis) evaluated in a sub-tropical climate. PLoS One 8: e61238. doi:10.1371/journal.pone.0061238.
17. Chow K-S, Wan K-L, Isa MNM, Bahari A, Tan S-H, et al. (2007) Insights into rubber biosynthesis from transcriptome analysis of Hevea brasiliensis latex. J Exp Bot 58: 2429-2440. doi:10.1093/jxb/erm093. (Pubitemid 47357554)
18. Chow K-S, Mat-Isa M-N, Bahari A, Ghazali A-K, Alias H, et al. (2012) Metabolic routes affecting rubber biosynthesis in Hevea brasiliensis latex. J Exp Bot 63: 1863-1871. doi:10.1093/jxb/err363.
19. Rahman AYA, Usharraj AO, Misra BB, Thottathil GP, Jayasekaran K, et al. (2013) Draft genome sequence of the rubber tree Hevea brasiliensis. BMC Genomics 14: 75. doi:10.1186/1471-2164-14-75.
20. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
21. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, et al. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523-536. doi:10.1016/j.cell.2008.03.029.
22. Lu T, Lu G, Fan D, Zhu C, Li W, et al. (2010) Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq: 1238-1249. doi:10.1101/gr.106120.110.
23. Hansey CN, Vaillancourt B, Sekhon RS, de Leon N, Kaeppler SM, et al. (2012) Maize (Zea mays L.) genome diversity as revealed by RNA-sequencing. PLoS One 7: e33071. doi:10.1371/journal.pone.0033071.
24. Egan AN, Schlueter J, Spooner DM (2012) Applications of next-generation sequencing in plant biology. Am J Bot 99: 175-185. doi:10.3732/ajb.1200020.
25. Xia Z, Xu H, Zhai J, Li D, Luo H, et al. (2011) RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis. Plant Mol Biol 77: 299-308. doi:10.1007/s11103-011-9811-z.
26. Chang S, Puryear J, Cairney J (1993) A simple and efficient method for isolating RNA from pine trees. Plant Mol Biol Report 11: 113-116. doi:10.1007/BF02670468.
27. Doyle J, Doyle J (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19: 11-15.
28. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, et al. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676. doi:10.1093/bioinformatics/bti610. (Pubitemid 41264107)
29. Ye J, Fang L, Zheng H, Zhang Y, Chen J, et al. (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34: W293-7. doi:10.1093/nar/ gkl031. (Pubitemid 44529781)
30. Zdobnov EM, Apweiler R (2001) signature-recognition methods in InterPro. 17: 847-848.
31. Silva CC, Mantello CC, Campos T, Souza LM, Gonçalves PS, et al. (2014) 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. Mol Breed. doi:10.1007/s11032-014-0095-2.
32. Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, et al. (2007) Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 35: W71-4. doi:10.1093/nar/gkm306.
33. Miller M (1997) 27. Miller MP: Tools for population genetic analysis (TFPGA) 1.3: A Windows program for the analysis of allozyme and molecular population genetic data. Computer Software distributed by the author 1997.
34. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41. doi:10.1186/1471-2105-4-41.
35. Stirnimann CU, Petsalaki E, Russell RB, Müller CW (2010) WD40 proteins propel cellular networks. Trends Biochem Sci 35: 565-574. doi:10.1016/j.tibs.2010.04.003.
36. Rushton PJ, Somssich IE, Ringler P, Shen QJ (2010) WRKY transcription factors. Trends Plant Sci 15: 247-258. doi:10.1016/j.tplants.2010.02.006.
37. Cheng Y, Zhou Y, Yang Y, Chi Y-J, Zhou J, et al. (2012) Structural and functional analysis of VQ motif-containing proteins in Arabidopsis as interacting proteins of WRKY transcription factors. Plant Physiol 159: 810-825. doi:10.1104/pp.112.196816.
38. Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30. (Pubitemid 30047706)
39. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36: D480-4. doi:10.1093/nar/gkm882. (Pubitemid 351149770)
40. Sando T, Takeno S, Watanabe N, Okumoto H, Kuzuyama T, et al. (2008) Cloning and Characterization of the 2-C-Methyl-D-erythritol 4-Phosphate (MEP) Pathway Genes of a Natural-Rubber Producing Plant, Hevea brasiliensis. Biosci Biotechnol Biochem 72: 2903-2917. doi:10.1271/bbb.80387.
41. Dao TTH, Linthorst HJM, Verpoorte R (2011) Chalcone synthase and its functions in plant resistance. Phytochem Rev 10: 397-412. doi:10.1007/s11101- 011-9211-7.
42. Kim JY, Kim WY, Kwak KJ, Oh SH, Han YS, et al. (2010) Glycine-rich RNA-binding proteins are functionally conserved in Arabidopsis thaliana and Oryza sativa during cold adaptation process. J Exp Bot 61: 2317-2325. doi:10.1093/jxb/erq058.
43. Caverzan A, Passaia G, Rosa SB, Ribeiro CW, Lazzarotto F, et al. (2012) Plant responses to stresses: Role of ascorbate peroxidase in the antioxidant protection. Genet Mol Biol 35: 1011-1019.
44. Lam KC, Ibrahim RK, Behdad B, Dayanandan S (2007) Structure, function, and evolution of plant O -methyltransferases. 1013: 1001-1013. doi:10.1139/G07-077.
45. Badger M (2003) The roles of carbonic anhydrases in photosynthetic CO(2) concentrating mechanisms. Photosynth Res 77: 83-94. doi:10.1023/A:1025821717773.
46. Tanaka Y, Matsuoka M, Yamanoto N, Ohashi Y, Kano-Murakami Y, et al. (1989) Structure and characterization of a cDNA clone for phenylalanine ammonia-lyase from cut-injured roots of sweet potato. Plant Physiol 90: 1403-1407.
47. Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30: 194-200. doi:10.1038/ng822.
48. Marconi TG, Costa E a, Miranda HR, Mancini MC, Cardoso-Silva CB, et al. (2011) Functional markers for gene mapping and genetic diversity studies in sugarcane. BMC Res Notes 4: 264. doi:10.1186/1756-0500-4-264.
49. La Rota M, Kantety R V, Yu J-K, Sorrells ME (2005) Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genomics 6: 23. doi:10.1186/1471-2164-6-23.
50. Wang Z, Fang B, Chen J, Zhang X, Luo Z, et al. (2010) De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas). BMC Genomics 11: 726. doi:10.1186/1471-2164-11-726.
51. Chen C, Zhou P, Choi Y a, Huang S, Gmitter FG (2006) Mining and characterizing microsatellites from citrus ESTs. Theor Appl Genet 112: 1248-1257. doi:10.1007/s00122-006-0226-1.
52. Wei W, Qi X, Wang L, Zhang Y, Hua W, et al. (2011) Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics 12: 451. doi:10.1186/1471-2164-12-451.
53. Fraser LG, Harvey CF, Crowhurst RN, De Silva HN (2004) EST-derived microsatellites from Actinidia species and their potential for mapping. Theor Appl Genet 108: 1010-1016. doi:10.1007/s00122-003-1517-4. (Pubitemid 38549870)
54. Aggarwal RK, Hendre PS, Varshney RK, Bhat PR, Krishnakumar V, et al. (2007) Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theor Appl Genet 114: 359-372. doi:10.1007/s00122-006-0440-x. (Pubitemid 46018221)
55. Meglécz E, Nève G, Biffin E, Gardner MG (2012) Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species. PLoS One 7: e40861. doi:10.1371/journal.pone. 0040861.
56. Tóth G, Gáspári Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10: 967-981. (Pubitemid 30608632)
57. Kumpatla SP, Mukhopadhyay S (2005) Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. 998: 985-998. doi:10.1139/G05-060.
58. Splicing PRNA, Coleman TP, Roesser JR, Commonwealth V, Uni V, et al. (1998) RNA Secondary Structure: An Important cis -Element in Rat Calcitonin/CGRP: 15941-15950.
59. Novaes E, Drost DR, Farmerie WG, Jr GJP, Grattapaglia D, et al. (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. 14: 1-14. doi:10.1186/1471-2164-9-312.
60. Chagné D, Crowhurst RN, Troggio M, Davey MW, Gilmore B, et al. (2012) Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS One 7: e31745. doi:10.1371/journal.pone.0031745.
61. Lijavetzky D, Cabezas JA, Ibáñez A, Rodríguez V, Martínez-Zapater JM (2007) High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology. BMC Genomics 8: 424. doi:10.1186/1471-2164-8-424.
62. Pootakham W, Chanprasert J, Jomchai N, Sangsrakru D, Yoocha T, et al. (2011) Single nucleotide polymorphism marker development in the rubber tree, Hevea brasiliensis (Euphorbiaceae). Am J Bot 98: e337-8. doi:10.3732/ajb. 1100228.
63. Salgado LR, Koop DM, Pinheiro DG, Rivallan R, Le Guen V, et al. (2014) De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers. BMC Genomics 15: 236. doi:10.1186/1471-2164-15- 236.
64. Allegre M, Argout X, Boccara M, Fouet O, Roguet Y, et al. (2012) 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. DNA Res 19: 23-35. doi:10.1093/dnares/dsr039.
65. Neale DB, Kremer A (2011) Forest tree genomics: growing resources and applications. Nat Rev Genet 12: 111-122. doi:10.1038/nrg2931.
66. Souza LM, Mantello CC, Santos MO, Goncalves PS, Souza A (2009) Microsatellites from rubber tree (Hevea brasiliensis) for genetic diversity analysis and cross-amplification in six Hevea wild species. Conserv Genet Resour 1: 75-79.
67. Le Guen, V Gay, C Xiong, T C., Souza, L M., Rodier-Goud M. and Seguin M (2011) Development and characterization of 296 new polymorphic microsatellite markers for rubber tree (Hevea brasiliensis). Plant Breed 130: 294-296.
68. Hirakawa H, Shirasawa K, Ohyama A, Fukuoka H, Aoki K, et al. (2013) Genome-wide SNP genotyping to infer the effects on gene functions in tomato. DNA Res 20: 221-233. doi:10.1093/dnares/dst005.