Abstract
In this study, RNA sequencing of several Hevea brasiliensis clones grown in Malaysia with different annual rubber production yields and disease resistance was performed on the Illumina platform. A total of 29,862,548 reads were generated, resulting in 101,269 assembled transcripts that were used as the reference transcripts. A similarity search against the non-redundant (nr) protein databases presented 83,771 (83%) positive BLASTx hits. The transcriptome was annotated using gene ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Pfam database. A search for putative molecular markers was performed to identify single-nucleotide polymorphisms (SNPs). Overall, 3,210,629 SNPs were detected and a total of 1314 SNPs associated with the genes involved in MVA and MEP pathways were identified. A total of 176 SNP primer pairs were designed from sequences that were related to the MVA and MEP pathways. The transcriptome of RRIM 3001 and RRIM 712 were subjected to pairwise comparison and the results revealed that there were 1262 significantly differentially expressed genes unique to RRIM 3001, 1499 significantly differentially expressed genes unique to RRIM 712 and several genes related to the MVA and MEP pathways such as AACT, HMGS, PMK, MVD, DXS and HDS were included. The results will facilitate the characterization of H. brasiliensis transcriptomes and the development of a new set of molecular markers in the form of SNPs from transcriptome assembly for the genotype identification of various rubber varieties with superior traits in Malaysia.
Data availability
The raw reads for this project have been deposited in the NCBI Genbank Bioproject under the accession number PRJNA511923.
References
Allegre M, Argout X, Boccara M, Fouet O, Roguet Y, Bérard A, Thévenin JM, Chauveau A, Rivallan R, Clement D, Courtois B, Gramacho K, Boland-Augé A, Tahi M, Umaharan P, Brunel D, Lanaud C (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. https://doi.org/10.1093/dnares/dsr039
Berthelot K, Lecomte S, Estevez Y, Benedicte CS, Bentaleb A, Cullin C, Deffieux A, Peruch F (2012) Rubber elongation factor (REF), a major allergen component in Hevea brasiliensis latex has amyloid properties. PLoS One 7(10):e48065. https://doi.org/10.1371/journal.pone.0048065
Chandra SS, Liljas A (2000) The end of the beginning: structural studies of ribosomal proteins. Curr Opin Struct Biol 10(6):633–636. https://doi.org/10.1016/S0959-440X(00)00143-3
Chow KS, Mat Isa MN, Bahari A, Ghazali AK, Alias H, Zainorlina MZ, Hoh CC, Wan KL (2012) Metabolic routes affecting rubber biosynthesis in Hevea brasiliensis latex. J Exp Bot 63:1863–1871. https://doi.org/10.1093/jxb/err363
Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676. https://doi.org/10.1093/bioinformatics/bti610
Cornish K (2001) Similarities and differences in rubber biochemistry among plant species. Phytochemistry 57(7):1123–1134. https://doi.org/10.1016/S0031-9422(01)00097-8
Duan CF, Rio M, Leclercq J, Bonnot F, Oliver G, Montoro P (2010) Gene expression pattern in response to wounding, methyl jasmonate and ethylene in the bark of Hevea brasiliensis. Tree Physiol 30(10):1349–1359. https://doi.org/10.1093/treephys/tpq066
Duan C, Argout X, Gebelin V, Summo M, Dufayard JF, Leclerq J et al (2013) Identification of the Hevea brasiliensis AP2/ERF superfamily by RNA sequencing. BMC Genomics 14:30. https://doi.org/10.1186/1471-2164-14-30
Gao JS, Meng Y, Sasaki N, Kanegae H, Hayashi N, Nyunoya H (2010) Characterization and cloning of TMV resistance gene N homologues from Nicotiana tabacum. Afr J Biotech 9(47):7998–8006. https://doi.org/10.5897/AJB10.732
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I et al (2011) Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nat Biotechnol 29(7):644–652. https://doi.org/10.1038/nbt.1883
Gronover CS, Wahler D, Prufer D (2011) Natural rubber biosynthesis and physic-chemical studies on plant derived latex. In: Elnashar M (ed) Biotechnology of biopolymers, InTech, Croatia, pp 75–88. http://www.intechopen.com/books/biotechnology-of-biopolymers/natural-rubber-biosynthesis-and-physic-chemical-studies-on-plant-derived-latex
Hayashi Y (2009) Production of natural rubber from Para rubber tree. Plant Biotechnology 26:67–70. https://doi.org/10.5511/plantbiotechnology.26.67
Hirakawa H, Shirasawa K, Ohyama A, Fukuoka H, Aoki K, Rothan C, Sato S, Isobe S, Tabata S (2013) Genome-wide SNP genotyping to infer the effects on gene functions in tomato. DNA Res 20(3):221–233. https://doi.org/10.1093/dnares/dst005
Horemans N, Foyer CH, Potters G, Asard H (2000) Ascorbate function and associated transport systems in plants. Plant Physiol Biochem 38(7–8):531–540. https://doi.org/10.1016/S0981-9428(00)00782-8
Hu J, Baker A, Bartel B, Linka N, Mullen RT, Reumann S, Zolman BK (2012) Plant peroxisomes: biogenesis and function. Plant Cell 24:2279–2303. https://doi.org/10.1105/tpc.112.096586
Kharel Y, Koyama T (2003) Molecular analysis of cis-prenyl chain elongating enzymes. Natural Prod Rep 20:111–118. https://doi.org/10.1039/B108934J
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(9):2317–2325. https://doi.org/10.1093/jxb/erq058
Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK (2012) Varscan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 22(3):568–576. https://doi.org/10.1101/gr.129684.111
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie2. Nat Methods 9:357–359
Lau NS, Makita Y, Kawashima M, Taylor TD, Kondo S, Othman AS, Alexander CSC, Matsui M (2016) The rubber tree genome shows expansion of gene family associated with rubber biosynthesis. Sci Rep. https://doi.org/10.1038/srep28594
Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658–1659. https://doi.org/10.1093/bioinformatics/btl158
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25(16):2078–2079. https://doi.org/10.1093/bioinformatics/btp352
Li R, Wang W, Wang W, Li F, Wang Q, Xu Y, Wang S (2015) Overexpression of a cysteine proteinase inhibitor gene from Jatropha curcas confers enhanced tolerance to salinity stress. Electron J Biotechnol 18(5):368–375. https://doi.org/10.1016/j.ejbt.2015.08.002
Lichtenthaler HK, Schwender J, Disch A, Rohmer M (1997) Biosynthesis of isoprenoids in higher plant chloroplasts proceeds via a mevalonate-independent pathway. FEBS Lett 400(3):271–274. https://doi.org/10.1016/S0014-5793(96)01404-4
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25:402–408. https://doi.org/10.1006/meth.2001.1262
Loh SC, Thottathil GP, Othman AS (2016) Identification of differentially expressed genes and signalling pathways in bark of Hevea brasiliensis seedlings associated with secondary laticifer differentiation using gene expression microarray. Plant Physiol Biochem 107:45–55. https://doi.org/10.1016/j.plaphy.2016.05.011
Mantello CC, Cardoso-Silva CB, da Silva CC, de Souza LM, Junior EJS, Gonçalves PDS, Vicentini R, de Souza AP (2014) De novo assembly and transcriptome analysis of the rubber tree (Hevea brasiliensis) and SNP markers development for rubber biosynthesis pathways. PLoS One 9(7):e102665. https://doi.org/10.1371/journal.pone.0102665
Mokryakova MV, Pogorelko GV, Bruskin SA, Piruzian ES, Abdeeva IA (2014) The role of peptidyl-prolyl cis/trans isomerase genes of Arabidopsis thaliana in plant defense during the course of Xanthomonas campestris infection. Russ J Genetics 50(2):140–148
Mooibroek H, Cornish K (2000) Alternatives sources of natural rubber. Appl Microbiol Biotechnol 53(4):355–365. https://doi.org/10.1007/s002530051627
Putranto RA, Duan C, Kuswanhadi TC, Rio M, Piyatrakul P et al (2015) Ethylene response factors are controlled by multiple harvesting stresses in Hevea brasiliensis. PLoS One 10(4):e0123618. https://doi.org/10.1371/journal.pone.0123618
Rahman AYA, Usharraj AO, Misra BB, Thottathil GP, Jayasekaran K, Feng Y et al (2013) Draft genome sequence of the rubber tree Hevea brasiliensis. BMC Genomics 14:75. https://doi.org/10.1186/1471-2164-14-75
Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140. https://doi.org/10.1093/bioinformatics/btp616
Rohmer M, Seemann M, Horbach S, Bringer-Meyer S, Sahms H (1996) Glyceraldehyde 3-phosphate and pyruvate as precursors of isoprenic units in an alternative non-mevalonate pathway for terpenoid biosynthesis. J Am Chem Soc 118(11):2564–2566. https://doi.org/10.1021/ja9538344
Saha T, Priyadarshan PM (2012) Genomics of Hevea rubber. In: Schnell RJ, Priyadarshan PM (eds) Genomics of tree crops. Springer, New York, pp 261–298. https://doi.org/10.1007/978-1-4614-0920-5_9
Sakdapipanich JT (2007) Structural characterization of natural rubber based on recent evidence from selective enzymatic treatments. J Biosci Bioeng 103(4):287–292. https://doi.org/10.1263/jbb.103.287
Sando T, Takeno S, Watanabe N, Okumoto H, Kuzuyama T, Yamashita A, Hattori M, Ogasawara N, Fukusaki E, Kobayashi A (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(11):2903–2917. https://doi.org/10.1271/bbb.80387
Spurgeon SL, Porter JW (1981) Biosynthesis of isoprenoid compounds. 1:1–46
Trapnell C et al (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7:562
Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC et al (2012) Primer3-new capabilities and interfaces. Nucleic Acids Res 40:e115. https://doi.org/10.1093/nar/gks596
van Beilen JB, Poirier Y (2007) Establishment of new crops for the production of natural rubber. Trends Biotechnol 25(11):522–529. https://doi.org/10.1016/j.tibtech.2007.08.009
Zdobnov EM, Apweiler R (2001) InterProScan—an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17(9):847–848. https://doi.org/10.1093/bioinformatics/17.9.847
Zhu W, Wang L, Dong Z, Chen X, Song F, Liu N, Yang H, Fu J (2016) Comparative transcriptome analysis identifies candidate genes related to skin color differentiation in red tilapia. Sci Rep 6:31347. https://doi.org/10.1038/srep31347
Acknowledgements
This project is funded by RISDA (304/PBIOLOGI/650728/P137) awarded to Ahmad Sofiman Othman of Universiti Sains Malaysia. We thank Yue Keong Choon (Universiti Sains Malaysia) for collecting the samples used in this work and Mohd Khairul Luqman Mohd Sakaf and Khairul Nasirudin Abu Mangsor (Universiti Sains Malaysia) for assisting in analysis. We also thank MyPhD15 for providing a scholarship to the first author.
Funding
Rubber Industry Smallholders Development Authority (Risda) (304/PBIOLOGI/650728/P137).
Author information
Authors and Affiliations
Contributions
SNAR and MFAB carried out the field and laboratory work including data analysis. GVS and SNAR prepared the manuscript. ASO initiated the research and designed the experiment.
Corresponding author
Ethics declarations
Conflict of interest
On behalf of all authors, the corresponding author states that there is no conflict of interest.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Abdul Rahman, S.N., Bakar, M.F.A., Singham, G.V. et al. Single-nucleotide polymorphism markers within MVA and MEP pathways among Hevea brasiliensis clones through transcriptomic analysis. 3 Biotech 9, 388 (2019). https://doi.org/10.1007/s13205-019-1921-3
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s13205-019-1921-3