Open Access Highly Accessed Research article

Draft genome sequence of the rubber tree Hevea brasiliensis

Ahmad Yamin Abdul Rahman1, Abhilash O Usharraj1, Biswapriya B Misra1, Gincy P Thottathil1, Kandakumar Jayasekaran1, Yun Feng2, Shaobin Hou3, Su Yean Ong1, Fui Ling Ng1, Ling Sze Lee1, Hock Siew Tan1, Muhd Khairul Luqman Muhd Sakaff1, Beng Soon Teh1, Bee Feong Khoo1, Siti Suriawati Badai1, Nurohaida Ab Aziz1, Anton Yuryev4, Bjarne Knudsen5, Alexandre Dionne-Laporte39, Nokuthula P Mchunu6, Qingyi Yu7, Brennick J Langston7, Tracey Allen K Freitas108, Aaron G Young3, Rui Chen2, Lei Wang2, Nazalan Najimudin1, Jennifer A Saito1* and Maqsudul Alam138*

Author Affiliations

1 Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia

2 TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, China

3 Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, USA

4 Ariadne Genomics Inc., Rockville, Maryland, USA

5 CLC bio, Aarhus, Denmark

6 Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa

7 AgriLife Research Center, Department of Plant Pathology and Microbiology, Texas A&M University System, Weslaco, Texas, USA

8 Department of Microbiology, University of Hawaii, Honolulu, Hawaii, USA

9 Current address: Centre of Excellence in Neuromics of Université de Montréal, Centre Hospitalier de l'Université de Montréal Research Center, Montréal, Québec, Canada

10 Current address: Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA

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BMC Genomics 2013, 14:75  doi:10.1186/1471-2164-14-75

Published: 2 February 2013

Additional files

Additional file 1: Table S1:

Construction of genomic libraries, generation and filtering of sequencing data used for genomic assembly. Table S2. Scaffolds showing the associated genes anchored on to the respective linkage groups based on the reported molecular markers. Table S3. Main classes of repeat elements in the H. brasiliensis genome assembly. Table S4. Summary statistics of gene models predicted by seven programs. Table S5. Comparison of publicly available H. brasiliensis transcripts with the genome. Table S6. General features of the transcriptome assembly. Table S7. Functional annotation of predicted proteins for H. brasiliensis. Table S8. Comparison of KOG functions across various sequenced plant genomes. Table S9. Pfam domains in the H. brasiliensis genome. Table S10. Predicted subcellular localization of H. brasiliensis gene models based on SignalP 3.0 analysis. Table S11. tRNA types found in the H. brasiliensis genome. Table S12. Gene Ontology (GO) analysis of Hevea specific genes. Table S13. InterPro domains within the Hevea specific lineage. Table S14. Pfam domains within the Hevea specific lineage. Table S15. KOG analysis of Hevea specific genes. Table S16. Rubber biosynthesis related genes in the H. brasiliensis genome. Table S17. Rubber biosynthesis related genes of H. brasiliensis in comparison to Parthenium argentatum (guayule) ESTs. Table S18. Lignocellulose biosynthetic genes of H. brasiliensis in comparison to other sequenced genomes. Table S19. Putative NBS-coding R genes of H. brasiliensis in comparsion to other sequenced genomes. Table S20. Pathogenesis-related proteins of H. brasiliensis in comparison with other genomes. Table S21. Systemic acquired resistance (SAR) and hypersensitive response (HR) related genes found in the H. brasiliensis genome. Table S22. Latex allergens in the H. brasiliensis genome. Table S23. Non-latex allergens in the H. brasiliensis genome. Table S24. Transcription factors present in H. brasiliensis in comparison to other sequenced plant genomes. Table S25. Genes involved in phytohormone metabolism, signaling and regulatory events represented in the H. brasiliensis genome. Table S26. Circadian clock and light signaling gene families from Hevea in comparison to Populus and Arabidopsis. Table S27. Major genes involved in carotenoid biosynthesis in H. brasiliensis and A. thaliana.

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Additional file 2: Figure S1:

Linkage map of H. brasiliensis showing 18 linkage groups with 143 anchored scaffolds corresponding to the reported 154 microsatellite markers. Figure S2. Complete network of rubber biosynthesis in H. brasiliensis. Figure S3. Lignin biosynthesis. Figure S4. Systemic acquired resistance pathway. Figure S5. Hypersensitive response. Figure S6. Auxin biosynthesis. Figure S7. Auxin signaling pathway. Figure S8. Zeatin biosynthesis. Figure S9. Cytokinin signaling pathway. Figure S10. Gibberellin biosynthesis. Figure S11. Gibberellin signaling pathway. Figure S12. Ethylene biosynthesis. Figure S13. Ethylene signaling pathway. Figure S14. Brassinosteroid biosynthesis. Figure S15. Brassinosteroid signaling pathway. Figure S16. Jasmonic acid biosynthesis. Figure S17. Salicylic acid biosynthesis. Figure S18. Carotenoid biosynthesis.

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