Genome analysis of Hevea species: H. nitida and H. spruceana for rubber improvement 2019 Sept. 30 to Oct. 1 International Rubber Conference at Nay Pyi Taw Myanmar Hevea species 1. : Euphobiaseae 1. : Hevea 1. Hevea brasiliensis 2. Hevea benthamiana 3. Hevea camporum 4. Hevea guianensis 5. Hevea microphylla 6. Hevea nitida 7. Hevea pauciflora 8. Hevea rigidiflora 9. Hevea spruceana
10. Hevea camargoana Drawing of the leaves and flowers Photograph by: Martius, C., Eichler, A.G., Urban, I., Flora Brasiliensis, vol. 11(2): fasicle 64, p. 299, t. 44 (1874) For latex productivity and disease resistance
H. brasiliensis H. spruceana H. nitida Hevea species distribution
Latex SALB (M. ulei)
H. brasiliensis Main Susceptible commercial source
H. nitida Anti- Not infected coagulant naturally latex
H. spruceana Watery and Susceptible Low quality (high proportion of resin) 5 Statistics of SNP analysis Latex from Hevea brasiliensis
SRPP IPP REF CPT
Natural rubber (cis-polyisoprene)
ProsOne 2012 e048065 CPT, SRPP, REF Proteins
Significant expansion of rubber biosynthesis-related genes in the Latex biosynthesis gene families genome correlates with the capacity to produce high levels of latex.
Phylogenic analysis of CPT protein Phylogenic analysis of SRPP and REF protein family families Possible nonsense mutations in H. nitida and H. spruceana in comparison with RRIM 600
H-brasiliensis Gene ID Function RRIM600 H-nitida H-spruceana (Brazil) - Hb_000548_030 CPT_1 - - - - Hb_005628_050 CPT_2 - - - - Hb_005686_130 CPT_3 - - - - Hb_000313_080 CPT_4 - - - - Hb_000539_030 CPT_5 - - - - Hb_000120_870 CPT_6 - - - stop Hb_001999_050 CPT_7 - - - - Hb_003411_090 CPTL - - - - Hb_100414_010 REF_1 - - - - Hb_149683_010 REF_2 - - - - Hb_001741_030 REF_3 - - - - Hb_000313_100 REF_4 - - - - Hb_152868_010 REF_5 - - - - Hb_001741_090 REF_6 - - - - Hb_001741_100 REF_7 - stop - - Hb_001741_040 REF_8 - stop - stop Hb_001723_060 REF_9 - - - - Hb_001741_080 SRPP_1 - - - - Hb_000613_200 SRPP_2 - stop - stop Hb_021596_070 SRPP_3 - - - - Hb_002016_040 SRPP_4 - stop stop - Hb_000617_260 SRPP_5 - - - - Hb_000345_040 SRPP_6 - stop - - Hb_001741_110 SRPP_7 - stop - - Hb_001741_070 SRPP_8 - - stop stop Possible nonsense mutations in H. nitida and H. spruceana in compared with RRIM600
Function RRIM600 H-brasiliensis H-nitida H-spruceana (Brazil) Hb_000184_040 AACT_1 (MVA_pathway) - - - - Hb_000371_100 AACT_2 (MVA_pathway) - - - - Hb_000608_190 AACT_3 (MVA_pathway) - - stop - Hb_000721_030 AACT_4 (MVA_pathway) - - - - Hb_000116_530 HMGR_1 (MVA_pathway) - - - - Hb_001123_160 HMGR_2 (MVA_pathway) - - - - Hb_003397_030 HMGR_3 (MVA_pathway) - - - - Hb_012796_050 HMGR_4 (MVA_pathway) - - - - Hb_134789_010 HMGR_5 (MVA_pathway) - stop stop stop Hb_000107_440 HMGS_1 (MVA_pathway) - - - - Hb_002876_240 HMGS_2 (MVA_pathway) - stop stop - Hb_000453_240 MDC_1 (MVA_pathway) - - - - Hb_000645_180 MDC_2 (MVA_pathway) - - - - Hb_142382_010 MK_1 (MVA_pathway) - stop stop stop Hb_029142_030 MK_2 (MVA_pathway) - - - - Hb_124247_030 MK_3 (MVA_pathway) - - - - Hb_000635_200 OLD_1 (MVA_pathway) - - - - Hb_001638_290 OLD_2 (MVA_pathway) - - - - Hb_002042_080 OLD_3 (MVA_pathway) - - - - Hb_011224_160 OLD_4 (MVA_pathway) - - - - Hb_000963_090 PD_1 (MVA_pathway) - - - - Hb_001153_150 PD_2 (MVA_pathway) - - - - Hb_001500_040 PD_3 (MVA_pathway) - - - - Hb_003185_080 PD_4 (MVA_pathway) - - - - Hb_006070_010 PD_5 (MVA_pathway) - - - - Hb_024714_090 PD_6 (MVA_pathway) - - - - Hb_116349_100 PD_7 (MVA_pathway) - - - - Hb_127194_010 PD_8 (MVA_pathway) - - - stop Hb_000110_310 PDC_1 (MVA_pathway) - - - - Hb_000207_300 PDC_2 (MVA_pathway) - - stop stop Hb_000795_060 PDC_3 (MVA_pathway) - - stop stop Hb_002217_100 PDC_4 (MVA_pathway) - - - - Hb_002759_250 PDC_5 (MVA_pathway) - - stop - Hb_003207_110 PDC_6 (MVA_pathway) - - - - Hb_004032_440 PDC_7 (MVA_pathway) - - - - Hb_002477_290 PMK_1 (MVA_pathway) - - - - Hb_115919_020 PMK_2 (MVA_pathway) - stop stop stop SNP analysis
SNP location
• SNP in CDS is less than 5%. • Genic region has 17% SNP while intergenic region is 67%. SRPP/REF gene cluster
H. brasiliensis
Scaffold345 Scaffold1741
V V V V V V
Inter chromosomal translocation V: deletions Intra chromosomal translocation
H. nitida 10K 30K 50K 70K 90K 110K 130K 150K
Collaboration with EMBRAPA Manaus, BRAZIL 12 Acknowledgement
• We thank Mr. Mohd Adi Faiz Ahmad Fauz in MRB for providing us Hevea species photos.
Collaboration
• Embrapa Amazônia Ocidental, Manaus, Amazonas, Brazil – Prof. Everton Rabelo Cordeiro – Prof. Aleksander Muniz – Dr. Gilvan Ferreira da Silva
• RIKEN – Yuko Makita – Mika Kawashima