Fig. 4: Analysis of the REF/SRPP gene cluster in Hevea.

a Copy number of REF/SRPP genes in 152 plant genomes, including 11 from four Hevea species (Hevea), 7 from seven Euphorbiaceae genera other than Hevea (Eup), 122 from 90 angiosperm families other than Euphorbiaceae (Ang), and 12 from six gymnosperm families (Gym). Solid circles represent the gene number, and see Fig. 3e legend for box blot details. Significance was determined using a two tailed t-test. b Diagram of the 190-kb genomic REF/SRPP cluster in H. brasiliensis RY73397 chr02 (middle panel). Assembly authenticity is validated by RNA-seq (upper panel) of three tissues and genomic (lower panel) reads mapping. Red solid boxes depict the SRPP/REF gene models, and blue and green boxes depict other genes. The SRPP/REF gene models 1-13 are SRPP11, SRPP9, SRPP8, SRPP1, REF7, SRPP3, REF3, REF4, REF1, RFE9, REF8, REF5, and SRPP5, respectively. See supplementary Data 13 for details. c The genomic region flanking the Hb REF/SRPP cluster in chr02 is highly collinear with regions in another Hb chr07 and the V. vinifera chr14. The chromosome karyotypes are plotted with JCVI, and grey lines indicate background collinearity. In the close-up view, the REF/SRPP genes are shown in red boxes. d Collinearity plots of the REF/SRPP cluster locus from 11 representative plant species, i.e., Hb, Hbe, Hn, Hp, M. esculenta (Me), R. communis (Rc), J. curcas (Jc), P. trichocarpa (Pt), A. thaliana (At), V. vinifera (Vv) and A. trichopoda (Atr). Red boxes indicate the REF/SRPP orthologues in each species. Collinear gene pairs were shown in red (REF/SRPPs) or grey (other genes). e Postulated evolution of the REF/SRPP cluster genes (right) according to their phylogenic tree (left) and genomic locations as in b. The cassava orthologue Manes.09G170000.1.v7.1 as shown in d was used as the outgroup. f log₂FPKM expressions of the REF/SRPP cluster genes in latex (Lx), leaf (Lf), and bark (Bk) of four Hevea species. Gray circles indicate the absence of corresponding genes. g Latex yield dynamics with successive tapping of virgin rubber trees. Results are the means ± SD from 3 biological replicates. h Expression dynamics of the top four laticifer-dominant REF/SRPP isoforms in three cultivars across the first, third, fifth, seventh, and ninth tappings. Two-tailed Pearson’s correlations (insets) were calculated between yield and gene expression with the confidence interval 95%. Source data are provided as a Source Data file.