Reference transcriptomes and comparative analyses of six species in the threatened rosewood genus Dalbergia

Abstract

Dalbergia is a pantropical genus with more than 250 species, many of which are highly threatened due to overexploitation for their rosewood timber, along with general deforestation. Many Dalbergia species have received international attention for conservation, but the lack of genomic resources for Dalbergia hinders evolutionary studies and conservation applications, which are important for adaptive management. This study produced the first reference transcriptomes for 6 Dalbergia species with different geographical origins and predicted ~ 32 to 49 K unique genes. We showed the utility of these transcriptomes by phylogenomic analyses with other Fabaceae species, estimating the divergence time of extant Dalbergia species to ~ 14.78 MYA. We detected over-representation in 13 Pfam terms including HSP, ALDH and ubiquitin families in Dalbergia. We also compared the gene families of geographically co-occurring D. cochinchinensis and D. oliveri and observed that more genes underwent positive selection and there were more diverged disease resistance proteins in the more widely distributed D. oliveri, consistent with reports that it occupies a wider ecological niche and has higher genetic diversity. We anticipate that the reference transcriptomes will facilitate future population genomics and gene-environment association studies on Dalbergia, as well as contributing to the genomic database where plants, particularly threatened ones, are currently underrepresented.

Figure 1

Bioinformatic pipeline of de novo transcriptome analysis and gene annotation for the 6 Dalbergia species. For the software details, see “Methods”.

Figure 2

Dated phylogeny of 16 Fabaceae species based on Bayesian analysis of a supergene from the 256 single-copy orthologs (479,064 bp) from their transcriptomes. Node bars indicate 95% CI for the estimated divergence time. Numbers on branches indicate posterior probability (1 for all branches).

Figure 3

Heatmap of annotated Pfam domains of the 13 Fabaceae species, only showing domains (n = 91) that are significantly contracted (negative) or expanded (positive) in the Dalbergia species (p < 0.05, two-tailed Fisher’s exact test of independence). See Supplementary Table 2 for species abbreviations.

Figure 4

Results of GO enrichment analysis on positively selected genes, which are single-copy orthologs, between D. cochinchinensis (N = 371, GO annotated n = 299) and D. oliveri (N = 439, GO annotated n = 361), only showing terms that are significant (p < 0.05, chi-square test of independence).