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.

A Dated Phylogeny of the Pantropical Genus Dalbergia L.f. (Leguminosae: Papilionoideae) and Its Implications for Historical Biogeography

“…Our estimated stem age of Dalbergia (c. 40.7 Ma) is largely consistent with the c. 40.4-43.0 Ma estimated by Lavin et al (2005) [37] which was based on the whole legumes family. However, our estimated crown age (c. 22.9 Ma; Early Miocene; see node 2, Figure 2) for Dalbergia is much older than c. 14.7 Ma (Middle Miocene) inferred by Hung et al (2020) [38], who only sampled six representative species from the most basal Clade I and other clades of Dalbergia. Additionally, the use of different fossil calibrations probably contributed to the difference in the estimation of crown age between the two studies.…”

Opportunities in phytochemistry, ecophysiology and wood research via laser ablation direct analysis in real time imaging‐mass spectrometry

“…Nevertheless, it tends to be harvested illegally for use in the fashioning of furniture and musical instruments. The Dalbergia genus is comprised of more than 250 species (Hung et al ., 2020), and while wood anatomy can be readily used to identify a given timber as a member of the genus, it can be much more difficult to use this technique to distinguish between species within the genus. The ability to do so is important because, while all the species in the genus are CITES regulated, the penalties associated with illegal trade differ depending upon the specific CITES designation.…”

Characterization of the complete chloroplast genome sequences of six Dalbergia species and its comparative analysis in the subfamily of Papilionoideae (Fabaceae)

“…Therefore, these species have been suffering from fast-evolving threats that have led to a major decline in wild populations ( Winfield, Grayson & Scott, 2016 ). Aiming to enhance the worldwide protection of rosewood species, an updated list of Dalbergia species has been adopted by CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora) since 2017, which will support better protection for the diversity and health of rosewood populations ( Hung et al, 2020 ). A complete infrageneric classification of the Dalbergia genus has been built by Bentham ( George & Bentham, 1860 ), but a wide range of species and distribution makes it difficult to perform a comprehensive investigation ( Carvalho, 1997 ; Chen, Zhang & Larsen, 2010 ; Niyomdham, 2002 ; Prain, 1904 ; Sunarno & Ohashi, 1997 ; Thothathri, 1987 ; Win, 2020 ).…”