Molecular evolution and comparative genomics of highly threatened Malagasy rosewoods (Dalbergia, Fabaceae) unveil genome diversity and a fine-scale evolutionary framework.

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conclusionThis study presents the first complete plastome sequences for highly threatened Malagasy rosewood species, filling a critical genomic gap, clarifying their evolutionary relationships, and identifies polymorphic loci for molecular marker development to enhance species delimitation, and sustainable management. The biodiversity hotspot of Madagascar is not only home to many endemic species of Dalbergia but also arguably the epicenter of an escalating rosewood massacre, driven by the global demand for some of the world's most coveted tropical timbers. Malagasy rosewoods, among the planet's most valuable and endangered timbers, face extreme extinction risks as a consequence of unsustainable exploitation, illegal logging, habitat loss, mining, weak governance, ineffective regulation, corruption, and political instability, despite being listed under CITES and protected by a national decree No. 2016-801. The lack of genomic resources undermines our understanding of evolutionary relationships and hinders the crucial law enforcement required in the ongoing conservation efforts. To date, no plastome sequences have been available for Malagasy Dalbergia species, creating a significant gap in genomic resources. This study bridges this knowledge gap by presenting the first de novo assembled complete plastid genome sequences for five highly threatened Malagasy rosewoods, namely, D. monticola, D. bathiei, D. maritima, D. louvelii, and D. greveana. All plastomes exhibited classical quadripartite structure with genome sizes ranging from 153,602 to 156,580 bp. Each plastome contains 127 genes, including 83 protein-coding genes, 8 rRNA genes, and 36 tRNA gene, with several gene losses (psbL and rpl22) and gene duplications (rpl2, rpl23, rps7, and ycf2) across the plastomes. Comparative analysis identified eight hypervariable intergenic regions, and 550 polymorphic simple-sequence repeats (SSRs), forming a toolkit for species delimitation, and conservation genetics. Phylogenomic analysis, based on 118 plastomes representing 42 species generated a robust, well-resolved phylogenetic hypothesis, clarifying the previously ambiguous evolutionary relationships. The analysis revealed that Malagasy species do not form a monophylum but rather share a complex evolutionary history with geographically distant Dalbergia species. Codon-usage analysis revealed strong GC bias, whereas relaxed purifying selection in genes, such as accD, clpP, and rpl2, indicated local adaptation across Madagascar's diverse environments. These findings not only fill a critical genomic gap but also provide essential tools for enhancing conservation research, law enforcement, and sustainable management of these highly valuable taxa, and establishing a genomic framework applicable to other CITES-listed tropical timber species.