The chromosome-level draft genome of Dalbergia odorifera.

BACKGROUND

Dalbergia odorifera T. Chen (Fabaceae) is an International Union for Conservation of Nature red-listed tree. This tree is of high medicinal and commercial value owing to its officinal, insect-proof, durable heartwood. However, there is a lack of genome reference, which has hindered development of studies on the heartwood formation.

FINDINGS

We presented the first chromosome-scale genome assembly of D. odorifera obtained on the basis of Illumina paired-end sequencing, Pacific Biosciences single-molecule real-time sequencing, 10x Genomics linked reads, and Hi-C technology. We assembled 97.68% of the 653.45 Mb D. odorifera genome with scaffold N50 and contig sizes of 56.16 and 5.92 Mb, respectively. Ten super-scaffolds corresponding to the 10 chromosomes were assembled, with the longest scaffold reaching 79.61 Mb. Repetitive elements account for 54.17% of the genome, and 30,310 protein-coding genes were predicted from the genome, of which ∼92.6% were functionally annotated. The phylogenetic tree showed that D. odorifera diverged from the ancestor of Arabidopsis thaliana and Populus trichocarpa and then separated from Glycine max and Cajanus cajan.

CONCLUSIONS

We sequence and reveal the first chromosome-level de novo genome of D. odorifera. These studies provide valuable genomic resources for the research of heartwood formation in D. odorifera and other timber trees. The high-quality assembled genome can also be used as reference for comparative genomics analysis and future population genetic studies of D. odorifera.