Identification and Characterization of Genes Associated With Wood Property Traits via Genome Sequencing in Fast-Growing Species of Genus Neolamarckia.

The Neolamarckia (Rubiaceae) genus is composed of only two species: N. cadamba and N. macrophylla. Both species are fast-growing plants with significant industrial and medicinal values. Here, we provided a high-quality chromosome-level assembly of the N. macrophylla genome for the first time. The assembled genome size was approximately 598.43 Mb, with contig N50 and scaffold N50 lengths of 23.41 and 24.54 Mb, respectively. The two species diverged at 6.5-23.5 Mya and one whole-genome duplication (WGD) event was detected to occur prior to their divergence. The assembled genomes showed that N. macrophylla had fewer protein-coding genes (34,411 vs. 35,461) but substantially more expanded gene families than N. cadamba. Most expanded gene families were under purifying selection in both N. macrophylla and N. cadamba. We identified genes associated with seven wood property traits of N. cadamba through GWAS based on resequencing datasets of 204 trees in total collected from a provenance trial, with 100 newly resequenced trees at age 12 and 104 previously resequenced trees at age 7. Almost all identified candidate genes were under purifying selection. Further analysis indicated that genes encoding 11 key enzymes in the lignin biosynthesis pathway were under purifying selection between N. cadamba and N. macrophylla. The overall results imply that strong selection effectively impeded evolutionary divergence between the two species in genes associated with wood property traits. The study provides insights into genes regulating wood property traits of industrial values, and a useful genomic resource for developing molecular markers for breeding Neolamarckia varieties.