Supporting data for "Chromosome-scale assemblies of three Ormosia species: Repetitive sequences distribution and structural rearrangement"

The genus <i>Ormosia</i> is in Fabaceae family. China is one of its centers with almost all of its species endemic, suggesting need for genomic studies to understand its evolution and help its conservation and usage. Therefore, the chromosome-scale assembly of <i>O. purpureiflora</i> was performed, and that for <i>O. emarginata</i> and <i>O. semicastrata</i> were updated. <br>The genome assembly sizes of the three species varied from 1.42 to 1.58 Gb, and <i>O. purpureiflora</i><em> </em>was the largest. Repeats accounted for 74.076.3% of sequences in the assemblies; the predicted genes varied from 50,517 to 55,061. <br>Repeats contributed largely to the <i>Ormosia</i> chromosome architectures, in which Helitron and Terminal Inverted Repeat (TIR) were associated with gene distribution, while <i>Gypsy</i> and unknown LTR were related to structural rearrangements. <br><i>Ormosia</i> contained substantial resistance (<i>R</i>) genes but fewer transcription factor genes. Alkaloid-, terpene- and flavonoid-related genes were found with tandem or proximal duplications. Some growth- and defense-related genes were missed in <i>O. purpureiflora</i>. <br>By resequencing 153 genotypes (~30 Gb data each) in 6 <i>O. purpureiflora</i> (sub)populations, 276,854 high-quality single nucleotide polymorphisms (SNPs) were identified, in which 2632 were presumably adaptive SNPs, and their function was mainly related to carbohydrate metabolism. High genetic diversity in <i>O. purpureiflora</i> was revealed even though it had very small populations. A weak and absent spatial genetic structures indicating high pollen flows within/among the (sub)populations. An approximately 30-Mb region on chromosome 5 was found to likely be under balancing selection. <br>The <i>Ormosia</i> assemblies provide valuable resources for evolutionary study, conservation and utility in both <i>Ormosia</i> and Fabaceae.