Genetic and genomic diversity of Xylia xylocarpa trees from Thailand

Whole genome sequencing was combined with targeted sequencing of amplified fragments to study the diversity of Xylia xylocarpa trees across Thailand.Whole genome sequencing was done for 6 trees. Genome size of Xylia xylocarpa (Fabaceae, Mimosoideae) is about 500 Mb. Heterozygosity is high. Eight gene coding loci were PCR amplified from 550 trees and analysed by Single Strand Conformational Polymorphism to reveal the different alleles in the populations. All alleles were also sequenced by Sanger sequencing to confirm the polymorphisms. From 10 to 33 alleles were identified for the loci. The effective number of alleles was much lower, ranging between 1.1 and 7.6, as several of the alleles were found at low frequency in just one or a small number of populations. Several loci showed deviation from the Hardy–Weinberg equilibrium. A high level of gene flow was estimated. The largest genetic distances calculated according to Nei (G st) and Jost (D est) were found between populations from the northeast and the west of Thailand. STRUCTURE analysis revealed support for population differentiation in two or three clusters, though genetic distances between the clusters were small.https://doi.org/10.1007/s11295-014-0825-y