Genetic Diversity and Population Structure of the Endangered Ulmus villosa in Pakistan Revealed by DNA Barcode Markers

Abstract

Ulmus villosa Brandis ex Gamble, an economically and ecologically important forest tree, is native to the western Himalayas of Pakistan. The long pressure imposed by unsustainable utilization and market demands has resulted in the rapid decline of the U. villosa population in the wild. To date, very limited information on the genomic diversity of U. villosa is available and this can tremendously limit our understanding of distribution and future conservation of U. villosa. Therefore, the current study aimed to assess genetic diversity within U. villosa wild populations of the Hazara Division using four barcoding markers (i.e., rbcL, matK XF + 5R, matK 390F + 1326R and trnH-psbA). A total of six high quality sequences were obtained with rbcL, four with matK XF + 5R, four with matK 390F + 1326R, and fourteen with trnH-psbA. The sequenced regions contained insertions and deletions as well as several SNPs across the length of sequences, and PCR-based markers may be developed from these novel SNPs markers. The phylogenetic results supported the polyphyletic origin of the genus Ulmus, and the data indicated that multiple speciation events may have led to the evolution of U. villosa in this region. For deeper understanding of the origin and evolution of U. villosa, sequencing of the complete nuclear and chloroplast genomes will be pivotal. The results herein provide novel insights into the genomic diversity as well as phylogenetic relationships of U. villosa with other species, and may facilitate both in situ and ex situ conservation efforts for this endangered species.