Analysis genetic variation and phylogenetic relationships of local lotus collected in Thua Thien hue province, Vietnam by DNA barcoding

Abstract

Universal conventional DNA barcodes will become more and more popular in plant species using short sequences of chloroplast DNA identifications. DNA mini-barcode is a solution for such specific purposes. Here we exemplify how to develop the best minibarcodes for specific taxa using the Nelumbo nucifera as an example. Six chloroplast DNA regions (accDpsaI, ndhA, psbE-petL, Rpl32-trnL, trnW – psaJ, trnSGCU-trnGGCC) were tested for their suitability as DNA barcoding regions of thirty three lotus samples (white and pink) which were collected in Thua Thien Hue province, Vietnam. Universal primers were used and sequenced products were analyzed using Minimum Evolution method in the MEGA X program. The sequences accD-psaI; ndhA and psbE-petL did not show any variable sites and none of the regions used in the study allowed the division of white and pink lotus varieties of N. nucifera species according to the adopted classification of the genus Nelumbo. The results confirm that the use of individual six gene regions or combining all six regions together is insufficient for DNA barcoding in white and pink lotus varieties of N. nucifera species. The neutrality tests were negative values for total six gene regions, indicating an excess of rare nucleotide site variants suggesting that either population expansion or background selection has occurred. However following Fu’s Fs test, the hypothesis of netural evolution was significantly rejected for all regions of the studied lotus population. Strobeck’s S, the probability of obtaining equal or fewer haplotypes based on gene frequency and mutation rate, was low in population ranging from 0.183 to 0.549. These results are not consistent with deviation from neutrality due to either selection or population expansion. Our results also indicate the necessity of using a different region.