AUTHOR=Wang Ruo-Nan , Milne Richard I. , Du Xin-Yu , Liu Jie , Wu Zeng-Yuan 

TITLE=Characteristics and Mutational Hotspots of Plastomes in Debregeasia (Urticaceae)

JOURNAL=Frontiers in Genetics

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2020.00729

DOI=10.3389/fgene.2020.00729

ISSN=1664-8021

ABSTRACT=<p><italic>Debregeasia</italic> is an economically important genus of the nettle family (Urticaceae). Previous systematic studies based on morphology, or using up to four plastome regions, have not satisfactorily resolved relationships within the genus. Here, we report 25 new plastomes for Urticaceae, including 12 plastomes from five <italic>Debregeasia</italic> species and 13 plastomes from other genera. Together with the one published plastome for <italic>Debregeasia</italic>, we analyzed plastome structure and character, identified mutation hotspots and loci under selection, and constructed phylogenies. The plastomes of <italic>Debregeasia</italic> were found to be very conservative, with a size from 155,743 bp to 156,065 bp, and no structural variation. Eleven mutation hotspots were identified, including three (<italic>rpoB</italic>-<italic>trnC</italic>-<italic>GCA</italic>, <italic>trnT</italic>-<italic>GGU</italic>-<italic>psbD</italic> and <italic>ycf1</italic>) that are highly variable both within <italic>Debregeasia</italic> and among genera; these show high potential value for future DNA barcoding, population genetics and phylogenetic reconstruction. Selection pressure analysis revealed nine genes (<italic>clpP</italic>, <italic>ndhF</italic>, <italic>petB</italic>, <italic>psbA</italic>, <italic>psbK</italic>, <italic>rbcL</italic>, <italic>rpl23</italic>, <italic>ycf2</italic>, and <italic>ycf1</italic>) that may experience positive selection. Phylogenomic analyses results suggest that <italic>Debregeasia</italic> was monophyletic, and closest to <italic>Boehmeria</italic> among genera examined. Within <italic>Debregeasia</italic>, <italic>D. longifolia</italic> was sister to <italic>D. saeneb</italic>, whereas <italic>D. elliptica</italic>, <italic>D. orientalis</italic> with <italic>D. squamata</italic> formed the other subclade. This study enriches organelle genome resources for Urticaceae, and highlights the utility of plastome data for detecting mutation hotspots for evolutionary and systematic analysis.</p>