AUTHOR=Zhan Min , Xue Ling , Zhou Jian-Jun , Zhang Qiang , Qin Xin-Mei , Liao Xiao-Wen , Wu Lei , Monro Alexander K. , Fu Long-Fei 

TITLE=Polyphyly of Boehmeria (Urticaceae) congruent with plastome structural variation

JOURNAL=Frontiers in Plant Science

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1297499

DOI=10.3389/fpls.2024.1297499

ISSN=1664-462X

ABSTRACT=<p><italic>Boehmeria</italic> is a taxonomically challenging group within the nettle family (Urticaceae). The polyphyly of the genus has been proposed by previous studies with respect to five genera (<italic>Debregeasia</italic>, <italic>Cypholophus</italic>, <italic>Sarcochlamys</italic>, <italic>Archiboehmeria</italic>, and <italic>Astrothalamus</italic>). Extensive homoplasy of morphological characters has made generic delimitation problematic. Previous studies in other plant groups suggest that plastome structural variations have the potential to provide characters useful in reconstructing evolutionary relationships. We aimed to test this across <italic>Boehmeria</italic> and its allied genera by mapping plastome structural variations onto a resolved strongly supported phylogeny. In doing so, we expanded the sampling of the plastome to include <italic>Cypholophus</italic>, <italic>Sarcochlamys</italic>, <italic>Archiboehmeria</italic>, and <italic>Astrothalamus</italic> for the first time. The results of our phylogenomic analyses provide strong support for <italic>Sarcochlamys</italic> as being more closely related to <italic>Leucosyke puya</italic> than to <italic>Boehmeria</italic> and for the clustering of <italic>Boehmeria</italic> s.l. into four subclades. The sizes of the plastomes in <italic>Boehmeria</italic> s.l. ranged from 142,627 bp to 170,958 bp. The plastomes recovered a typical quadripartite structure comprising 127~146 genes. We observe several obvious structural variations across the taxa such as gene loss and multiple gene duplication, inverted repeat (IR) contraction and wide expansions, and inversions. Moreover, we recover a trend for these variations that the early clades were relatively conserved in evolution, whereas the later diverging clades were variable. We propose that the structural variations documented may be linked to the adaptation of <italic>Boehmeria</italic> s.l. to a wide range of habitats, from moist broadleaf forests in Asia to xeric shrublands and deserts in Africa. This study confirms that variation in plastome gene loss/duplication, IR contraction/expansion, and inversions can provide evidence useful for the reconstruction of evolutionary relationships.</p>