AUTHOR=Niu Zhitao , Xue Qingyun , Zhu Shuying , Sun Jing , Liu Wei , Ding Xiaoyu 

TITLE=The Complete Plastome Sequences of Four Orchid Species: Insights into the Evolution of the Orchidaceae and the Utility of Plastomic Mutational Hotspots

JOURNAL=Frontiers in Plant Science

VOLUME=8

YEAR=2017

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2017.00715

DOI=10.3389/fpls.2017.00715

ISSN=1664-462X

ABSTRACT=<p>Orchidaceae (orchids) is the largest family in the monocots, including about 25,000 species in 880 genera and five subfamilies. Many orchids are highly valued for their beautiful and long-lasting flowers. However, the phylogenetic relationships among the five orchid subfamilies remain unresolved. The major dispute centers on whether the three one-stamened subfamilies, Epidendroideae, Orchidoideae, and Vanilloideae, are monophyletic or paraphyletic. Moreover, structural changes in the plastid genome (plastome) and the effective genetic loci at the species-level phylogenetics of orchids have rarely been documented. In this study, we compared 53 orchid plastomes, including four newly sequenced ones, that represent four remote genera: <italic>Dendrobium</italic>, <italic>Goodyera</italic>, <italic>Paphiopedilum</italic>, and <italic>Vanilla</italic>. These differ from one another not only in their lengths of inverted repeats and small single copy regions but also in their retention of <italic>ndh</italic> genes. Comparative analyses of the plastomes revealed that the expansion of inverted repeats in <italic>Paphiopedilum</italic> and <italic>Vanilla</italic> is associated with a loss of <italic>ndh</italic> genes. In orchid plastomes, mutational hotspots are genus specific. After having carefully examined the data, we propose that the three loci <italic>5′trnK</italic>-<italic>rps16</italic>, <italic>trnS</italic>-<italic>trnG</italic>, and <italic>rps16</italic>-<italic>trnQ</italic> might be powerful markers for genera within Epidendroideae, and <italic>clpP</italic>-<italic>psbB</italic> and <italic>rps16</italic>-<italic>trnQ</italic> might be markers for genera within Cypripedioideae. After analyses of a partitioned dataset, we found that our plastid phylogenomic trees were congruent in a topology where two one-stamened subfamilies (i.e., Epidendroideae and Orchidoideae) were sisters to a multi-stamened subfamily (i.e., Cypripedioideae) rather than to the other one-stamened subfamily (Vanilloideae), suggesting that the living one-stamened orchids are paraphyletic.</p>