Abstract
Plastid genomes have been widely applied to elucidate plant evolution at higher taxonomic levels, but have rarely been considered useful for addressing close relationships. Here, we resolve the phylogeny and taxonomy of the Chinese lianoid Gnetum clade (Gnetales), using high throughput and Sanger sequencing techniques and studies of plant morphology. Despite previous efforts, relationships among taxa and the taxonomy within the clade have remained unclear. We generated 11 plastid genomes representing one arborescent and four lianoid species. Phylogenetic analyses were conducted using (a) the entire plastid genomes and (b) the protein-coding genes only. Sequence divergence among the lianoid species was substantial, with 9345 variable sites. Four variable regions were identified, targeted and sequenced for an additional 54 specimens and analyzed together with one nuclear ribosomal marker. Results from the phylogenetic analyses corroborate G. parvifolium as sister to the remaining lianoid species and support the presence of at least five additional species in the Chinese lianoid clade: G. catasphaericum, G. formosum, G. luofuense, G. montanum and G. pendulum. Following morphological investigations, G. giganteum and G. gracilipes are included in and synonymized with G. pendulum. Gnetum hainanense is included in and synonymized with G. luofuense. Two names, G. indicum and G. cleistostachyum, remain questionable. A taxonomic revision and a key to Chinese lianoid Gnetum are presented. Internal nodes in the Chinese lianoid Gnetum clade are from the Miocene and onwards and coincide with the expansion of tropical to subtropical forests in South China, which may have facilitated speciation in the clade.
Highlights
In recent years, next-generation sequencing (NGS) has revolutionized systematic biology and molecular ecology
Representatives of nine lianoid species (G. catasphaericum H.Shao, G. formosum Markgr., G. giganteum H.Shao, G. gracilipes C.Y.Cheng, G. hainanense C.Y.Cheng ex L.K.Fu, Y.F.Yu & M.G.Gilbert, G. luofuense C.Y.Cheng, G. parvifolium (Warb.) W.C.Cheng, G. pendulum and G. montanum) were included in the phylogenetic analyses (Online Resource 1), among which G. catasphaericum, G. formosum, G. giganteum, G. gracilipes and G. pendulum had previously never been included in such analyses
A total of 190,899 to 2,003,005 paired-end reads were mapped onto the reference plastid genome, resulting in the average coverage number of 298–2156
Summary
Next-generation sequencing (NGS) has revolutionized systematic biology and molecular ecology. Compared to traditional Sanger sequencing techniques, NGS allows us to generate orders of magnitude of more informative characters in a both cost- and time-efficient way (Davey et al 2011; Ekblom and Galindo 2011; Straub et al 2012). We use data from NGS, combined with data from traditional Sanger sequencing and morphology, with the primary aim of resolving the phylogeny and species delimitation among Chinese lianoid species of Gnetum L. Most of the species diversity is found in the eastern and southeastern regions of Asia, where vegetative parts and seeds from Gnetum have been used for medical purposes (Yao and Lin 2005; Yao et al 2006; Liu et al 2010), for production of daily necessities (Markgraf 1951) and as food and drinks (Fu et al 1999a). Seeds are either sessile (Fig. 1i, j) or stipitate (Fig. 1k–p)
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