Molecular systematics of Trilliaceae II. Phylogenetic analyses of Trillium and its allies using sequences of rbcL and matK genes of cpDNA and internal transcribed spacers of 18S–26S nrDNA

Abstract

Coding regions of the rbcL and matK genes of cpDNA and internal transcribed spacers (ITS) of nuclear ribosomal DNA were sequenced to study phylogenetic relationships within and among all four genera of Trilliaceae: Trillium, Paris, Daiswa and Kinugasa. The rbcL gene has evolved much slower than matK and in particular ITS; hence the phylogenetic trees based on the rbcL gene show a much lower resolution than trees based on either matK or ITS. The general topology of phylogenetic trees resulting from separate parsimony analyses of the matK and ITS sequences are relatively congruent, with the exception of the placement of T. pusillum. Both matK and ITS phylogenies reveal that T. rivale diverges at the base of the trees. In both trees, Paris, Daiswa and Kinugasa form a relatively weakly supported group. Within this group, the allo‐octaploid Kinugasa japonica is the sister group of Daiswa species. The Paris–Daiswa–Kinugasa group, the major Trillium group, and T. undulatum and T. govanianum showed a loosely related topology, but their affinities are not evident according to these two molecular markers. However, phylogenetic analysis of amino acid sequences derived from matK shows that T. rivale together with clades T. undulatum–T. govanianum, Daiswa–Kinugasa and Paris is basally diverged as a sister group to the remainder of Trillium.

Analysis of Complete Chloroplast Genome Sequences Improves Phylogenetic Resolution in Paris (Melanthiaceae)

“…Our phylogenomic analyses also well resolved the inter-tribe relationships in the family Melanthiaceae and the inter-generic relationships within the tribe Parideae, with higher support than previous phylogenetic studies that used single or multiple locus DNA sequences data (Osaloo and Kawano, 1999; Farmer and Schilling, 2002; Ji et al, 2006; Kim et al, 2013). This result was consistent with previous findings (Attigala et al, 2016) in which a much higher of support to inter-generic relationships was observed in the cp genomic phylogeny within Arundinarieae tribe (Bambusoideae: Poaceae).…”

“…Compared to previous molecular phylogeneitc analyses (Osaloo and Kawano, 1999; Ji et al, 2006; Farmer and Schilling, 2002), our results clearly indicated that all nodes within the Daiswa clade showing a MLBS > 90% and PP > 0.95 ( Figure 3 ). Similar results have also been observed from the whole chloroplast genome analysis of Pinus species (Parks et al, 2009), Araucaria species (Ruhsam et al, 2015), and Acasia species (Williams et al, 2016).…”

“…The key interest in the current study is to resolve the previously phylogenetic controversies in Paris (Osaloo and Kawano, 1999; Farmer and Schilling, 2002; Ji et al, 2006) by using the complete cp genome sequences. Our phylogenomic analyses did not resolve Paris as a monophyletic group, and strongly supported its division into two monophyletic genera: Paris s.s. and Daiswa ( Figure 3 ).…”

“…The molecular phylogeny of Paris based on either single or multiple-locus DNA sequence data (e.g., rbc L, mat K, trn L/ trn F, psb A/ trn H and ITS) has remained controversial in recent investigations. The monophyly of Paris was justified by the studies of Osaloo and Kawano (1999) and Ji et al (2006); however, analyses by Farmer and Schilling (2002) supported the taxonomical treatment of Takhtajan (1983). Despite recent insights into the evolutionary relationships within this plant group, a fully resolved and well-supported phylogeny remains elusive.…”

“…Inaccurate identification of these species could confound their effective exploration, conservation, and domestication. Moreover, at the species level, nearly all reported chloroplast (cp) DNA sequences ( rbc L, mat K, trn L/ trn F, and psb A/ trn H) exhibit inadequate genetic variation (Osaloo and Kawano, 1999; Ji et al, 2006), to allow reliable discrimination of these species.…”