Topological incongruence between nuclear and chloroplast DNA trees suggesting hybridization in the urophyllum group of the genus Fagopyrum (Polygonaceae)

Abstract

We performed phylogenetic analyses of Fagopyrum species in the urophyllum group based on nucleotide sequences of two nuclear genes, FLORICAULA/LEAFY ( FLO/LFY ) and AGAMOUS ( AG ), and three segments of chloroplast DNA (cpDNA), rbc L-acc D, trn K intron, and trn C-rpo B spacer. The FLO/LFY and AG sequences turned out to be phylogenetically more informative at the intrageneric level than the cpDNA sequences. Congruence among these gene trees, inferred by a maximum-likelihood (ML) method, demonstrated that topologies were partially incongruent between the nuclear and chloroplast DNA phylogenies. The nuclear DNA sequence data supported a monophyletic relation of F. statice , F. gilesii , and F. jinshaense , whereas the former two species formed another monophyletic relation with the F. capillatum -F. gracilipes -F. gracilipedoides -F. rubifolium clade excluding F. jinshaense in the synthetic cpDNA phylogeny. In addition, two divergent sequences of FLO/LFY were found in F. rubifolium (tetraploid). One of these was sister to F. gracilipedoides and another was sister to F. statice , and a monophyletic relation of these two genes was rejected by a bootstrap analysis. These results suggest that hybridization may have occurred during diversification of Fagopyrum species in the urophyllum group, and that F. rubifolium is possibly allotetraploid species.

Two distinct groups of natural populations of Fagopyrum urophyllum (Bur. et Franch.) Gross revealed by the nucleotide sequence of a noncoding region in chloroplast DNA

“…Two cultivated species, F. esculentum and F. tataricum belong to the cymosum group. This grouping has been supported by molecular classification of the buckwheat species (Ohnishi and Matsuoka, 1996;Yasui and Ohnishi, 1998a, b;Ohsako and Ohnishi, 2000;Nishimoto et al, 2003).…”

“…The nucleotide diversity ( p ) among all the accessions was 0.00685. The nucleotide sequence of the trnC-rpoB spacer region had already been determined in 5 species of the urophyllum group, for more than 5 accessions for each species Ohnishi, 2000, 2001;Nishimoto et al, 2003;Kawasaki et al, unpublished). In the present study, Pn Fig.…”

“…For the phylogenetic analysis of the nucleotide sequences of trn C-rpo B spacer, in addition to 16 accessions evaluated in this study and 3 accessions determined by Ohsako and Ohnishi(2000), 48 accessions of other species of the urophyllum group were also analyzed, namely 34 accessions obtained from DDBJ/ EMBL/GenBank databases Ohnishi, 2000 andNishimoto et al, 2003) and 9 accessions of F. gilesii and 5 accessions of F. jinshaense (Kawasaki et al, unpublished). The species' names, basic characteristics of the species and their distributions are summarized in Table Table 1 2.…”

Construction of a BAC library for buckwheat genome research -An application to positional cloning of agriculturally valuable traits-

“…AGAMOUS(AG), FLORICAULA/LEAFY(FLO/LFY), and Rubisco large subunit (rbcL) were screened, where primers were designed from the nucleotide sequences of Nishimoto et al (2003) for AG and FLO/LFY, and Yasui and Ohnishi (1996) for rbcL. Preliminary genomic Southern hybridization analyses indicated that the two nuclear genes AG and FLO/LFY were likely to be single copy genes (Yasui et al unpublished).…”

Allopolyploid speciation inPersicaria(Polygonaceae): Insights from a low-copy nuclear region

“…LEAFY is regarded as a singlecopy gene in angiosperms (32) and has proven to be useful for phylogeny at the intraspecific level (33)(34)(35). On the basis of our analyses, we consider variation in the frequency of reticulation and the potential consequences of allopolyploid speciation for invasiveness.…”