Complete plastome sequences from Glycine syndetika and six additional perennial wild relatives of soybean.
Bottom Line: Repetitive sequences were detected in high frequencies as in soybean, but further analysis showed that repeat sequence numbers are inflated.Previous chloroplast-based phylogenetic trees for perennial Glycine were incongruent with nuclear gene-based phylogenetic trees.Alignment of complete plastome sequences and Bayesian analysis allowed us to date putative hybridization events supporting the hypothesis of introgression and chloroplast "capture."
Affiliation: Cornell University, Department of Plant Biology, Ithaca, New York 14853 email@example.com.Show MeSH
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Mentions: The total number of genes reported above does not include ycf4, which in legumes is divergent from other angiosperm ycf4 sequences (Stefanovic et al. 2009) and was not annotated by Dogma (Wyman et al. 2004) or GenBank for our submissions. Stefanovic et al.(2009) were the first to draw attention to the fact that the gene was present and highly divergent in legumes (Stefanovic et al. 2009) rather than absent, as suggested by DNA hybridization surveys (Doyle et al. 1995) and the G. max annotation (Saski et al. 2005). This gene is thought to be a nonessential Photosystem I assembly factor in higher plants (Krech et al. 2012), and this level of sequence divergence may indicate that if its function is retained in Glycine, it is replaced by a nuclear copy of a plastid gene (NuPT). This region flanks one of several NuPTs found in the soybean genome sequence (A. Bombarely, D. Robinson, S. Sherman-Broyles, and J. J. Doyle, unpublished data). Although ycf4 is divergent from other legume ycf4 sequences, there is no indication that it is a mutational hotspot in Glycine, as it is known to be in the legume genus Lathyrus (Magee et al. 2010).There are high levels of sequence similarity in genes between rps16 and cemA, the hypervariable region in Magee et al. (2010) (Figure 3). Pairwise Ka/Ks values for all Glycine species (data not shown) are misleading because there are so few differences that ratios were based on too few polymorphic sites.
Affiliation: Cornell University, Department of Plant Biology, Ithaca, New York 14853 firstname.lastname@example.org.