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Complete plastome sequences from Glycine syndetika and six additional perennial wild relatives of soybean.

Sherman-Broyles S, Bombarely A, Grimwood J, Schmutz J, Doyle J - G3 (Bethesda) (2014)

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.We tested whether the hypothesis of introgression was supported by the complete plastomes.

View Article: PubMed Central - PubMed

Affiliation: Cornell University, Department of Plant Biology, Ithaca, New York 14853 sls98@cornell.edu.

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Sequence similarity plot generated by VISTA tools. Base sequence is G. syndetika. Intergenic regions are pink. Shuffle LAGAN option used to align Phaseolus and Vigna that have 78-kb inversions. Hypervariable region identified by Magee et al. (2010) is demarcated by red line. Gene with low sequence similarity to other angiosperms, ycf4 is indicated, along with five other genes for orientation. Only one inverted repeat is shown.
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fig3: Sequence similarity plot generated by VISTA tools. Base sequence is G. syndetika. Intergenic regions are pink. Shuffle LAGAN option used to align Phaseolus and Vigna that have 78-kb inversions. Hypervariable region identified by Magee et al. (2010) is demarcated by red line. Gene with low sequence similarity to other angiosperms, ycf4 is indicated, along with five other genes for orientation. Only one inverted repeat is shown.

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.


Complete plastome sequences from Glycine syndetika and six additional perennial wild relatives of soybean.

Sherman-Broyles S, Bombarely A, Grimwood J, Schmutz J, Doyle J - G3 (Bethesda) (2014)

Sequence similarity plot generated by VISTA tools. Base sequence is G. syndetika. Intergenic regions are pink. Shuffle LAGAN option used to align Phaseolus and Vigna that have 78-kb inversions. Hypervariable region identified by Magee et al. (2010) is demarcated by red line. Gene with low sequence similarity to other angiosperms, ycf4 is indicated, along with five other genes for orientation. Only one inverted repeat is shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4199708&req=5

fig3: Sequence similarity plot generated by VISTA tools. Base sequence is G. syndetika. Intergenic regions are pink. Shuffle LAGAN option used to align Phaseolus and Vigna that have 78-kb inversions. Hypervariable region identified by Magee et al. (2010) is demarcated by red line. Gene with low sequence similarity to other angiosperms, ycf4 is indicated, along with five other genes for orientation. Only one inverted repeat is shown.
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.

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.We tested whether the hypothesis of introgression was supported by the complete plastomes.

View Article: PubMed Central - PubMed

Affiliation: Cornell University, Department of Plant Biology, Ithaca, New York 14853 sls98@cornell.edu.

Show MeSH