title: Complete plastome sequences from Glycine syndetika and six additional perennial wild relatives of soybean.
abstract: Organelle sequences have a long history of utility in phylogenetic analyses. Chloroplast sequences when combined with nuclear data can help resolve relationships among flowering plant genera, and within genera incongruence can point to reticulate evolution. Plastome sequences are becoming plentiful because they are increasingly easier to obtain. Complete plastome sequences allow us to detect rare rearrangements and test the tempo of sequence evolution. Chloroplast sequences are generally considered a nuisance to be kept to a minimum in bacterial artificial chromosome libraries. Here, we sequenced two bacterial artificial chromosomes per species to generate complete plastome sequences from seven species. The plastome sequences from Glycine syndetika and six other perennial Glycine species are similar in arrangement and gene content to the previously published soybean plastome. 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. Alignment of complete plastome sequences and Bayesian analysis allowed us to date putative hybridization events supporting the hypothesis of introgression and chloroplast "capture."
authors.affiliation: Cornell University, Department of Plant Biology, Ithaca, New York 14853 sls98@cornell.edu.
authors.forename: Sue
authors.initials: S
authors.lastname: Sherman-Broyles
authors.affiliation: Cornell University, Department of Plant Biology, Ithaca, New York 14853.
authors.forename: Aureliano
authors.initials: A
authors.lastname: Bombarely
authors.affiliation: Hudson Alpha Institute for Biotechnology, Huntsville, Alabama 35806.
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.affiliation: Hudson Alpha Institute for Biotechnology, Huntsville, Alabama 35806.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.affiliation: Cornell University, Department of Plant Biology, Ithaca, New York 14853.
authors.forename: Jeff
authors.initials: J
authors.lastname: Doyle
mesh_terms: D001499:Bayes Theorem; D005075:Biological Evolution; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D007887:Fabaceae / Q000145:classification / Q000235:genetics*; D015723:Gene Library; D054627:Genome, Plastid; D006657:Histones / Q000737:chemistry / Q000235:genetics; D055029:Inverted Repeat Sequences; D010802:Phylogeny; D018087:Plastids / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000145:classification / Q000235:genetics
chemical_list: D006657:Histones
keywords: divergence dates; incongruence; inversions; repetitive sequences