Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus

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dc.creatorRaubeson, Linda A.en
dc.creatorPeery, Rhiannonen
dc.creatorChumley, Timothy W.en
dc.creatorDziubek, Chrisen
dc.creatorFourcade, Matthew H.en
dc.creatorBoore, Jeffrey L.en
dc.creatorJansen, Robert K.en
dc.date.accessioned2014-12-15T17:10:22Zen
dc.date.available2014-12-15T17:10:22Zen
dc.date.issued2007-06-15en
dc.descriptionLinda A. Raubeson, Rhiannon Peery, and Chris Dziubek are with the Biological Sciences, Central Washington University, Ellensburg, WA 98926-7537, USA -- Timothy W. Chumley and Robert K. Jansen are with the Section of Integrative Biology and Institute of Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA -- H. Matthew Fourcade and Jeffery L. Boore are with the DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Program in Evolutionary Genomics, Walnut Creek, CA 94547, USAen
dc.description.abstractBackground: The number of completely sequenced plastid genomes available is growing rapidly. This array of sequences presents new opportunities to perform comparative analyses. In comparative studies, it is often useful to compare across wide phylogenetic spans and, within angiosperms, to include representatives from basally diverging lineages such as the genomes reported here: Nuphar advena (from a basal-most lineage) and Ranunculus macranthus (a basal eudicot). We report these two new plastid genome sequences and make comparisons (within angiosperms, seed plants, or all photosynthetic lineages) to evaluate features such as the status of ycf15 and ycf68 as protein coding genes, the distribution of simple sequence repeats (SSRs) and longer dispersed repeats (SDR), and patterns of nucleotide composition. -- Results: The Nuphar [GenBank:NC_008788] and Ranunculus [GenBank:NC_008796] plastid genomes share characteristics of gene content and organization with many other chloroplast genomes. Like other plastid genomes, these genomes are A+T-rich, except for rRNA and tRNA genes. Detailed comparisons of Nuphar with Nymphaea, another Nymphaeaceae, show that more than two-thirds of these genomes exhibit at least 95% sequence identity and that most SSRs are shared. In broader comparisons, SSRs vary among genomes in terms of abundance and length and most contain repeat motifs based on A and T nucleotides. -- Conclusion: SSR and SDR abundance varies by genome and, for SSRs, is proportional to genome size. Long SDRs are rare in the genomes assessed. SSRs occur less frequently than predicted and, although the majority of the repeat motifs do include A and T nucleotides, the A+T bias in SSRs is less than that predicted from the underlying genomic nucleotide composition. In codon usage third positions show an A+T bias, however variation in codon usage does not correlate with differences in A+T-richness. Thus, although plastome nucleotide composition shows "A+T richness", an A+T bias is not apparent upon more in-depth analysis, at least in these aspects. The pattern of evolution in the sequences identified as ycf15 and ycf68 is not consistent with them being protein-coding genes. In fact, these regions show no evidence of sequence conservation beyond what is normal for non-coding regions of the IR.en
dc.description.catalogingnoteraubeson@cwu.eduen
dc.description.departmentIntegrative Biologyen
dc.description.departmentInstitute for Cellular and Molecular Biologyen
dc.description.sponsorshipen
dc.identifier.Filename1471-2164-8-174en
dc.identifier.citationRaubeson, Linda A., Rhiannon Peery, Timothy W. Chumley, Chris Dziubek, H. Matthew Fourcade, Jeffrey L. Boore, and Robert K. Jansen. “Comparative Chloroplast Genomics: Analyses Including New Sequences from the Angiosperms Nuphar Advena and Ranunculus Macranthus.” BMC Genomics 8, no. 1 (June 15, 2007): 174. doi:10.1186/1471-2164-8-174.en
dc.identifier.doidoi:10.1186/1471-2164-8-174en
dc.identifier.urihttp://hdl.handle.net/2152/27871en
dc.language.isoEnglishen
dc.publisherBMC Genomicsen
dc.rightsAdministrative deposit of works to UT Digital Repository: This works author(s) is or was a University faculty member, student or staff member; this article is already available through open access at http://www.biomedcentral.com. The public license is specified as CC-BY: http://creativecommons.org/licenses/by/4.0/. The library makes the deposit as a matter of fair use (for scholarly, educational, and research purposes), and to preserve the work and further secure public access to the works of the University.en
dc.subjectplastid genomesen
dc.subjectNuphar advenaen
dc.subjectRanunculus macranthusen
dc.titleComparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthusen
dc.typeArticleen

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