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

<p>Abstract</p> <p>Background</p> <p>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: <it>Nuphar advena </it>(from a basal-most lineage) and <it>Ranunculus macranthus </it>(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 <it>ycf15 </it>and <it>ycf68 </it>as protein coding genes, the distribution of simple sequence repeats (SSRs) and longer dispersed repeats (SDR), and patterns of nucleotide composition.</p> <p>Results</p> <p>The <it>Nuphar </it>[GenBank:<ext-link ext-link-type="gen" ext-link-id="NC_008788">NC_008788</ext-link>] and <it>Ranunculus </it>[GenBank:<ext-link ext-link-type="gen" ext-link-id="NC_008796">NC_008796</ext-link>] 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 <it>Nuphar </it>with <it>Nymphaea</it>, 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.</p> <p>Conclusion</p> <p>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 <it>ycf15 </it>and <it>ycf68 </it>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.</p

Comparison of inverted repeat-single copy boundaries in six representative angiosperms

<p><b>Copyright information:</b></p><p>Taken from "Comparative chloroplast genomics: analyses including new sequences from the angiosperms and "</p><p>http://www.biomedcentral.com/1471-2164/8/174</p><p>BMC Genomics 2007;8():174-174.</p><p>Published online 15 Jun 2007</p><p>PMCID:PMC1925096.</p><p></p> Variation occurs at each of the four junctions. In is not in the IR. Joccurs within in all of the genomes but the amount of the 5' end of that is duplicated ranges from 156 bp in to 1583 bp in . Eleven bp of is duplicated in but none of the other genomes shown have any duplication of the gene. Jvaries from including 5 bp of spacer downstream of in to the inclusion of and an additional 140 bp upstream sequence in the IR in

Scatter plots showing relationships between aspects of SSR frequency and other characteristics

<p><b>Copyright information:</b></p><p>Taken from "Comparative chloroplast genomics: analyses including new sequences from the angiosperms and "</p><p>http://www.biomedcentral.com/1471-2164/8/174</p><p>BMC Genomics 2007;8():174-174.</p><p>Published online 15 Jun 2007</p><p>PMCID:PMC1925096.</p><p></p> (top) The relationship of "short" SSRs and "long" SSRs. "Long" SSRs are the 10,10.12 repeats. "Short" SSRs are the 8,8,9 repeats with the 10,10,12 repeats excluded. These are shown for the 24 taxa in Table 7. (middle) The relationship between total SSR number and genome size (in nucleotides) for the 24 taxa. (bottom) The relationship of A+T-richness (the overall A+T percentage of the genome) and the frequency of A and T mononucleotide repeats for the 10 taxa involved in the more detailed comparison. No other SSR category showed a relationship to any aspect of nucleotide composition

Sequence similarity comparisons of IGS and introns within the IR and the LSC

<p><b>Copyright information:</b></p><p>Taken from "Comparative chloroplast genomics: analyses including new sequences from the angiosperms and "</p><p>http://www.biomedcentral.com/1471-2164/8/174</p><p>BMC Genomics 2007;8():174-174.</p><p>Published online 15 Jun 2007</p><p>PMCID:PMC1925096.</p><p></p> In both the top and bottom section, each 14 pairwise Mulan alignments is displayed as a histogram showing the similiarity (ranging from 50% to 100%) between each taxon (A-N) and the reference (top or bottom). The height of the blue histogram topped by the horizontal black lines indicates the degree of similarity; similarity histograms are blue except where we have re-colored yellow the regions equivalent to (top) and (bottom) to highlight those regions. [The black horizontal lines without blue bars subtending them indicate short regions of similarity, basically SDRs. Red bars above the histogram indicate evolutionary conserved regions as determined in Mulan.] In interpreting the diagram, essentially the more blue (or yellow) in a region, the more similar are the two sequences. (Top) Comparisons, relevant to the conservation of , of six IGS regions from were made to (A), (B), (C), (D), (E), (F), (G), (H), (I), (J), (K), (L), (M), and (N). (Bottom) Comparisons, relevant to the conservation of , of introns from were made to those of (A), (B), (C), (D), (E), (F), (G), (H), (I), (J), (K), (L), (M), and (N)

The number of SDRs of different length classes found in eight different angiosperm plastid genomes

<p><b>Copyright information:</b></p><p>Taken from "Comparative chloroplast genomics: analyses including new sequences from the angiosperms and "</p><p>http://www.biomedcentral.com/1471-2164/8/174</p><p>BMC Genomics 2007;8():174-174.</p><p>Published online 15 Jun 2007</p><p>PMCID:PMC1925096.</p><p></p> The majority of repeats are 40 nt or less in length, but some genomes so have repeats that are longer. , the only genome to have repeats over 100 nt in length, is also the only genome to exhibit inversions changing aspects of gene order from the angiosperm consensus order exhibited by (and the other genomes included.