PMC:3091637 / 43484-47921 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/3091637","sourcedb":"PMC","sourceid":"3091637","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3091637","text":"Nucleotide composition and skews\nAll four vermetid genomes were AT-rich, with these two nucleotides accounting for 59 - 62% of the genome (Figure 2; Additional file 7, Table S1); this trend was consistent across regions of each genome associated with protein-encoding genes, rRNA genes, tRNAs, and non-coding regions. Interestingly, however, the AT-biases of vermetid genomes were noticeably lower than those reported for other complete caenogastropod genomes (range: 65.2-70.1%, n = 14; Additional file 7, Table S1). Likewise, AT content was only moderately higher at third-codon positions and 4FD sites of protein-encoding genes, a result unusual in comparison with many other protostomes where %AT can often exceed \u003e80% at 4FD sites [44]. Skew analyses revealed that the \"+\" strand was strongly biased against A (AT-skew ranging from -0.148 to -0.238) and towards G (GC-skew ranging from +0.065 to +0.251). This pattern was similar to other caenogastropods (Additional file 7, Table S1), heterobranchs [15], and the chiton, Katharina tunicata [55], but opposite to that found on the \"+\" strand of the abalone Haliotis [56] and the cephalopods, Nautilus and Octopus, suggestive of switches in the assignments of leading and lagging strands within the Mollusca [41].\nFigure 2 Nucleotide composition of four complete vermetid genomes. For each species, the %AT content, AT-skew, and GC-skew are shown for the \"+\" strand of the complete genome and its functional components, including: protein-encoding genes (complete protein, 3rd codon positions only, and 3rd positions of 4-fold degenerate (4FD) codons only), rRNA genes, unassigned regions (UR), and tRNA genes (including \"+\" and \"-\" strand encoded genes). Error bars refer to standard errors based on a sample size from each genome of: 13 protein encoding genes, 14 -15 \"+\" strand tRNA genes, and 7-8 \"-\" strand tRNA genes. Skew patterns were different between regions of the genome depending on their function. For AT-skews, the most strongly biased areas were found associated with protein-encoding genes, but these were not necessarily most pronounced at third positions or at 4FD sites (except for D. maximum; Figure 2). The two rRNA genes showed a marked difference from protein-encoding genes, with a slight positive AT-skew, on average. Differences in skew patterns between rRNA and protein-encoding genes have been noted elsewhere [41,57], and may reflect base-pairing constraints associated with the secondary structures of these rRNAs [41]. Unassigned regions, assumed to be non-coding, were expected to experience similar selective pressures to those of 4FD third codon positions; this correspondence was not strong, however, with unassigned regions showing variation in AT-bias across taxa from slight positive AT-skews to moderate negative skews. tRNA genes regardless of whether they were coded for on the \"+\" or \"-\" strand exhibited no consistent skew patterns, with an average close to zero.\nGC-skews were moderately positive for most regions of the genome, including protein-encoding genes, rRNA genes, unassigned regions, and tRNAs encoded on the \"+\" strand. Skews were particularly strong, however, for the third codon positions and 4FD third codon positions in Dendropoma maximum and Eualetes tulipa. On average, neutral to negative GC-skews were associated with regions of the \"+\" strand associated with tRNA genes encoded on the \"-\" strand.\nAs predicted by skew patterns described above, G+T composition varied across the length of the \"+\" strand in all four complete genomes (Figure 3). Areas of weak or no G+T bias were typically associated with rRNAs and regions with tRNAs encoded on the \"-\" strand. Dendropoma maximum exhibited a particularly strong bias for G+T (\u003e65%) in the region from 10,000 to 14,000 bp.\nFigure 3 Plots of A+C and G+T composition along the \"+\" strand of the mt genomes of D. maximum, D. gregarium, E. tulipa, and T. squamigerus using a sliding window of 100 nucleotides. Each plot is positioned above a linear representation of its corresponding genome highlighting regions corresponding to the presence of: 1) protein encoding genes and tRNA genes encoded on the \"+\" strand, 2) rRNA genes encoded on the \"+\" strand, and 3) tRNA genes encoded on the \"-\" strand. See [41] for a comparison with Nautilus and Katharina. As is the standard convention for metazoan mt genomes, cox1 has been designated the start point for the \"+\" strand.","divisions":[{"label":"title","span":{"begin":0,"end":32}},{"label":"p","span":{"begin":33,"end":1267}},{"label":"figure","span":{"begin":1268,"end":1878}},{"label":"label","span":{"begin":1268,"end":1276}},{"label":"caption","span":{"begin":1278,"end":1878}},{"label":"p","span":{"begin":1278,"end":1878}},{"label":"p","span":{"begin":1879,"end":2962}},{"label":"p","span":{"begin":2963,"end":3417}},{"label":"p","span":{"begin":3418,"end":3791}},{"label":"label","span":{"begin":3792,"end":3800}}],"tracks":[{"project":"2_test","denotations":[{"id":"20642828-7563121-10659355","span":{"begin":737,"end":739},"obj":"7563121"},{"id":"20642828-18302768-10659356","span":{"begin":1006,"end":1008},"obj":"18302768"},{"id":"20642828-7828825-10659357","span":{"begin":1047,"end":1049},"obj":"7828825"},{"id":"20642828-16206015-10659358","span":{"begin":1122,"end":1124},"obj":"16206015"},{"id":"20642828-16854241-10659359","span":{"begin":1263,"end":1265},"obj":"16854241"},{"id":"20642828-16854241-10659360","span":{"begin":2395,"end":2397},"obj":"16854241"},{"id":"20642828-18628961-10659361","span":{"begin":2398,"end":2400},"obj":"18628961"},{"id":"20642828-16854241-10659362","span":{"begin":2501,"end":2503},"obj":"16854241"},{"id":"20642828-16854241-10659363","span":{"begin":4272,"end":4274},"obj":"16854241"}],"attributes":[{"subj":"20642828-7563121-10659355","pred":"source","obj":"2_test"},{"subj":"20642828-18302768-10659356","pred":"source","obj":"2_test"},{"subj":"20642828-7828825-10659357","pred":"source","obj":"2_test"},{"subj":"20642828-16206015-10659358","pred":"source","obj":"2_test"},{"subj":"20642828-16854241-10659359","pred":"source","obj":"2_test"},{"subj":"20642828-16854241-10659360","pred":"source","obj":"2_test"},{"subj":"20642828-18628961-10659361","pred":"source","obj":"2_test"},{"subj":"20642828-16854241-10659362","pred":"source","obj":"2_test"},{"subj":"20642828-16854241-10659363","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ec939a","default":true}]}]}}