A study of the phylogeny of Brassica rapa, B. nigra, Raphanus sativus, and their related genera using noncoding regions of chloroplast DNA (original) (raw)
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Patterns of Nucleotide Substitution in Angiosperm cpDNA trnL (UAA)-trnF (GAA) Regions
Molecular Biology and Evolution, 2000
Patterns of substitution in chloroplast encoded trnL-F regions were compared between species of Actaea (Ranunculales), Digitalis (Scrophulariales), Drosera (Caryophyllales), Panicoideae (Poales), the small chromosome species clade of Pelargonium (Geraniales), each representing a different order of flowering plants, and Huperzia (Lycopodiales). In total, the study included 265 taxa, each with Ͼ900-bp sequences, totaling 0.24 Mb. Both pairwise and phylogeny-based comparisons were used to assess nucleotide substitution patterns. In all six groups, we found that transition/transversion ratios, as estimated by maximum likelihood on most-parsimonious trees, ranged between 0.8 and 1.0 for ingroups. These values occurred both at low sequence divergences, where substitutional saturation, i.e., multiple substitutions having occurred at the same (homologous) nucleotide position, was not expected, and at higher levels of divergence. This suggests that the angiosperm trnL-F regions evolve in a pattern different from that generally observed for nuclear and animal mtDNA (transition/transversion ratio Ն 2). Transition/transversion ratios in the intron and the spacer region differed in all alignments compared, yet base compositions between the regions were highly similar in all six groups. A↔T and G↔C transversions were significantly less frequent than the other four substitution types. This correlates with results from studies on fidelity mechanisms in DNA replication that predict A↔T and G↔C transversions to be least likely to occur. It therefore strengthens confidence in the link between mutation bias at the polymerase level and the actual fixation of substitutions as recorded on evolutionary trees and, concomitantly, in the neutrality of nucleotide substitutions as phylogenetic markers.
Relative rates of nucleotide substitution at the rbcl locus of monocotyledonous plants
Journal of Molecular Evolution, 1992
We subjected 35 rbcL nucleotide sequences from monocotyledonous taxa to maximum likelihood relative rate tests and estimated relative differences in rates of nucleotide substitution between groups of sequences without relying on knowledge of divergence times between taxa. Rate tests revealed that there is a hierarchy of substitution rate at the rbcL locus within the monocots. Among the taxa analYzed the grasses have the most rapid substitution rate; they are followed in rate by the Orchidales, the Liliales, the Bromeliales, and the Arecales. The overall substitution rate for the rbcL locus of grasses is over 5 times the substitution rate in the rbcL of the palms. The substitution rate at the third codon positions in the rbcL of the grasses is over 8 times the third position rate in the palms. The pattern of rate variation is consistent with the generation-time-effect hypothesis. Heterogenous rates of substitution have important implications for phylogenetic reconstruction.
Journal of Molecular Evolution, 2002
It has been known that in noncoding regions of the chloroplast genome, the pattern of nucleotide substitution is in¯uenced by the two nucleotides¯anking the substitution site. In a GCrich environment, a bias toward transition was observed, whereas in an AT-rich environment, a bias toward transversion was observed. In this study, the in¯uence of the two adjacent neighbors on the substitution pattern was observed in the ®rst intron of the mitochondrial nad4 gene, although the AT content of this intron is only 48%. The proportion of transversions increases from 0.32 to 0.75 as the A + T content (number of A's + T's) of the two nearest neighbors increases from 0 to 2. This trend was also observed in another mitochondrial group I intron with an AT content of 64%. In addition, a similar, though weaker, eect was observed in vertebrate pseudogenes. So this eect is present in all three types of genomes. Furthermore, in contrast to the situation in the noncoding regions of chloroplast DNA, where most nucleotide substitutions occurred in the categories with an A + T content of either 1 or 2, nucleotide substitutions in the mitochondrial ®rst nad4 intron occurred more evenly in three categories of dierent A + T contents. This might be due largely to the dierence in the AT content (0.48 vs. 0.72) between the mitochondrial ®rst nad4 intron and the chloroplast DNA regions studied.
Journal of Molecular Evolution, 1999
We obtained 16 nucleotide sequences (∼1400 bp each) of the first intron of the mitochondrial (mt) gene for NADH subunit 4 (nad4) from 10 species of Brassicaceae. Using these new sequences and five published sequences from GenBank, we constructed a phylogenetic tree of the Brassicaceae species under study and showed that the rate of nucleotide substitution in the first intron of nad4 is very low, about 0.16-0.23 × 10 −9 substitution per site per year, which is about half of the silent rate in exons of nad4. The ratios of substitution rates in this intron, ITS, and IGS are approximately 1: 23:73, where ITS is the nuclear intergenic spacer between 18S and 25S rRNA genes and IGS is the intergenic spacer of 5S rRNA genes. A segment (335 bp) in the first intron of nad4 in Brassicaceae species that is absent in wheat was considered as a nonfunctional sequence and used to estimate the neutral rate (the rate of mutation) in mtDNA to be 0.5-0.7 × 10 −9 substitution per site per year, which is about three times higher than the substitution rate in the rest of the first intron of nad4. We estimated that the dates of divergence are 170-235 million years (Myr) for the monocot-dicot split, 112-156 Myr for the Brassicaceae-Lettuce split, 14.5-20.4 Myr for the Brassica-Arabidopsis split, and 14.5-20.4 Myr for the Arabidopsis-Arabideae split.
Assessing substitution variation across sites in grass chloroplast DNA
Journal of Molecular Evolution, 2007
We assess the similarity of base substitution processes, described by empirically derived 4 · 4 matrices, using chi-square homogeneity tests. Such significance analyses allow us to assess variation in sequence evolution across sites and we apply them to matrices derived from noncoding sites in different contexts in grass chloroplast DNA. We show that there is statistically significant variation in rates and patterns of mutation among noncoding sites in different contexts and then demonstrate a similar and significant influence of context on substitutions at fourfold degenerate sites of coding regions from grass chloroplast DNA. These results show that context has the same general effect on substitution bias in coding and noncoding DNA: the A+T content of flanking bases is correlated with rate of substitution, transition bias, and GC fi AT pressure, while the number of flanking pyrimidines on a single strand is correlated with a mutational bias, or skew, toward pyrimidines. Despite the similarity in general trends, however, when we compare coding and noncoding matrices we find that there is a statistically significant difference between them even when we control for context. Most noticeably, fourfold degenerate sites in coding sequences are undergoing substitution at a higher rate and there are also significant differences in the relationship between pyrimidines skew and the number of flanking pyrimidines. Possible reasons for the differences between coding and noncoding sites are discussed. Furthermore, our analysis illustrates a simple statistical way for comparing substitution processes across sites allowing us to better study variation in evolutionary processes across a genome.
International Journal of Molecular Sciences, 2015
Ribosomal DNA (rDNA) of plants is present in high copy number and shows variation between and within species in the length of the intergenic spacer (IGS). The 45S rDNA of flowering plants includes the 5.8S, 18S and 25S rDNA genes, the internal transcribed spacer (ITS1 and ITS2), and the intergenic spacer 45S-IGS (25S-18S). This study identified six different types of 45S-IGS, A to F, which at 363 bp, 1121 bp, 1717 bp, 1969 bp, 2036 bp and 2111 bp in length, respectively, were much shorter than the reported reference IGS sequences in B. oleracea var. alboglabra. The shortest two IGS types, A and B, lacked the transcription initiation site, non-transcribed spacer, and external transcribed spacer. Functional behavior of those two IGS types in relation to rRNA synthesis is a subject of further investigation. The other four IGSs had subtle variations in the transcription termination site, guanine-cytosine (GC) content, and number of tandem repeats, but the external transcribed spacers of these four IGSs were quite similar in length. The 45S IGSs were found to follow Mendelian inheritance in a population of 15 F 1 s and their 30 inbred parental lines, which suggests that these sequences could be useful for development of new breeding tools. In addition, this study represents the first report of intra-specific (within subspecies) variation of the 45S IGS in B. oleracea.
Chromosomal localization of rDNA in the Brassicaceae
Genome, 2005
A survey is given about the number and chromosomal position of rDNA loci in 45 Brassicaceae species. For 34 species, 5S and 45S rDNA loci have been localized by two-colour fluorescence in situ hybridization for the first time. These data show the variability of rDNA within karyotypes of the Brassicaceae, provide anchor points for (comparative) genetic maps, and might be important for studies on concerted evolution of internal transcribed sequence types of rDNA in cruciferous plants.
Intralineage variation in the pattern ofrbcL nucleotide substitution
Plant Systematics and Evolution, 1998
Abstraet: Variation in chloroplast rbcL sequences was studied in representative species of four different lineages: the tribe Rubieae (Rubiaceae), and the genera Drosera (Droseraceae), Nothofagus (Nothofagaceae) and llex (Aquifoliaceae). Each lineage has its particular non-overlapping set of rbcL polymorphic sites, indicating that common unconstrained rbcL sites are not shared. Large differences in the rate and pattern of nucleotide substitution are observed among the four lineages. The genus Ilex has the lowest rate of substitution, the lowest transition/transversion ratio, the lowest synonymous/ replacement ratio and the lowest number of substitutions at the third codon position. An apparent relationship of these measures to the age of the lineages is observed. The A + T content and codon use among the four lineages are very similar and, apparently, cannot account for the observed differences in pattems of nucleotide substitution. However, the A + T content of the two bases immediately flanking the polymorphic sites is higher in Ilex than in the other lineages. This could be correlated with the transversion/transition bias observed in Ilex. The particularly low synonymous/replacement ratio found in Ilex could also be explained by the small population sizes of species in this genus.
Rates of synonymous substitution in plant nuclear genes
Journal of Molecular Evolution, 1989
The rate of synonymous nucleotide substitution in nuclear genes of higher plants has been estimated. The rate varies among genes by a factor of up to two, in a manner that is not immediately explicable in terms of base composition or codon usage bias. The average rate, in both monocots and dicots, is about four times higher than that in chloroplast genes. This leads to an estimated absolute silent substitution rate of 6 x 10 -9 substitutions per site per year that falls within the range of average rates (2-8 x 10 -9) seen in different mammalian nuclear genomes.
Current Genetics, 1993
The noncoding DNA region of the chloroplast genome, flanked by the genes rbcL and psaI (ORF36), has been sequenced for seven species of the grass family (Poaceae). This region had previously been observed as a hotspot area for length mutations. Sequence comparison reveals that short duplications, probably resulting from slipped-strand mispairing, account for many small length differences between sequences but that major mutational hotspots are localized in three small areas, two of which show potential secondary structure. Mutation in one of these hotspots appears to be a result of more complex recombination events. All seven species contain a pseudogene for rp123 and evidence is presented that this pseudogene is being maintained by gene conversion with the functional gene. Different transition/transversion biases and AT contents between the pseudogene and the surrounding noncoding sequences are noted. In the subfamily Panicoideae there is a deletion in which almost 1 kb of ancestral sequence, including the 3' end of the rp123 pseudogene, has been replaced by a non-homologous 60-base sequence of unknown origin. Two other deletions of almost the same region have occurred in the grass family. The deleted noncoding region has mutational and compositional properties similar to the rbcL coding sequence and the rpl23 pseudogene. The three independent deletions, as well as the pattern of mutation in the localized hotspots, indicate that such noncoding DNA may be misleading for studies of phylogenetic inference.