Akira Kawabe — Page 2 | Search PubMed

PubMed2002

Characterization of duplicated two cytosolic phosphoglucose isomerase (PgiC) loci in Arabidopsis halleri ssp. gemmifera.

Arabidopsis halleri ssp. gemmifera has two cytosolic phosphoglucose isomerase (PgiC) loci. A 48-bp deletion was observed in the junction of exon 17 and intron 17 for a locus (PgiC2). PCR-RFLP analysis using cDNA template did not detect the PgiC2 locus. Another locus (PgiC1) has common structure with A. thaliana and expressed normally. A phylogenetic tree of PgiC sequences revealed that duplication of the two loci in A. gemmifera occurred after species splitting of A. thaliana and A. gemmifera. More than 12 kb region encompassing PgiC was sequenced for both loci. In both PgiC1 and PgiC2, sequence homologous to A. thaliana PgiC 5' upstream region was not detected. A gene located on chromosome 4 of A. thaliana was detected in the 5' upstream of PgiC2. This result suggested that the microsyntheny around the PgiC region between A. thaliana and A. gemmifera is not established.

3' Flanking Region↗

PubMed2002

DNA variation in the acidic chitinase locus (ChiA) region in Arabis gemmifera and its related species.

We analyzed DNA variation at the acidic chitinase (ChiA) locus of Arabis gemmifera and among its eight related species. Nucleotide diversity (pi) of the entire locus in A. gemmifera was 0.0032, which was one third that of A. thaliana. In A. gemmifera, an excess of unique polymorphisms yielded significantly negative results with the tests of Tajima and Fu and Li. The McDonald and Kreitman test revealed that the ratio of nucleotide replacement to synonymous changes in A. gemmifera was significantly greater than those between A. gemmifera and A. glabra, A. gemmifera and A. griffithiana, A. gemmifera and A. korshinskyi, A. gemmifera and A. wallichii, and A. gemmifera and A. himalaica. These results indicated that the neutrality assumption, the equilibrium population assumption, or both, could not be applied to the ChiA locus of A. gemmifera. The small size and relative isolation of local subpopulations of A. gemmifera could explain the excess of unique polymorphisms and the high proportion of replacement changes. The specific sampling scheme of this study, where one strain each was sampled from each local subpopulation might also have led to an excess of singletons. Interspecific comparison among Arabidopsis, Arabis and Cardaminopsis species showed that Ka was always lower than Ks, providing evidence against the adaptive evolution of ChiA. However, Ka/Ks was greater between closely related species than between more distant related species. ChiA had a higher level of replacement divergence and a lower level of synonymous divergence compared than did Adh. We suggest that both the mutation rate at the nucleotide level and the selective constraints at the protein level are lower in ChiA than in Adh.

Analysis of Variance↗