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In many organisms, the difference in codon usage patterns among genes reflects variation in local base compositional biases and the intensity of natural selection. In this study, a comparative analysis was performed to investigate the characteristics of codon bias and factors in shaping the codon usage patterns among mitochondrion, chloroplast and nuclear genes in common wheat (Triticum aestivum L.). GC contents in nuclear genes were higher than that in mitochondrion and chloroplast genes. The neutrality and correspondence analyses indicated that the codon usage in nuclear genes would be a result of relative strong mutational bias, while the codon usage patterns of mitochondrion and chloroplast genes were more conserved in GC content and influenced by translation level. The Parity Rule 2 (PR2) plot analysis showed that pyrimidines were used more frequently than purines at the third codon position in the three genomes. In addition, using a new alterative strategy, 11, 12, and 24 triplets were defined as preferred codons in the mitochondrion, chloroplast and nuclear genes, respectively. These findings suggested that the mitochondrion, chloroplast and nuclear genes shared particularly different features of codon usage and evolutionary constraints. Comparative analysis of codon usage patterns among mitochondrion, chloroplast and nuclear genes in Triticum aestivum L.The vast majority of prokaryotic and eukaryotic species have non-random codon usage. Alternative synonymous codons in most genes are used with unequal frequency, i.e., certain synonymous codons are significantly preferred over others. It has been widely accepted that the biased codon usage is a result of natural selection (Sharp and Li 1986;Akashi 1994) or mutation pressure (Jukes and Bhushar 1986;Osawa et al. 1988;Sueoka 1988;Kano et al. 1991). In plants, most studies on codon bias have focused on nuclear genes. Chiapello et al. (1998) investigated the association between codon usage and gene functions in Arabidopsis thaliana, and identified two classes of genes: one was highly biased to G/C and the other had a weak preference for A/T-biased codons. Kliman and Henry (2005) also inferred the preferred codons in A. thaliana using the factor analysis and found that these codons corresponded to the commonly represented tRNA anticodons. For poaceous plants that include a number of important crops, a correspondence analysis of 101 genes in maize (Zea mays) revealed that the major pattern in codon usage was a result of differences among the genes in the frequencies of G+C in the third Comparative Analysis of Codon Usage in T. aestivum 247 silent nucleotide position (Fennoy and Bailey-Serres 1993). Liu et al. (2004aLiu et al. ( , 2005a also analyzed a large dataset of rice (Oryza sativa) genes and found that synonymous codon usage and gene functions were strongly correlated. Kawabe and Miyashita (2003) compared features of codon choice among three dicot and four monocot plant species and figured out that despite the difference in GC contents, the codon usage tend...

Background: The domestication of plants and animals was extremely important anthropologically. Previous studies have revealed a general tendency for populations of livestock species to include deeply divergent maternal lineages, indicating that they were domesticated in multiple, independent events from genetically discrete wild populations. However, in water buffalo, there are suggestions that a similar deep maternal bifurcation may have originated from a single population. These hypotheses have rarely been rigorously tested because of a lack of sufficient wild samples. To investigate the origin of the domestic yak (Poephagus grunnies), we analyzed 637 bp of maternal inherited mtDNA from 13 wild yaks (including eight wild yaks from a small population in west Qinghai) and 250 domesticated yaks from major herding regions.

Protein modifiers are involved in diverse biological processes and regulate the activity or function of target proteins by covalently conjugating to them. Although ubiquitin and a number of ubiquitin-like protein modifiers (Ubls) in eukaryotes have been identified, no protein modifier has been found in prokaryotes; thus, their evolutionary origin remains a puzzle. To infer the evolutionary relationships between the protein modifiers and sulfur carrier proteins, we solved the solution NMR structure of the Urm1 (ubiquitin-related modifier-1) protein from Saccharomyces cerevisiae. Both structural comparison and phylogenetic analysis of the ubiquitin superfamily, with emphasis on the Urm1 family, indicate that Urm1 is the unique ''molecular fossil'' that has the most conserved structural and sequence features of the common ancestor of the entire superfamily. The similarities of 3D structure and hydrophobic and electrostatic surface features between Urm1 and MoaD (molybdopterin synthase small subunit) suggest that they may interact with partners in a similar manner, and similarities between Urm1-Uba4 and MoaD-MoeB establish an evolutionary link between ATP-dependent protein conjugation in eukaryotes and ATP-dependent cofactor sulfuration.evolution ͉ NMR structure