Patterns of divergence among conifer ESTs and polymorphism in Pinus sylvestris identify putative selective sweeps

Finding genes that are under positive selection is a difficult task, especially in non-model organisms. Here, we have analyzed expressed sequence tag (EST) data from 4 species (Pinus pinaster, Pinus taeda, Picea glauca, and Pseudotsuga menziesii) to investigate selection patterns during their evolution and to identify genes likely to be under positive selection. To confirm selection, population samples of these genes have been sequenced in Pinus sylvestris, a species that was not included in the EST data set. The estimates of branch-specific Ka/Ks (nonsynonymous/synonymous substitution rates) across all genes in the EST data set were similar or smaller than estimates from other higher plant species. There was no evidence for the traditional indication of positive selection, Ka/Ks above 1. However, several lines of evidence based on polymorphism patterns suggest that genes with high Ka/Ks (0.20-0.52) in the EST data set are in fact more affected by positive selection in P. sylvestris than genes with low Ka/Ks (0.01-0.04). The high Ka/Ks genes have a lower level of polymorphism and more negative Tajima's D than the low Ka/Ks genes. Further, in the high Ka/Ks group, the Hudson-Kreitman-Aguade test is significant. This suggests that the EST data set is a good starting point for finding genes under positive selection in conifers and that even moderate Ka/Ks values could be indicative of selection. A group of 5 genes with high Ka/Ks collectively show evidence for positive selection within P. sylvestris.     

Widespread positive selection in synonymous sites of mammalian genes

Evolution of protein sequences is largely governed by purifying selection, with a small fraction of proteins evolving under positive selection. The evolution at synonymous positions in protein-coding genes is not nearly as well understood, with the extent and types of selection remaining, largely, unclear. A statistical test to identify purifying and positive selection at synonymous sites in protein-coding genes was developed. The method compares the rate of evolution at synonymous sites (Ks) to that in intron sequences of the same gene after sampling the aligned intron sequences to mimic the statistical properties of coding sequences. We detected purifying selection at synonymous sites in approximately 28% of the 1,562 analyzed orthologous genes from mouse and rat, and positive selection in approximately 12% of the genes. Thus, the fraction of genes with readily detectable positive selection at synonymous sites is much greater than the fraction of genes with comparable positive selection at nonsynonymous sites, i.e., at the level of the protein sequence. Unlike other genes, the genes with positive selection at synonymous sites showed no correlation between Ks and the rate of evolution in nonsynonymous sites (Ka), indicating that evolution of synonymous sites under positive selection is decoupled from protein evolution. The genes with purifying selection at synonymous sites showed significant anticorrelation between Ks and expression level and breadth, indicating that highly expressed genes evolve slowly. The genes with positive selection at synonymous sites showed the opposite trend, i.e., highly expressed genes had, on average, higher Ks. For the genes with positive selection at synonymous sites, a significantly lower mRNA stability is predicted compared to the genes with negative selection. Thus, mRNA destabilization could be an important factor driving positive selection in nonsynonymous sites, probably, through regulation of expression at the level of mRNA degradation and, possibly, also translation rate. So, unexpectedly, we found that positive selection at synonymous sites of mammalian genes is substantially more common than positive selection at the level of protein sequences. Positive selection at synonymous sites might act through mRNA destabilization affecting mRNA levels and translation.     

Positive selection signatures in the TLR7 family

While adaptive immunity genes evolve rapidly under the influence of positive selection, innate immune system genes are known to evolve slowly due to strong purifying selection. Among the sensors of the innate immune system, Toll-like receptors (TLRs) are particularly important due to their ability to recognize and respond to pathogen-associated molecular patterns (PAMP), such as lipopolysaccharides, peptidoglycans, and nucleic acids from bacteria or viruses. In the present study, we examine the evolutionary process that has operated on the TLR7 family genes TLR7, TLR8, and TLR9. The results demonstrate that the average Ka/Ks (the ratio between nonsynonymous and synonymous substitution rates) of each TLR family gene is far lower than one regardless of estimating methods, supporting previous observations of strong purifying selection in this gene family. Interestingly, however, analysis of Ka/Ks ratios along the coding regions of TLR7 family genes by sliding-window analysis reveals a few narrow high peaks (Ka/Ks > 1). The most prominent peak corresponds to a specific region in the ectodomain, which exists only in the TLR7 family, suggesting that this unique structure of the TLR7 family might have been a target of positive selection in a variety of lineages. Furthermore, maximum likelihood model tests suggest that positive selection is the best explanation for a certain fraction of the amino acid substitutions in the TLR9.     

Evaluation of whether accelerated protein evolution in chordates has occurred before, after, or simultaneously with gene duplication

Gene duplication and loss are predicted to be at least of the order of the substitution rate and are key contributors to the development of novel gene function and overall genome evolution. Although it has been established that proteins evolve more rapidly after gene duplication, we were interested in testing to what extent this reflects causation or association. Therefore, we investigated the rate of evolution prior to gene duplication in chordates. Two patterns emerged; firstly, branches, which are both preceded by a duplication and followed by a duplication, display an elevated rate of amino acid replacement. This is reflected in the ratio of nonsynonymous to synonymous substitution (mean nonsynonymous to synonymous nucleotide substitution rate ratio [Ka:Ks]) of 0.44 compared with branches preceded by and followed by a speciation (mean Ka:Ks of 0.23). The observed patterns suggest that there can be simultaneous alteration in the selection pressures on both gene duplication and amino acid replacement, which may be consistent with co-occurring increases in positive selection, or alternatively with concurrent relaxation of purifying selection. The pattern is largely, but perhaps not completely, explained by the existence of certain families that have elevated rates of both gene duplication and amino acid replacement. Secondly, we observed accelerated amino acid replacement prior to duplication (mean Ka:Ks for postspeciation preduplication branches was 0.27). In some cases, this could reflect adaptive changes in protein function precipitating a gene duplication event. In conclusion, the circumstances surrounding the birth of new proteins may frequently involve a simultaneous change in selection pressures on both gene-copy number and amino acid replacement. More precise modeling of the relative importance of preduplication, postduplication, and simultaneous amino acid replacement will require larger and denser genomic data sets from multiple species, allowing simultaneous estimation of lineage-specific fluctuations in mutation rates and adaptive constraints.     

Expansion Mechanisms and Functional Divergence of the Glutathione S-Transferase Family in Sorghum and Other Higher Plants

Glutathione S-transferases (GSTs) exist in various eukaryotes and function in detoxification of xenobiotics and in response to abiotic and biotic stresses. We have carried out a genome-wide survey of this gene family in 10 plant genomes. Our data show that tandem duplication has been regarded as the major expansion mechanism and both monocot and dicot plants may have practiced different expansion and evolutionary history. Non-synonymous substitutions per site (Ka) and synonymous substitutions per site (Ks) analyses showed that N- and C-terminal functional domains of GSTs (GST_N and GST_C) seem to have evolved under a strong purifying selection (Ka/Ks < 1) under different selective pressures. Differential evolutionary rates between GST_N and GST_C and high degree of expression divergence have been regarded as the major drivers for the retention of duplicated genes and the adaptability to various stresses. Expression profiling also indicated that the gene family plays a role not only in stress-related biological processes but also in the sugar-signalling pathway. Our survey provides additional annotation of the plant GST gene family and advance the understanding of plant GSTs in lineage-specific expansion and species diversification.     

Expression diversity and evolutionary dynamics of rice duplicate genes

Duplicate genes are believed to be a major source of new gene functions over evolutionary time. In order to evaluate the evolutionary dynamics of rice duplicate genes, formed principally by paleoployploidization prior to the speciation of the Poaceae family, we have employed a public microarray dataset including 155 gene expression omnibus sample plates and bioinformatics tools. At least 57.4% of old ~70 million years ago (MYA) duplicate gene pairs exhibit divergences in expression over the given experimental set, whereas at least 50.9% of young ~7.7-MYA duplicate gene pairs were shown to be divergent. When grouping the rice duplicate genes according to functional categories, we noted a striking and significant enrichment of divergent duplicate metabolism-associated genes, as compared to that observed in non-divergent duplicate genes. While both non-synonymous substitution (Ka) and synonymous substitution (Ks) values between non- and divergent duplicate gene pairs evidenced significant differences, the Ka/Ks values between them exhibited no significant differences. Interestingly, the average numbers of conserved motifs of the duplicate gene pairs revealed a pattern of decline along with an increase in expression diversity, partially supporting the subfunctionalization model with degenerative complementation in regulatory motifs. Duplicate gene pairs with high local similarity (HLS) segments, which might be formed via conversion between rice paleologs, evidenced higher expression correlations than were observed in the gene pairs without the HLS segments; this probably resulted in an increased likelihood of gene conversion in promoters of the gene pairs harboring HLS segments. More than 60% of the rice gene families exhibited similar high expression diversity between members as compared to that of randomly selected gene pairs. These findings are likely reflective of the evolutionary dynamics of rice duplicate genes for gene retention. An erratum to this article can be found at     

The characterization of complete mitochondrial genome and phylogenetic relationship within Rattus genus (Rodentia: Muridae)

The genus Rattus is one of the main pest genus of rodent. Most species of the genus carry all kinds of pathogenic bacteria to human being. They are traditionally considered to be a least understood group. The complete mitochondrial genome of the White-Footed Indochinese Rat, Rattus nitidus was determined in this study. The characterization of mitochondrial genomes of Rattus genus was also analyzed based on comprehensive comparison. The result of evolutionary patterns of protein-coding genes (PCGs) suggested purifying selection was the predominant evolutionary forces in the mitochondrial genomes of Rattus genus. The NADH dehydrogenase 4 gene (ND4) showed a highly elevated Ka/Ks ratio compared to the other protein-coding genes, which indicated ND4 was most likely under relaxed selection pressure. Phylogenetic analysis provided a well-supported outline of Rattus genus, and revealed two groups in the genus. R. nitidus had a sister relationship with R. norvegicus.     

Reductive genome evolution from the mother of Rickettsia

The Rickettsia genus is a group of obligate intracellular α-proteobacteria representing a paradigm of reductive evolution. Here, we investigate the evolutionary processes that shaped the genomes of the genus. The reconstruction of ancestral genomes indicates that their last common ancestor contained more genes, but already possessed most traits associated with cellular parasitism. The differences in gene repertoires across modern Rickettsia are mainly the result of differential gene losses from the ancestor. We demonstrate using computer simulation that the propensity of loss was variable across genes during this process. We also analyzed the ratio of nonsynonymous to synonymous changes (Ka/Ks) calculated as an average over large sets of genes to assay the strength of selection acting on the genomes of Rickettsia, Anaplasmataceae, and free-living γ-proteobacteria. As a general trend, Ka/Ks were found to decrease with increasing divergence between genomes. The high Ka/Ks for closely related genomes are probably due to a lag in the removal of slightly deleterious nonsynonymous mutations by natural selection. Interestingly, we also observed a decrease of the rate of gene loss with increasing divergence, suggesting a similar lag in the removal of slightly deleterious pseudogene alleles. For larger divergence (Ks > 0.2), Ka/Ks converge toward similar values indicating that the levels of selection are roughly equivalent between intracellular α-proteobacteria and their free-living relatives. This contrasts with the view that obligate endocellular microorganisms tend to evolve faster as a consequence of reduced effectiveness of selection, and suggests a major role of enhanced background mutation rates on the fast protein divergence in the obligate intracellular α-proteobacteria.     

Genome- Wide Analysis and Characterization of the TRX Gene Family in Upland Cotton

Thioredoxins (TRX) are small molecules of proteins that are present in all organisms. TRXs play an important role in diverse functions of plant growth and development. In this study, we performed genome-wide, characterization and expression levels of TRX gene family in cotton. A total of 150 GhTRX proteins were identified in upland cotton and classified into five subfamilies based on their domain compositions. Phylogenetic tree analysis divided TRX genes into seven subgroups. GhTRX genes covered all upland cotton chromosomes, with duplicated gene events. Ka/Ks ratio of three gene pairs was less than 1, suggesting purifying selection. The functions of GhTRX genes were studied using gene ontology, protein localization, and promoter analysis. Furthermore, six GhTRX genes were randomly selected to examine their expression level in cotton development and under various exogenous treatments. The genes showed high expressions in various tissues and at different stages of leaf senescence, also showed high expression under abscisic acid, ethylene, drought, and salinity. This study reveals the first report of TRX family genes in upland cotton. However further studies are needed to elucidate their specific functions in cotton plant.     

Average allozyme heterozygosity in vertebrates correlates with Ka/Ks measured in the human-mouse lineage

It is well established that different allozyme proteins vary in heterozygosity in averages made over large numbers of species. For example, the enzyme 6-phosphogluconate dehydrogenase has a much higher average heterozygosity than glutamate dehydrogenase. Allozyme data alone provide insufficient power to determine the evolutionary cause of such a difference. Many studies have now been carried out on the DNA sequences coding for allozymes. These have identified diverse selective and nonselective causes of polymorphisms at individual loci. However the studies are mainly in a small number of model species; thus, it is difficult to identify from these DNA studies specific causes of global average heterozygosity differences among allozyme proteins. Here we demonstrate that estimates of average heterozygosity for 37 allozyme proteins in vertebrates correlate positively with Ka and Ka/Ks but not with Ks, measured in the human-mouse lineage. The values of Ka/Ks are less than 0.25, and Ka/Ks is negatively correlated with subunit number (quaternary structure), a measure of structural constraint. Proteins with lower levels of constraint have higher values of both Ka/Ks and heterozygosity. These results better support the hypothesis that differences in average allozyme diversity between proteins are more closely related to differences in the level of purifying selection than to differences in the underlying mutation rate or level of positive selection.     

Transposon-mediated expansion and diversification of a family of ULP-like genes

Transposons comprise a major component of eukaryotic genomes, yet it remains controversial whether they are merely genetic parasites or instead significant contributors to organismal function and evolution. In plants, thousands of DNA transposons were recently shown to contain duplicated cellular gene fragments, a process termed transduplication. Although transduplication is a potentially rich source of novel coding sequences, virtually all appear to be pseudogenes in rice. Here we report the results of a genome-wide survey of transduplication in Mutator-like elements (MULEs) in Arabidopsis thaliana, which shows that the phenomenon is generally similar to rice transduplication, with one important exception: KAONASHI (KI). A family of more than 97 potentially functional genes and apparent pseudogenes, evidently derived at least 15 MYA from a cellular small ubiquitin-like modifier-specific protease gene, KI is predominantly located in potentially autonomous non-terminal inverted repeat MULEs and has evolved under purifying selection to maintain a conserved peptidase domain. Similar to the associated transposase gene but unlike cellular genes, KI is targeted by small RNAs and silenced in most tissues but has elevated expression in pollen. In an Arabidopsis double mutant deficient in histone and DNA methylation with elevated KI expression compared to wild type, at least one KI-MULE is mobile. The existence of KI demonstrates that transduplicated genes can retain protein-coding capacity and evolve novel functions. However, in this case, our evidence suggests that the function of KI may be selfish rather than cellular.     

Identification and characterisation of imprinted genes in the mouse.

Imprinted genes are expressed specifically from one or other parental allele. Over 70 are now known, and about one-half of these are expressed from the paternal allele and one-half from the maternal allele. Most imprinted genes are clustered within imprinting regions of the mouse genome, regions which are associated with abnormal phenotypes when inherited uniparentally. Imprinted genes have been identified from surveys based on differential expression or differential methylation according to parental origin, as well as analyses of candidate genes, mutants and imprinted gene clusters. Many imprinted genes affect growth and development, and more than 25 per cent determine non-coding RNAs that may have a function in controlling imprinted gene expression.     

Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes

Horizontal transfer (HT) alters the repertoire of symbiosis genes in rhizobial genomes and may play an important role in the on-going evolution of the rhizobia–legume symbiosis. To gain insight into the extent of HT of symbiosis genes with different functional roles (nodulation, N-fixation, host benefit and rhizobial fitness), we conducted comparative genomic and selection analyses of the full-genome sequences from 27 rhizobial genomes. We find that symbiosis genes experience high rates of HT among rhizobial lineages but also bear signatures of purifying selection (low Ka : Ks). HT and purifying selection appear to be particularly strong in genes involved in initiating the symbiosis (e.g. nodulation) and in genome-wide association candidates for mediating benefits provided to the host. These patterns are consistent with rhizobia adapting to the host environment through the loss and gain of symbiosis genes, but not with host-imposed positive selection driving divergence of symbiosis genes through recurring bouts of positive selection.