Synonymous Nucleotide Substitution Rates Research Articles

Natural selection on apical membrane antigen 1 (AMA1) of an emerging zoonotic malaria parasite Plasmodium inui

Apical membrane antigen 1 (AMA1) of malaria parasites plays an important role in host cell invasion. Antibodies to AMA1 can inhibit malaria merozoite invasion of erythrocytes while vaccine-induced specific cytotoxic T cell responses to this protein are associated with clinical protection. Polymorphisms in AMA1 of Plasmodium falciparum (PfAMA1) and P. vivax (PvAMA1) are of concern for vaccine development. To date, little is known about sequence diversity in ama1 of P. inui (Piama1), an emerging zoonotic malaria parasite. In this study, 80 complete Piama1 coding sequences were obtained from 57 macaques in Thailand that defined 60 haplotypes clustering in two phylogenetic lineages. In total, 74 nucleotide substitutions were identified and distributed unevenly across the gene. Blockwise analysis of the rates of synonymous (dS) and nonsynonymous (dN) nucleotide substitutions did not show a significant deviation from neutrality among Thai isolates. However, significantly negative Tajima’s D values were detected in domain I and the loop region of domain II, implying purifying selection. Codon-based analysis of dN/dS has identified 12 and 14 codons under positive and negative selections, respectively. Meanwhile, 85 amino acid substitutions were identified among 80 Thai and 11 non-Thai PiAMA1 sequences. Of these, 48 substituted residues had a significant alteration in physicochemical properties, suggesting positive selection. More than half of these positively selected amino acids (32 of 48) corresponded to the predicted B-cell or T-cell epitopes, suggesting that selective pressure could be mediated by host immunity. Importantly, 14 amino acid substitutions were singletons and predicted to be deleterious that could be subject to ongoing purifying selection or elimination. Besides genetic drift and natural selection, intragenic recombination identified in domain II could generate sequence variation in Piama1. It is likely that malarial ama1 exhibits interspecies differences in evolutionary histories. Knowledge of the sequence diversity of the Piama1 locus further provides an evolutionary perspective of this important malaria vaccine candidate.

Draft Genome of Akame (Lates Japonicus) Reveals Possible Genetic Mechanisms for Long-Term Persistence and Adaptive Evolution with Low Genetic Diversity.

It is known that some endangered species have persisted for thousands of years despite their very small effective population sizes and low levels of genetic polymorphisms. To understand the genetic mechanisms of long-term persistence in threatened species, we determined the whole genome sequences of akame (Lates japonicus), which has survived for a long time with extremely low genetic variations. Genome-wide heterozygosity in akame was estimated to be 3.3 to 3.4 × 10-4/bp, one of the smallest values in teleost fishes. Analysis of demographic history revealed that the effective population size in akame was around 1,000 from 30,000 years ago to the recent past. The relatively high ratio of nonsynonymous to synonymous heterozygosity in akame indicated an increased genetic load. However, a detailed analysis of genetic diversity in the akame genome revealed that multiple genomic regions, including genes involved in immunity, synaptic development, and olfactory sensory systems, have retained relatively high nucleotide polymorphisms. This implies that the akame genome has preserved the functional genetic variations by balancing selection, to avoid a reduction in viability and loss of adaptive potential. Analysis of synonymous and nonsynonymous nucleotide substitution rates has detected signs of positive selection in many akame genes, suggesting adaptive evolution to temperate waters after the speciation of akame and its close relative, barramundi (Lates calcarifer). Our results indicate that the functional genetic diversity likely contributed to the long-term persistence of this species by avoiding the harmful effects of the population size reduction.

Natural selection shapes the evolution of SARS-CoV-2 Omicron in Bangladesh.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved to give rise to a highly transmissive and immune-escaping variant of concern, known as Omicron. Many aspects of the evolution of SARS-CoV-2 and the driving forces behind the ongoing Omicron outbreaks remain unclear. Substitution at the receptor-binding domain (RBD) in the spike protein is one of the primary strategies of SARS-CoV-2 Omicron to hinder recognition by the host angiotensin-converting enzyme 2 (ACE2) receptor and avoid antibody-dependent defense activation. Here, we scanned for adaptive evolution within the SARS-CoV-2 Omicron genomes reported from Bangladesh in the public database GISAID (www.gisaid.org; dated 2 April 2023). The ratio of the non-synonymous (Ka) to synonymous (Ks) nucleotide substitution rate, denoted as ω, is an indicator of the selection pressure acting on protein-coding genes. A higher proportion of non-synonymous to synonymous substitutions (Ka/Ks or ω > 1) indicates positive selection, while Ka/Ks or ω near zero indicates purifying selection. An equal amount of non-synonymous and synonymous substitutions (Ka/Ks or ω = 1) refers to neutrally evolving sites. We found evidence of adaptive evolution within the spike (S) gene of SARS-CoV-2 Omicron isolated from Bangladesh. In total, 22 codon sites of the S gene displayed a signature of positive selection. The data also highlighted that the receptor-binding motif within the RBD of the spike glycoprotein is a hotspot of adaptive evolution, where many of the codons had ω > 1. Some of these adaptive sites at the RBD of the spike protein are known to be associated with increased viral fitness. The M gene and ORF6 have also experienced positive selection. These results suggest that although purifying selection is the dominant evolutionary force, positive Darwinian selection also plays a vital role in shaping the evolution of SARS-CoV-2 Omicron in Bangladesh.

Parallel Evolution of Sex-Linked Genes across XX/XY and ZZ/ZW Sex Chromosome Systems in the Frog Glandirana rugosa.

Genetic sex-determination features male (XX/XY) or female heterogamety (ZZ/ZW). To identify similarities and differences in the molecular evolution of sex-linked genes between these systems, we directly compared the sex chromosome systems existing in the frog Glandirana rugosa. The heteromorphic X/Y and Z/W sex chromosomes were derived from chromosomes 7 (2n = 26). RNA-Seq, de novo assembly, and BLASTP analyses identified 766 sex-linked genes. These genes were classified into three different clusters (XW/YZ, XY/ZW, and XZ/YW) based on sequence identities between the chromosomes, probably reflecting each step of the sex chromosome evolutionary history. The nucleotide substitution per site was significantly higher in the Y- and Z-genes than in the X- and W- genes, indicating male-driven mutation. The ratio of nonsynonymous to synonymous nucleotide substitution rates was higher in the X- and W-genes than in the Y- and Z-genes, with a female bias. Allelic expression in gonad, brain, and muscle was significantly higher in the Y- and W-genes than in the X- and Z-genes, favoring heterogametic sex. The same set of sex-linked genes showed parallel evolution across the two distinct systems. In contrast, the unique genomic region of the sex chromosomes demonstrated a difference between the two systems, with even and extremely high expression ratios of W/Z and Y/X, respectively.

A likely autotetraploidization event shaped the Chinese mahogany (Toona sinensis) genome

Chinese mahogany (Toona sinensis) is of considerable medical and economic importance, and its genome has been deciphered. However, the process underlying its polyploidy is unclear, and the chromosomal evolutionary trajectory is poorly understood. Here, by reanalysing the T. sinensis genome, we found evidence of a tetraploidization event (T. sinensis special tetraploidization, TST) that occurred approximately 15–17 million years ago (MYA) after the core eudicot-common hexaploidization (ECH or gamma) event. We characterized the synonymous nucleotide substitution rates (Ks values) of collinear genes and found that T. sinensis genes affected by the TST evolve at a slower rate than Acer yangbiense genes. Furthermore, we identified homologous genes related to polyploidization and speciation and constructed multiple alignments with different reference genomes. Notably, the significant balance of gene retention and loss characterized in the two TST-derived subgenomes suggests an autopolyploid nature of the TST. Moreover, we deduced the chromosomal karyotypes of the two subgenomes and identified 7 chromosomal fusions that have shaped the T. sinensis genome; more information is available on a newly constructed karyotype platform (http://www.cgrpoee.top/Toona_sinensis/index.html). The T. sinensis genome preserves the ancestral chromosome structure of dicotyledons well and could serve as a good reference for understanding genomic changes in other Meliaceae and Sapindales plants. In addition, we verified that tandem duplication and the ECH have promoted the expansion of terpene synthase (TPS) genes; conversely, the TST seems to have inhibited expansion of these genes. This present effort has clarified the polyploidy events of the T. sinensis genome, filled gaps in the history of karyotype evolution, and laid a solid foundation for further genomic studies in the Meliaceae research community and beyond.

Comprehensive Comparative Analysis and Development of Molecular Markers for Dianthus Species Based on Complete Chloroplast Genome Sequences

Dianthus spp. is a genus with high economic and ornamental value in the Caryophyllaceae, which include the famous fresh-cut carnation and the traditional Chinese herbal medicine, D. superbus. Despite the Dianthus species being seen everywhere in our daily lives, its genome information and phylogenetic relationships remain elusive. Thus, we performed the assembly and annotation of chloroplast genomes for 12 individuals from seven Dianthus species. On this basis, we carried out the first comprehensive and systematic analysis of the chloroplast genome sequence characteristics and the phylogenetic evolution of Dianthus. The chloroplast genome of 12 Dianthus individuals ranged from 149,192 bp to 149,800 bp, containing 124 to 126 functional genes. Sequence repetition analysis showed the number of simple sequence repeats (SSRs) ranged from 75 to 80, tandem repeats ranged from 23 to 41, and pair-dispersed repeats ranged from 28 to 43. Next, we calculated the synonymous nucleotide substitution rates (Ks) of all 76 protein coding genes to obtain the evolution rate of these coding genes in Dianthus species; rpl22 showed the highest Ks (0.0471), which suggested that it evolved the swiftest. By reconstructing the phylogenetic relationships within Dianthus and other species of Caryophyllales, 16 Dianthus individuals (12 individuals reported in this study and four individuals downloaded from NCBI) were divided into two strongly supported sister clades (Clade A and Clade B). The Clade A contained five species, namely D. caryophyllus, D. barbatus, D. gratianopolitanus, and two cultivars (‘HY’ and ‘WC’). The Clade B included four species, in which D. superbus was a sister branch with D. chinensis, D. longicalyx, and F1 ‘87M’ (the hybrid offspring F1 from D. chinensis and ‘HY’). Further, based on sequence divergence analysis and hypervariable region analysis, we selected several regions that had more divergent sequences, to develop DNA markers. Additionally, we found that one DNA marker can be used to differentiate Clade A and Clade B in Dianthus. Taken together, our results provide useful information for our understanding of Dianthus classification and chloroplast genome evolution.

Molecular Evolution of rbcL in Orthotrichales (Bryophyta): Site Variation, Adaptive Evolution, and Coevolutionary Patterns of Amino Acid Replacements.

Molecular evolution of the large subunit of the RuBisCO enzyme is understudied in early diverging land plants. These groups show morphological and eco-physiological adaptations to the uneven and intermittent distribution of water in the terrestrial environment. This might have prompted a continuous fine-tuning of RuBisCO under a selective pressure modifying the species-specific optima for photosynthesis in contrasting microdistributions and environmental niches. To gain a better insight into the molecular evolution of RuBisCO large subunits, the aim of this study was to assess the pattern of evolutionary change in the amino acid residues in a monophyletic group of Bryophyta (Orthotrichaceae). Tests for positive, neutral, or purifying selection at the amino acid level were assessed by comparing rates (ω) of non-synonymous (dN) and synonymous (dS) nucleotide substitutions along a Maximum Likelihood phylogenetic tree. Molecular adaptation tests using likelihood ratio tests, reconstruction of ancestral amino acid sites, and intra-protein coevolution analyses were performed. Variable amino acid sites (39) were unevenly distributed across the LSU. The residues are located on rbcL sites that are highly variable in higher plants and close to key regions implying dimer-dimer (L2L2), RuBisCO-activase interactions, and conformational functions during catalysis. Ten rbcL sites (32, 33, 91, 230, 247, 251, 255, 424, 449 and 475) have been identified by the Bayesian Empirical Bayes inference to be under positive selection and under adaptive evolution under the M8 model. The pattern of amino acid variation suggests that it is not lineage specific, but rather representative of a case of convergent evolution, suggesting recurrent changes that potentially favor the same amino acid substitutions that are likely optimized the RuBisCO activity.

Genome-wide analysis of cotton C2H2-zinc finger transcription factor family and their expression analysis during fiber development

BackgroundC2H2-zinc finger protein family is commonly found in the plant, and it is known as the key actors in the regulation of transcription and vital component of chromatin structure. A large number of the C2H2-zinc finger gene members have not been well characterized based on their functions and structure in cotton. However, in other plants, only a few C2H2-zinc finger genes have been studied.ResultsIn this work, we performed a comprehensive analysis and identified 386, 196 and 195 C2H2-zinc finger genes in Gossypium hirsutum (upland cotton), Gossypium arboreum and Gossypium raimondii, respectively. Phylogenetic tree analysis of the C2H2-zinc finger proteins encoding the C2H2-zinc finger genes were classified into seven (7) subgroups. Moreover, the C2H2-zinc finger gene members were distributed in all cotton chromosomes though with asymmetrical distribution patterns. All the orthologous genes were detected between tetraploid and the diploid cotton, with 154 orthologous genes pair detected between upland cotton and Gossypium arboreum while 165 orthologous genes were found between upland cotton and Gossypium raimondii. Synonymous (Ks) and non-synonymous (Ka) nucleotide substitution rates (Ka/Ks) analysis indicated that the cotton C2H2-zinc finger genes were highly influenced mainly by negative selection, which maintained their protein levels after the duplication events. RNA-seq data and RT-qPCR validation of the RNA seq result revealed differential expression pattern of some the C2H2-zinc finger genes at different stages of cotton fiber development, an indication that the C2H2-zinc finger genes play an important role in initiating and regulating fiber development in cotton.ConclusionsThis study provides a strong foundation for future practical genome research on C2H2-zinc finger genes in upland cotton. The expression levels of C2H2-zinc finger genes family is a pointer of their involvement in various biochemical and physiological functions which are directly related to cotton fiber development during initiation and elongation stages. This work not only provides a basis for determining the nominal role of the C2H2-zinc finger genes in fiber development but also provide valuable information for characterization of potential candidate genes involved in regulation of cotton fiber development.

Phylogenomic Rhizobium Species Are Structured by a Continuum of Diversity and Genomic Clusters.

The bacterial genus Rhizobium comprises diverse symbiotic nitrogen-fixing species associated with the roots of plants in the Leguminosae family. Multiple genomic clusters defined by whole genome comparisons occur within Rhizobium, but their equivalence to species is controversial. In this study we investigated such genomic clusters to ascertain their significance in a species phylogeny context. Phylogenomic inferences based on complete sets of ribosomal proteins and stringent core genome markers revealed the main lineages of Rhizobium. The clades corresponding to R. etli and R. leguminosarum species show several genomic clusters with average genomic nucleotide identities (ANI > 95%), and a continuum of divergent strains, respectively. They were found to be inversely correlated with the genetic distance estimated from concatenated ribosomal proteins. We uncovered evidence of a Rhizobium pangenome that was greatly expanded, both in its chromosomes and plasmids. Despite the variability of extra-chromosomal elements, our genomic comparisons revealed only a few chromid and plasmid families. The presence/absence profile of genes in the complete Rhizobium genomes agreed with the phylogenomic pattern of species divergence. Symbiotic genes were distributed according to the principal phylogenomic Rhizobium clades but did not resolve genome clusters within the clades. We distinguished some types of symbiotic plasmids within Rhizobium that displayed different rates of synonymous nucleotide substitutions in comparison to chromosomal genes. Symbiotic plasmids may have been repeatedly transferred horizontally between strains and species, in the process displacing and substituting pre-existing symbiotic plasmids. In summary, the results indicate that Rhizobium genomic clusters, as defined by whole genomic identities, might be part of a continuous process of evolutionary divergence that includes the core and the extrachromosomal elements leading to species formation.

Comparative transcriptome analysis reveals expression signatures of albino Russian sturgeon, Acipenseriformes gueldenstaedtii

Albinism is a genetically inherited condition that is caused by a series of genetic abnormalities leading to a reduction in melanin production. Russian sturgeon is one of the most valuable freshwater fish species worldwide, and albino individuals have been found in fish farms. Due to its complicated genome and scarce genome-wide genetic resources, the underlying molecular basis of albinism in Russian sturgeon is unknown. In the present study, we first generated transcriptome profile of Acipenser gueldenstaedtii using pooled tissues, which provided reliable reference sequences for future molecular genetic studies. A total of 369,441 contigs were assembled, corresponding to 32,965 unique genes. A comparative analysis of the transcripts from the skin of albino and wildtype individuals was conducted afterwards. A total of 785 unique genes were differentially expressed, including the upregulation of 385 genes and the downregulation of 400 genes in albino individuals. The expression pattern of 16 selected differentially expressed genes was validated using qRT-PCR. Additional annotation, GO enrichment analysis and gene pathway analysis indicated that the melanogenesis pathway may be interrupted in albinism. Eight potential causative genes that were highly likely to be responsible for sturgeon albinism were identified, including Dct, Tyrp1b, Slc45a2, Ctns, Pmela, Pmelb, Cd63, and Bloc1s3, which were found to be significantly down-regulated in albino Russian sturgeon. Moreover, a sliding window analysis of the ratio of nonsynonymous to synonymous nucleotide substitution rates (Ka/Ks) ratios indicated that seven out of the eight genes underwent positive selection during evolution. Our results provide a valuable basis for understanding the molecular mechanism of albinism in fish species and will facilitate future genetic selection and breeding of sturgeon with market-favored traits in aquaculture.

Protocols for the Molecular Evolutionary Analysis of Membrane Protein Gene Duplicates.

Gene duplication is an important process in the evolution of gene content in eukaryotic genomes. Understanding when gene duplicates contribute new molecular functions to genomes through molecular adaptation is one important goal in comparative genomics. In large gene families, however, characterizing adaptation and neofunctionalization across species is challenging, as models have traditionally quantified the timing of duplications without considering underlying gene trees. This protocol combines multiple approaches to detect adaptation in protein duplicates at a phylogenetic scale. We include a description of models for gene tree-species tree reconciliation that enable different types of inference, as well as a practical guide to their use. Although simulation-based approaches successfully detect shifts in the rate of duplication/retention, the conflation between the duplication and retention processes, the distinct trajectories of duplicates under non-, sub-, and neofunctionalization, as well as dosage effects offer hitherto unexplored analytical avenues. We introduce mathematical descriptions of these probabilities and offer a road map to computational implementation whose starting point is parsimony reconciliation. Sequence evolution information based on the ratio of nonsynonymous to synonymous nucleotide substitution rates (dN/dS) can be combined with duplicate survival probabilities to better predict the emergence of new molecular functions in retained duplicates. Together, these methods enable characterization of potentially adaptive candidate duplicates whose neofunctionalization may contribute to phenotypic divergence across species.

Purifying Selective Pressure Suggests the Functionality of a Vitamin B12 Biosynthesis Pathway in a Global Population of Mycobacterium tuberculosis.

Mycobacterium tuberculosis is one of the deadliest and most challenging pathogens to study in current microbiological research. One of the issues that remains to be resolved is the importance of cobalamin in the metabolism of M. tuberculosis. The functionality of a vitamin B12 biosynthesis pathway in M. tuberculosis is under dispute, and the ability of this pathogen to scavenge vitamin B12 from the host is unknown. Here, we quantified the ratios of nonsynonymous and synonymous nucleotide substitution rates (dN/dS) in the genes involved in vitamin B12 biosynthesis and transport and in genes encoding cobalamin-dependent enzymes in nearly four thousand strains of M. tuberculosis. We showed that purifying selection is the dominant force acting on cobalamin-related genes at the levels of individual codons, genes and groups of genes. We conclude that cobalamin-related genes may not be essential but are adaptive for M. tuberculosis in clinical settings. Furthermore, the cobalamin biosynthesis pathway is likely to be functional in this species.

Paralog analyses reveal gene duplication events and genes under positive selection in Ixodes scapularis and other ixodid ticks.

BackgroundHard ticks (family Ixodidae) are obligatory hematophagous ectoparasites of worldwide medical and veterinary importance. The haploid genomes of multiple species of ixodid ticks exceed 1 Gbp, prompting questions regarding gene, segmental and whole genome duplication in this phyletic group. The availability of the genome assembly for the black legged tick, Ixodes scapularis, and transcriptome datasets for multiple species of ticks offers an opportunity to assess the contribution of gene duplication to the genome. Here we developed a bioinformatics pipeline to identify and analyze duplicated genes (paralogs) using gene models from the prostriate tick, I. scapularis IscaW1.1 annotation and expressed sequence tags (ESTs) from I. scapularis and the metastriate ticks, Rhipicephalus microplus (southern cattle tick), R. appendiculatus (brown ear tick) and Amblyomma variegatum (tropical bont tick).ResultsApproximately 1-2 % of I. scapularis gene models and 2-14 % of ESTs from the four species represent duplicated genes. The ratio of non-synonymous to synonymous nucleotide substitution rates suggests ~ 25 % of duplicated genes are under positive selection pressure in each species. Analyses of synonymous substitution rates provide evidence for two duplication events in I. scapularis and R. microplus involving several hundred genes. Conservative molecular clock estimates based on synonymous substitution rates for species of Anopheles mosquitoes and the fruit fly, Drosophila melanogaster, suggest these events occurred within the last 50 MYA. Mapping of paralogs to the I. scapularis genome assembly supports tandem, or possibly segmental duplication events.ConclusionsThe present study marks the first genome-level analyses of gene duplication for the Ixodidae and provides insights into mechanisms shaping genome evolution in this group. At least two duplication events involving hundreds of genes may have occurred independently in the lineages prostriata and metastriata, with tandem and segmental duplication the most likely mechanisms for paralog generation. Duplicated genes under positive selection pressure may be linked to emerging functions in the tick and represent important candidates for further study.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2350-2) contains supplementary material, which is available to authorized users.

Convergent evolution of marine mammals is associated with distinct substitutions in common genes.

Phenotypic convergence is thought to be driven by parallel substitutions coupled with natural selection at the sequence level. Multiple independent evolutionary transitions of mammals to an aquatic environment offer an opportunity to test this thesis. Here, whole genome alignment of coding sequences identified widespread parallel amino acid substitutions in marine mammals; however, the majority of these changes were not unique to these animals. Conversely, we report that candidate aquatic adaptation genes, identified by signatures of likelihood convergence and/or elevated ratio of nonsynonymous to synonymous nucleotide substitution rate, are characterized by very few parallel substitutions and exhibit distinct sequence changes in each group. Moreover, no significant positive correlation was found between likelihood convergence and positive selection in all three marine lineages. These results suggest that convergence in protein coding genes associated with aquatic lifestyle is mainly characterized by independent substitutions and relaxed negative selection.

Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast.

BackgroundSelection on proteins is typically measured with the assumption that each protein acts independently. However, selection more likely acts at higher levels of biological organization, requiring an integrative view of protein function. Here, we built a kinetic model for de novo pyrimidine biosynthesis in the yeast Saccharomyces cerevisiae to relate pathway function to selective pressures on individual protein-encoding genes.ResultsGene families across yeast were constructed for each member of the pathway and the ratio of nonsynonymous to synonymous nucleotide substitution rates (dN/dS) was estimated for each enzyme from S. cerevisiae and closely related species. We found a positive relationship between the influence that each enzyme has on pathway function and its selective constraint.ConclusionsWe expect this trend to be locally present for enzymes that have pathway control, but over longer evolutionary timescales we expect that mutation-selection balance may change the enzymes that have pathway control.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0515-x) contains supplementary material, which is available to authorized users.

The effect of ecosystem biodiversity on virus genetic diversity depends on virus species: A study of chiltepin-infecting begomoviruses in Mexico.

Current declines in biodiversity put at risk ecosystem services that are fundamental for human welfare. Increasing evidence indicates that one such service is the ability to reduce virus emergence. It has been proposed that the reduction of virus emergence occurs at two levels: through a reduction of virus prevalence/transmission and, as a result of these epidemiological changes, through a limitation of virus genetic diversity. Although the former mechanism has been studied in a few host-virus interactions, very little is known about the association between ecosystem biodiversity and virus genetic diversity. To address this subject, we estimated genetic diversity, synonymous and non-synonymous nucleotide substitution rates, selection pressures, and frequency of recombinants and re-assortants in populations of Pepper golden mosaic virus (PepGMV) and Pepper huasteco yellow vein virus (PHYVV) that infect chiltepin plants in Mexico. We then analyzed how these parameters varied according to the level of habitat anthropization, which is the major cause of biodiversity loss. Our results indicated that genetic diversity of PepGMV (but not of PHYVV) populations increased with the loss of biodiversity at higher levels of habitat anthropization. This was mostly the consequence of higher rates of synonymous nucleotide substitutions, rather than of adaptive selection. The frequency of recombinants and re-assortants was higher in PepGMV populations infecting wild chiltepin than in those infecting cultivated ones, suggesting that genetic exchange is not the main mechanism for generating genetic diversity in PepGMV populations. These findings provide evidence that biodiversity may modulate the genetic diversity of plant viruses, but it may differentially affect even two closely related viruses. Our analyses may contribute to understanding the factors involved in virus emergence.

A simple method for estimating the strength of natural selection on overlapping genes.

Overlapping genes, where one DNA sequence codes for two proteins with different reading frames, are not uncommon in viruses and cellular organisms. Estimating the direction and strength of natural selection acting on overlapping genes is important for understanding their functionality, origin, evolution, maintenance, and potential interaction. However, the standard methods for estimating synonymous (dS) and nonsynonymous (dN) nucleotide substitution rates are inapplicable here because a nucleotide change can be simultaneously synonymous and nonsynonymous when both reading frames involved are considered. We have developed a simple method that can estimate dN/dS and test for the action of natural selection in each relevant reading frame of the overlapping genes. Our method is an extension of the modified Nei-Gojobori method previously developed for nonoverlapping genes. We confirmed the reliability of our method using extensive computer simulation. Applying this method, we studied the longest human sense–antisense overlapping gene pair, LRRC8E and ENSG00000214248. Although LRRC8E (leucine-rich repeat containing eight family, member E) is known to regulate cell size, the function of ENSG00000214248 is unknown. Our analysis revealed purifying selection on ENSG00000214248 and suggested that it originated in the common ancestor of bony vertebrates.

The Implication of Codon Usage Design and Expression Level in Determining the Nature of Selection and Functionality Amongst the Amino Acid Biosynthetic Pathway Coding Sequences of Arthrobacter sp. FB24

Amino acid biosynthesis is an immensely important life process requiring the participation of nearly hundred gene products, differing in terms of codon usage pattern, expressivity and selection pressure. In this study an attempt was made to categorize the gene products according to their expression level, nature of selection and functionality analyzing the amino acid biosynthetic pathway genes of the soil bacterium Arthrobacter, known for its varied metabolic activities and a key agent for industrial production of amino acids. The relationship between the different parameters like expression level, codon usage and selection pressure was calculated to find out the correlation of biasness, expression level, nature of selection and functionality amongst the genes involved in amino acid biosynthetic pathways. We found that genes coding for enzymes and proteins with large number of functions have higher codon usage bias and are subjected mostly to purifying selection. Gene sequences of proteins and enzymes with low functionality showed less codon usage bias and are under positive selection. The multifunctional genes mostly show high expression level and it is highly correlated with codon usage bias. The results of this study demonstrate that functionality and nature of selective forces acting on the coding sequences can be determined by studying the correlation between the different parameters like effective number of codon, codon adaptation index and nucleotide substitution ratios and careful study of all these parameters is a pretty good indicator for determining the functionality of the genes and this can be extended towards the genes of unknown function(s). Keywords: Amino acid biosynthetic pathways, Arthrobacter, CAI, Nc, Ka/Ks, synonymous and non-synonymous nucleotide substitution rates, positive selection, purifying selection.

Molecular Evolution, Characterization and Expression Profiling of Uterine Aldoketoreductase 1B5 Gene in Endometrium of Goat (Capra hircus)

Aldoketoreductase 1B5 (AKR1B5), a member of the Aldoketoreductase family, is involved in the production of Prostaglandin F2α (PGF2α) as one of vital prostaglandin F synthase (PGFS). PGs (Prostaglandins) play a crucial role in female reproductive system. In the present study, we cloned and characterized the full-length open reading frame of AKR1B5 gene in Black Bengal (BB) goat. The complete coding sequence of AKR1B5 comprises an entire open reading frame of 951 bp, encoding 316 amino acid (AA) residues. BB AKR1B5 showed >82.9% identity with that of cattle, rabbit, human, and rat at nucleotide and amino acid levels, respectively. Further, a systematic study of AKR1B5 sequence evolution was also conducted using Phylogenetic Analysis by Maximum Likelihood (PAML), entropy plot, and Blossum 62 in a phylogenetic context. Analysis of nonsynonymous to synonymous nucleotide substitution rate ratios (Ka/Ks) revealed that negative selection may have been operating on this gene during evolution in goat, cattle, rabbit, human, and rat, which showed its conservation across species. Further, expression of AKR1B5 was determined by quantitative real-time PCR in goat endometrial tissues at different stages of the estrous cycle and early pregnancy. Our results indicated its high expression at luteolytic phase (stage III; day 16–21) during the estrous cycle. However, during early (day ∼30–40) pregnancy the expression was highest as compared to estrous cycle.

New insights on the evolution of Leafy cotyledon1 (LEC1) type genes in vascular plants

NF-Y is a conserved oligomeric transcription factor found in all eukaryotes. In plants, this regulator evolved with a broad diversification of the genes coding for its three subunits (NF-YA, NF-YB and NF-YC). The NF-YB members can be divided into Leafy Cotyledon1 (LEC1) and non-LEC1 types. Here we presented a comparative genomic study using phylogenetic analyses to validate an evolutionary model for the origin of LEC-type genes in plants and their emergence from non-LEC1-type genes. We identified LEC1-type members in all vascular plant genomes, but not in amoebozoa, algae, fungi, metazoa and non-vascular plant representatives, which present exclusively non-LEC1-type genes as constituents of their NF-YB subunits. The non-synonymous to synonymous nucleotide substitution rates (Ka/Ks) between LEC1 and non-LEC1-type genes indicate the presence of positive selection acting on LEC1-type members to the fixation of LEC1-specific amino acid residues. The phylogenetic analyses demonstrated that plant LEC1-type genes are evolutionary divergent from the non-LEC1-type genes of plants, fungi, amoebozoa, algae and animals. Our results point to a scenario in which LEC1-type genes have originated in vascular plants after gene expansion in plants. We suggest that processes of neofunctionalization and/or subfunctionalization were responsible for the emergence of a versatile role for LEC1-type genes in vascular plants, especially in seed plants. LEC1-type genes besides being phylogenetic divergent also present different expression profile when compared with non-LEC1-type genes. Altogether, our data provide new insights about the LEC1 and non-LEC1 evolutionary relationship during the vascular plant evolution.