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Dioscorea alata, commonly known as “greater yam”, is a vital crop in tropical and subtropical regions of the world, yet it faces significant threats from anthracnose disease, mainly caused by Colletotrichum gloeosporioides. However, exploring disease resistance genes in this species has been challenging due to the difficulty of genetic mapping resulting from the loss of the flowering trait in many varieties. The receptor-like kinase (RLK) gene family represents essential immune receptors in plants. In this study, genomic analysis revealed 467 RLK genes in D. alata. The identified RLKs were distributed unevenly across chromosomes, likely due to tandem duplication events. However, a considerable number of ancient whole-genome or segmental duplications dating back over 100 million years contributed to the diversity of RLK genes. Phylogenetic analysis unveiled at least 356 ancient RLK lineages in the common ancestor of Dioscoreaceae, which differentially inherited and expanded to form the current RLK profiles of D. alata and its relatives. The analysis of cis-regulatory elements indicated the involvement of RLK genes in diverse stress responses. Transcriptome analysis identified RLKs that were up-regulated in response to C. gloeosporioides infection, suggesting their potential role in resisting anthracnose disease. These findings provide novel insights into the evolution of RLK genes in D. alata and their potential contribution to disease resistance.

The greater yam (Dioscorea alata), a widely cultivated and nutritious food crop, suffers from widespread yield reduction due to anthracnose caused by Colletotrichum gloeosporioides. Latent infection often occurs before anthracnose phenotypes can be detected, making early prevention difficult and causing significant harm to agricultural production. Through comparative genomic analysis of 60 genomes of 38 species from the Colletotrichum genus, this study identified 17 orthologous gene groups (orthogroups) that were shared by all investigated C. gloeosporioides strains but absent from all other Colletotrichum species. Four of the 17 C. gloeosporioides-specific orthogroups were used as molecular markers for PCR primer designation and C. gloeosporioides detection. All of them can specifically detect C. gloeosporioides out of microbes within and beyond the Colletotrichum genus with different sensitivities. To establish a rapid, portable, and operable anthracnose diagnostic method suitable for field use, specific recombinase polymerase amplification (RPA) primer probe combinations were designed, and a lateral flow (LF)-RPA detection kit for C. gloeosporioides was developed, with the sensitivity reaching the picogram (pg) level. In conclusion, this study identified C. gloeosporioides-specific molecular markers and developed an efficient method for C. gloeosporioides detection, which can be applied to the prevention and control of yam anthracnose as well as anthracnose caused by C. gloeosporioides in other crops. The strategy adopted by this study also serves as a reference for the identification of molecular markers and diagnosis of other plant pathogens.

Forty-eight male Lezhi black goat kids with similar body weight ((12.09±1.70) kg) and age ((60±5) d) were used to determine the effect of dietary copper (Cu), in the form of reagent grade Cu sulfate (CuSO4·5H2O), on performance, serum lipid profile, and the relative mRNA abundance of genes involved in lipid metabolism. Goat kids were stratified by body weight and randomly assigned to one of 4 treatment groups. Each treatment consisted of 12 replicate pens with each pen containing one goat kid. Treatment groups received the basal diet with no supplemental Cu (control), basal diet plus 10 mg of Cu kg−1 of dry matter (DM), basal diet plus 20 mg of Cu kg−1 of DM, or basal diet plus 30 mg of Cu kg−1 of DM. Goats were housed individually in pens and fed a high-concentrate pelleted diet for 60 d. Average daily gain, average daily feed intake and feed:gain of goats were not affected by dietary Cu supplementation (P>0.10). No differences were detected in serum total cholesterol, triglyceride, and high density lipoprotein cholesterol concentrations of goat kids fed with different Cu concentrations (P>0.05). However, serum low density lipoprotein cholesterol concentrations decreased linearly (P=0.01) as the concentration of dietary Cu increased. Intramuscular fat content of longissimus muscle increased (P=0.002) quadratically and liver Cu concentrations increased (P

Dioscorea alata L. (Dioscoreaceae) is a widely cultivated tuber crop with variations in tuber color, offering potential value as health-promoting foods. This study focused on the comparison of D. alata tubers possessing two distinct colors, white and purple, to explore the underlying mechanisms of color variation. Flavonoids, a group of polyphenols known to influence plant color and exhibit antioxidant properties, were of particular interest. The total phenol and total flavonoid analyses revealed that purple tubers (PTs) have a significantly higher content of these metabolites than white tubers (WTs) and a higher antioxidant activity than WTs, suggesting potential health benefits of PT D. alata. The transcriptome analysis identified 108 differentially expressed genes associated with the flavonoid synthesis pathway, with 57 genes up-regulated in PTs, including CHS, CHI, DFR, FLS, F3H, F3′5′H, LAR, ANS, and ANR. The metabolomics analysis demonstrated that 424 metabolites, including 104 flavonoids and 8 tannins, accumulated differentially in PTs and WTs. Notably, five of the top ten up-regulated metabolites were flavonoids, including 6-hydroxykaempferol-7-O-glucoside, pinocembrin-7-O-(6″-O-malonyl)glucoside, 6-hydroxykaempferol-3,7,6-O-triglycoside, 6-hydroxykaempferol-7-O-triglycoside, and cyanidin-3-O-(6″-O-feruloyl)sophoroside-5-O-glucoside, with the latter being a precursor to anthocyanin synthesis. Integrating transcriptome and metabolomics data revealed that the 57 genes regulated 20 metabolites within the flavonoid synthesis pathway, potentially influencing the tubers’ color variation. The high polyphenol content and antioxidant activity of PTs indicate their suitability as nutritious and health-promoting food sources. Taken together, the findings of this study provide insights into the molecular basis of tuber color variation in D. alata and underscore the potential applications of purple tubers in the food industry and human health promotion. The findings contribute to the understanding of flavonoid biosynthesis and pigment accumulation in D. alata tubers, opening avenues for future research on enhancing the nutritional quality of D. alata cultivars.

Carbon Capture and Storage (CCS) is one of the effective means to deal with global warming, and saline aquifer storage is considered to be the most promising storage method. Junggar Basin, located in the northern part of Xinjiang and with a large distribution area of saline aquifer, is an effective carbon storage site. Based on well logging data and 2D seismic data, a 3D heterogeneous geological model of the Cretaceous Donggou Formation reservoir near D7 well was constructed, and dynamic simulations under two scenarios of single-well injection and multi-well injection were carried out to explore the storage potential and CO2 storage mechanism of deep saline aquifer with real geological conditions in this study. The results show that within 100 km2 of the saline aquifer of Donggou Formation in the vicinity of D7 well, the theoretical static CO2 storage is 71.967 × 106 tons (P50)①, and the maximum dynamic CO2 storage is 145.295 × 106 tons (Case2). The heterogeneity of saline aquifer has a great influence on the spatial distribution of CO2 in the reservoir. The multi-well injection scenario is conducive to the efficient utilization of reservoir space and safer for storage. Based on the results from theoretical static calculation and the dynamic simulation, the effective coefficient of CO2 storage in deep saline aquifer in the eastern part of Xinjiang is recommended to be 4.9%. This study can be applied to the engineering practice of CO2 sequestration in the deep saline aquifer in Xinjiang.

Abstract Preeclampsia (PE) is a major cause of perinatal and maternal mortality and morbidity, which affects 2% to 8% of pregnancies in the world. The aberrant maternal inflammation and angiogenic imbalance have been demonstrated to contribute to the pathogenesis of PE. This research aimed to investigate the effect of Astragaloside IV (AsIV) in the treatment of PE and the underlying mechanisms. A rat PE‐like model was established by tail vein injection of lipopolysaccharide (LPS) and different doses of AsIV (40 and 80 mg/kg) were treated at the same time. Systolic blood pressure, total urine protein and urine volume were observed. Serum and placenta inflammatory cytokines were measured by ELISA kit. The mRNA and protein expression of relative genes were analyzed by qRT‐PCR and Western blotting. In PE‐like rats, there were obvious increases in systolic blood pressure, total urine protein and urine volume, which were obviously alleviated by treatment with AsIV. Serum levels of interleukin (IL)‐1β, tumor necrosis factor alpha (TNF‐α), IL‐6 and IL‐18, as well as IL‐4, IL‐10, PIGF, VEGF and sFlt‐1, were all reversed by treatment with AsIV. Meanwhile, AsIV treatment improved abnormal pregnancy outcomes, such as low litter size and low fetal weight. In addition, AsIV treatment downregulated the mRNA expression of inflammatory gene IL‐1β and IL‐6 in PE rats model, and AsIV treatment inhibited the activation of TLR‐4, NF‐κB, and sFlt‐1 in the placenta of PE rats. Our findings indicated the first evidence that AsIV alleviated PE‐like signs, and this improvement effect is possibly through inhibition of inflammation response via the TLR4/NF‐κB signaling pathway.

Dioscorea alata L. (Dioscoreaceae), commonly known as greater yam, water yam, or winged yam, is a popular tuber vegetable/food crop worldwide, with nutritional, health, and economical importance. China is an important domestication center of D. alata, and hundreds of cultivars (accessions) have been established. However, genetic variations among Chinese accessions remain ambiguous, and genomic resources currently available for the molecular breeding of this species in China are very scarce. In this study, we generated the first pan-plastome of D. alata, based on 44 Chinese accessions and 8 African accessions, and investigated the genetic variations, plastome evolution, and phylogenetic relationships within D. alata and among members of the section Enantiophyllum. The D. alata pan-plastome encoded 113 unique genes and ranged in size from 153,114 to 153,161 bp. A total of four whole-plastome haplotypes (Haps I–IV) were identified in the Chinese accessions, showing no geographical differentiation, while all eight African accessions shared the same whole-plastome haplotype (Hap I). Comparative genomic analyses revealed that all four whole plastome haplotypes harbored identical GC content, gene content, gene order, and IR/SC boundary structures, which were also highly congruent with other species of Enantiophyllum. In addition, four highly divergent regions, i.e., trnC–petN, trnL–rpl32, ndhD–ccsA, and exon 3 of clpP, were identified as potential DNA barcodes. Phylogenetic analyses clearly separated all the D. alata accessions into four distinct clades corresponding to the four haplotypes, and strongly supported that D. alata was more closely related to D. brevipetiolata and D. glabra than D. cirrhosa, D. japonica, and D. polystachya. Overall, these results not only revealed the genetic variations among Chinese D. alata accessions, but also provided the necessary groundwork for molecular-assisted breeding and industrial utilization of this species.

Secale cereale is an important crop in the Triticeae tribe of the Poaceae family, and it has unique agronomic characteristics and genome properties. It possesses resistance to many diseases and serves as an important resource for the breeding of other Triticeae crops. We performed a genome-wide study on S. cereale to identify the largest group of plant disease resistance genes (R genes), the nucleotide-binding site-leucine-rich repeat receptor (NBS-LRR) genes. In its genome, 582 NBS-LRR genes were identified, including one from the RNL subclass and 581 from the CNL subclass. The NBS-LRR gene number in the S. cereale genome is greater than that in barley and the diploid wheat genomes. S. cereale chromosome 4 contains the largest number of NBS-LRR genes among the seven chromosomes, which is different from the pattern in barley and the genomes B and D of wheat but similar to that in the genome A of wheat. Further synteny analysis suggests that more NBS-LRR genes on chromosome 4 have been inherited from a common ancestor by S. cereale and the wheat genome A than the wheat genomes B and D. Phylogenetic analysis revealed that at least 740 NBS-LRR lineages are present in the common ancestor of S. cereale, Hordeum vulgare and Triticum urartu. However, most of them have only been inherited by one or two species, with only 65 of them preserved in all three species. The S. cereale genome inherited 382 of these ancestral NBS-LRR lineages, but 120 of them have been lost in both H. vulgare and T. urartu. This study provides the full NBS-LRR profile of the S. cereale genome, which is a resource for S. cereale breeding and indicates that S. cereale can be an important material for the molecular breeding of other Triticeae crops.

Nucleotide-binding site (NBS)-type disease resistance genes (R genes) play key roles in plant immune responses and have co-evolved with pathogens over the course of plant lifecycles. Comparative genomic studies tracing the dynamic evolution of NBS-encoding genes have been conducted using many important plant lineages. However, studies on Sapindaceae species have not been performed. In this study, a discrepant number of NBS-encoding genes were identified in the genomes of Xanthoceras sorbifolium (180), Dinnocarpus longan (568), and Acer yangbiense (252). These genes were unevenly distributed and usually clustered as tandem arrays on chromosomes, with few existed as singletons. The phylogenetic analysis revealed that NBS-encoding genes formed three monophyletic clades, RPW8-NBS-LRR (RNL), TIR-NBS-LRR (TNL), and CC-NBS-LRR (CNL), which were distinguished by amino acid motifs. The NBS-encoding genes of the X. sorbifolium, D. longan, and A. yangbiense genomes were derived from 181 ancestral genes (three RNL, 23 TNL, and 155 CNL), which exhibited dynamic and distinct evolutionary patterns due to independent gene duplication/loss events. Specifically, X. sorbifolium exhibited a “first expansion and then contraction” evolutionary pattern, while A. yangbiense and D. longan exhibited a “first expansion followed by contraction and further expansion” evolutionary pattern. However, further expansion in D. longan was stronger than in A. yangbiense after divergence, suggesting that D. longan gained more genes in response to various pathogens. Additionally, the ancient and recent expansion of CNL genes generated the dominance of this subclass in terms of gene numbers, while the low copy number status of RNL genes was attributed to their conserved functions.

Dioscorea rotundata is an important food crop that is mainly cultivated in subtropical regions of the world. D. rotundata is frequently infected by various pathogens during its lifespan, which results in a substantial economic loss in terms of yield and quality. The disease resistance gene (R gene) profile of D. rotundata is largely unknown, which has greatly hampered molecular study of disease resistance in this species. Nucleotide-binding site–leucine-rich repeat (NBS-LRR) genes are the largest group of plant R genes, and they play important roles in plant defense responses to various pathogens. In this study, 167 NBS-LRR genes were identified from the D. rotundata genome. Subsequently, one gene was assigned to the resistance to powdery mildew8 (RPW8)-NBS-LRR (RNL) subclass and the other 166 genes to the coiled coil (CC)-NBS-LRR (CNL) subclass. None of the Toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) genes were detected in the genome. Among them, 124 genes are located in 25 multigene clusters and 43 genes are singletons. Tandem duplication serves as the major force for the cluster arrangement of NBS-LRR genes. Segmental duplication was detected for 18 NBS-LRR genes, although no whole-genome duplication has been documented for the species. Phylogenetic analysis revealed that D. rotundata NBS-LRR genes share 15 ancestral lineages with Arabidopsis thaliana genes. The NBS-LRR gene number increased by more than a factor of 10 during D. rotundata evolution. A conservatively evolved ancestral lineage was identified from D. rotundata, which is orthologs to the Arabidopsis RPM1 gene. Transcriptome analysis for four different tissues of D. rotundata revealed a low expression of most NBS-LRR genes, with the tuber and leaf displaying a relatively high NBS-LRR gene expression than the stem and flower. Overall, this study provides a complete set of NBS-LRR genes for D. rotundata, which may serve as a fundamental resource for mining functional NBS-LRR genes against various pathogens.

Plant resistance conferred by nucleotide binding site (NBS)-encoding resistance genes plays a key role in the defense against various pathogens throughout the entire plant life cycle. However, comparative analyses for the systematic evaluation and determination of the evolutionary modes of NBS-encoding genes among Solanaceae species are rare. In this study, 447, 255, and 306 NBS-encoding genes were identified from the genomes of potato, tomato, and pepper, respectively. These genes usually clustered as tandem arrays on chromosomes; few existed as singletons. Phylogenetic analysis indicated that three subclasses [TNLs (TIR-NBS-LRR), CNLs (CC-NBS-LRR), and RNLs (RPW8-NBS-LRR)] each formed a monophyletic clade and were distinguished by unique exon/intron structures and amino acid motif sequences. By comparing phylogenetic and systematic relationships, we inferred that the NBS-encoding genes in the present genomes of potato, tomato, and pepper were derived from 150 CNL, 22 TNL, and 4 RNL ancestral genes, and underwent independent gene loss and duplication events after speciation. The NBS-encoding genes therefore exhibit diverse and dynamic evolutionary patterns in the three Solanaceae species, giving rise to the discrepant gene numbers observed today. Potato shows a “consistent expansion” pattern, tomato exhibits a pattern of “first expansion and then contraction,” and pepper presents a “shrinking” pattern. The earlier expansion of CNLs in the common ancestor led to the dominance of this subclass in gene numbers. However, RNLs remained at low copy numbers due to their specific functions. Along the evolutionary process of NBS-encoding genes in Solanaceae, species-specific tandem duplications contributed the most to gene expansions.

In order to distinguish the spammers efficiently,a classifier based on the behavior characteristics was established.By analyzing the previous research,the ratio of followers,total number of blog posts,the number of friends,comprehensive quality evaluation and favorites according to latest data set,the Weibo spammers’ identification algorithm was realized based on Bayesian model and genetic algorithm.The experiment result based on the real-time data of Sina Weibo verify that the Bayesian model recognition algorithm can ensure spammers recognition accuracy without sacrificing recognition rate of non-spammers,and the proposed threshold value matrix proposed optimization can significantly improve recognition accuracy navy.

Glycosides of Cistanche (GC) is a preparation used extensively for its neuroprotective effect against neurological diseases, but its mechanisms of action remains incompletely understood. Here, we established a bilateral common carotid artery occlusion model of vascular dementia in rats and injected the model rats with a suspension of GC (10 mg/kg/day, intraperitoneally) for 14 consecutive days. Immunohistochemistry showed that GC significantly reduced p-tau and amyloid beta (Aβ) immunoreactivity in the hippocampus of the model rats. Proteomic analysis demonstrated upregulation of mitochondrial precursor protein and downregulation of keratin type II cytoskeletal 6A after GC treatment compared with model rats that had received saline. Western blot assay confirmed these findings. Our results suggest that the neuroprotective effect of GC in vascular dementia occurs via the promotion of neuronal cytoskeleton regeneration.

The study was conducted to compare and evaluate effects of four different macro-algaes on growth, immune response, and intestinal microbiota of Litopenaeus vannamei. In the rearing trial 1, shrimp were fed five diets containing four sources of macro-algaes for 8 weeks, named D1 (without macro-algae), D2 (Porphyra haitanensis), D3 (Undaria pinnatifida), D4 (Saccharina japonica), and D5 (Gracilaria lemaneiformis), respectively. Growth performance of shrimp in D5 diet was significantly higher than that of shrimp fed the control and D4 diet (P < 0.05); however, there is no significant difference among D2, D3, and D5 diets (P > 0.05). Apparent digestibility coefficients of dry matter from the D2, D3, and D5 diets were significantly higher than that from the control and D4 diets (P < 0.05). Supplementary macro-algaes enhanced hepatopancreas immunity through positively increasing total antioxidant status (TAS) and prophenoloxidase activity (ProPO), as well as up-regulating the hepatopancreas RNA expression of ProPO and IκBα and down-regulating the expression of transforming growth factor β. Furthermore, dietary macro-algaes modified intestinal microbiota of L. vannamei, boosting the relative abundance of beneficial bacterial such as Bacteroidetes, Firmicutes, and Bacillaceae, and decreasing those detrimental bacterial such as Gammaproteobacteria and Vibrionaceae. In the white spot syndrome virus (WSSV) challenge trial, shrimps were injected for 6-day after the rearing trial. On the fourth day, shrimp death started to occur, and the mortality in D2, D3, and D5 diets was significantly lower than that in control and SJ diets during 4–6 challenged days (P < 0.05). Dietary macro-algaes ameliorated hepatopancreas damage in L. vannamei by increasing TAS and ProPO activities and decreasing SOD activity, inhibiting the lipid peroxidation (malondialdehyde), as well as regulating the immune-related genes expression. Taken together, dietary macro-algaes availably relieved enterohepatic oxidative damage by improving antioxidant ability and immunity and regulated intestinal microbiota in L. vannamei. These results indicated that G. lemaneiformis is the most suitable macro-algae and then followed by U. pinnatifida and P. haitanensis as the feed ingredient for L. vannamei.

A novel approach to locate the fault for null pointer exception is presented.The approach first computes the static slice guided by the runtime stack,then conducts a null-pointer analysis and aliases analysis on the sliced program and obtains the suspicious statements that throw null-pointer exceptions,and finally generates a fault localization report.The experimental study indicates that,although time spent in runtime stack information collecting and aliases transferring,the proposed approach can narrow the searching space of the problem with runtime stack,and discover the value transfer process with aliases analysis,thereby eliminating false negative and false positive,and improving the effectiveness of fault localization.

The Toll-interleukin-1 receptor (TIR) and Nucleotide-binding site (NBS) domains are two major components of the TIR-NBS-leucine-rich repeat family plant disease resistance genes. Extensive functional and evolutionary studies have been performed on these genes; however, the characterization of a small group of genes that are composed of atypical TIR and NBS domains, namely XTNX genes, is limited. The present study investigated this specific gene family by conducting genome-wide analyses of 59 green plant genomes. A total of 143 XTNX genes were identified in 51 of the 52 land plant genomes, whereas no XTNX gene was detected in any green algae genomes, which indicated that XTNX genes originated upon emergence of land plants. Phylogenetic analysis revealed that the ancestral XTNX gene underwent two rounds of ancient duplications in land plants, which resulted in the formation of clades I/II and clades IIa/IIb successively. Although clades I and IIb have evolved conservatively in angiosperms, the motif composition difference and sequence divergence at the amino acid level suggest that functional divergence may have occurred since the separation of the two clades. In contrast, several features of the clade IIa genes, including the absence in the majority of dicots, the long branches in the tree, the frequent loss of ancestral motifs, and the loss of expression in all detected tissues of Zea mays, all suggest that the genes in this lineage might have undergone pseudogenization. This study highlights that XTNX genes are a gene family originated anciently in land plants and underwent specific conservative pattern in evolution.

To provide a resource of sisal-specific expressed sequence data and facilitate this powerful approach in new gene research, the preparation of normalized cDNA libraries enriched with full-length sequences is necessary. Four libraries were produced with RNA pooled from Agave sisalana multiple tissues to increase efficiency of normalization and maximize the number of independent genes by SMART™ method and the duplex-specific nuclease (DSN). This procedure kept the proportion of full-length cDNAs in the subtracted/normalized libraries and dramatically enhanced the discovery of new genes. Sequencing of 3875 cDNA clones of libraries revealed 3320 unigenes with an average insert length about 1.2 kb, indicating that the non-redundancy of libraries was about 85.7%. These unigene functions were predicted by comparing their sequences to functional domain databases and extensively annotated with Gene Ontology (GO) terms. Comparative analysis of sisal unigenes and other plant genomes revealed that four putative MADS-box genes and knotted-like homeobox (knox) gene were obtained from a total of 1162 full-length transcripts. Furthermore, real-time PCR showed that the characteristics of their transcripts mainly depended on the tight expression regulation of a number of genes during the leaf and flower development. Analysis of individual library sequence data indicated that the pooled-tissue approach was highly effective in discovering new genes and preparing libraries for efficient deep sequencing.

Plant genomes harbor dozens to hundreds of nucleotide-binding site-leucine-rich repeat (NBS-LRR, NBS for short) type disease resistance genes (Shao et al., 2014; Zhang et al., 2015). Proper regulation of these genes is important for normal growth of plants by reducing unnecessary fitness costs in the absence of pathogen infection. Recent studies have revealed that microRNAs are involved in regulation of NBS genes in plants (Zhai et al., 2011; Shivaprasad et al., 2012). This protocol describes computational methods for the genome-wide identification of plant NBS genes potentially regulated by microRNAs.

The Histidine Triad Proteins (HTPs), also known as Pht proteins in Streptococcus pneumoniae, constitute a family of surface-exposed proteins that exist in many pathogenic streptococcal species. Although many studies have revealed the importance of HTPs in streptococcal physiology and pathogenicity, little is known about their origin and evolution. In this study, after identifying all htp homologs from 105 streptococcal genomes representing 38 different species/subspecies, we analyzed their domain structures, positions in genome, and most importantly, their evolutionary histories. By further projecting this information onto the streptococcal phylogeny, we made several major findings. First, htp genes originated earlier than the Streptococcus genus and gene-loss events have occurred among three streptococcal groups, resulting in the absence of the htp gene in the Bovis, Mutans and Salivarius groups. Second, the copy number of htp genes in other groups of Streptococcus is variable, ranging from one to four functional copies. Third, both phylogenetic evidence and domain structure analyses support the division of two htp subfamilies, designated as htp I and htp II. Although present mainly in the pyogenic group and in Streptococcus suis, htp II members are distinct from htp I due to the presence of an additional leucine-rich-repeat domain at the C-terminus. Finally, htp genes exhibit a faster nucleotide substitution rate than do housekeeping genes. Specifically, the regions outside the HTP domains are under strong positive selection. This distinct evolutionary pattern likely helped Streptococcus to easily escape from recognition by host immunity.

BackgroundIn yeast coding sequences, once a particular codon has been used, subsequent occurrence of the same amino acid tends to use codons sharing the same tRNA. Such a phenomenon of co-tRNA codons pairing bias (CTCPB) is also found in some other eukaryotes but it is not known whether it occurs in prokaryotes.Methodology/principal findingsIn this study, we focused on a total of 773 bacterial genomes to investigate their synonymous codon pairing preferences. After calculating the actual frequencies of synonymous codon pairs and comparing them with their expected values, we detected an obvious pairing bias towards identical codon pairs. This seems consistent with the previously reported CTCPB phenomenon, since identical codons are certainly read by the same tRNA. However, among co-tRNA but non-identical codon pairs, only 22 were often found overrepresented, suggesting that many co-tRNA codons actually do not preferentially pair together in prokaryotes. Therefore, the previously reported co-tRNA codons pairing rule needs to be more rigorously defined. The affinity differences between a tRNA anticodon and its readable codons should be taken into account. Moreover, both within-gene-shuffling tests and phylogenetic analyses support the idea that translational selection played an important role in shaping the observed synonymous codon pairing pattern in prokaryotes.ConclusionsOverall, a high level of synonymous codon pairing bias was detected in 73% investigated bacterial species, suggesting the synonymous codon ordering strategy has been prevalently adopted by prokaryotes to improve their translational efficiencies. The findings in this study also provide important clues to better understand the complex dynamics of translational process.