Human enterovirus 71 viruses have been long circulating throughout the world. In this study, we performed a positive selection analysis of the VP1 genes of capsid proteins from Enterovirus 71 viruses. Our results show...Human enterovirus 71 viruses have been long circulating throughout the world. In this study, we performed a positive selection analysis of the VP1 genes of capsid proteins from Enterovirus 71 viruses. Our results showed that although most sites were under negative or neutral evolution, four positions of the VP1 genes were under positive selection pressure. This might account for the spread and frequent outbreaks of the viruses and the enhanced neurovirulence. In particular, position 98 might be involved in neutralizing antibodies, modulating the virus-receptor interaction and enhancing the virulence of the viruses. Moreover, both positions 145 and 241 might correlate to determine the receptor specificity. However, these positions did not display much difference in amino acid polymorphism. In addition, no position in the VP1 genes of viruses isolated from China was under positive selection.展开更多
T cells are derived from progenitor thymocytes, of which only a minority receive the appropriate TCR signal, undergo positive selection and mature. Owing to the very short lifespan of thymocytes, the prerequisite for ...T cells are derived from progenitor thymocytes, of which only a minority receive the appropriate TCR signal, undergo positive selection and mature. Owing to the very short lifespan of thymocytes, the prerequisite for posi- tive selection is survival. TCR signal-induced Bcl-2 expression is believed to play a dominant role in the survival of positively selecting thymocytes, but how Bcl-2 is directly regulated is unknown. Here we report that the immediate early gene （IEG） c-Fos can stimulate the expression of Bcl-2, depending on a specific AP-l-binding site in the Bcl-2 promoter. In c-Fos transgenic （Fos-Tg） mice, c-Fos binds to this site and promotes the expression of Bcl-2. As a result, Fos-Tg thymocytes exhibited enhanced survival, and more mature single-positive （SP） thymocytes were generated, even on a unique TCR background. The TCR repertoire remained normal in Fos-Tg mice. Our results identified c-Fos as the mediator of the stimulatory effect of TCR signaling on Bcl-2 expression. Therefore, c-Fos, as an IEG, because of its early response ability, can quickly rescue the survival of short-lived thymocytes during positive selection. Our results provide novel insight into the mechanism regulating the survival of positively selecting thymocytes.展开更多
People living on the high plateaus of the world have long fascinated biological anthropologists and geneticists because they live in ＂thin air＂ and epitomize an extreme of human biological adaptation.
The Mariana Trench,the deepest trench on the earth,is ideal for deep-sea adaptation research due to its unique characters,such as the highest hydrostatic pressure on the Earth,constant ice-cold temperature,and eternal...The Mariana Trench,the deepest trench on the earth,is ideal for deep-sea adaptation research due to its unique characters,such as the highest hydrostatic pressure on the Earth,constant ice-cold temperature,and eternal darkness.In this study,tissues of a the hadal holothurian(Paelopatides sp.)were fi xed with RNA later in situ at~6501-m depth in the Mariana Trench,which,to our knowledge,is the deepest in-situ fi xed animal sample.A high-quality transcript was obtained by de-novo transcriptome assembly.A maximum likelihood tree was constructed based on the single copy orthologs across nine species with their available omics data.To investigate deep-sea adaptation,113 positively selected genes(PSGs)were identifi ed in Paelopatides sp.Some PSGs such as microphthalmia-associated transcription factor(MITF)may contribute to the distinct phenotype of Paelopatides sp.,including its translucent white body and degenerated ossicles.At least eight PSGs(transcription factor 7-like 2[TCF7L2],ETS-related transcription factor Elf-2-like[ELF2],PERQ amino acid-rich with GYF domain-containing protein[GIGYF],cytochrome c oxidase subunit 7a,[COX7A],type I thyroxine 5′-deiodinase[DIO1],translation factor GUF1[GUF1],SWI/SNF related-matrix-associated actin-dependent regulator of chromatin subfamily C and subfamily E,member 1[SMARCC]and[SMARCE1])might be related to cold adaptation.In addition,at least nine PSGs(cell cycle checkpoint control protein[RAD9A],replication factor A3[RPA3],DNA-directed RNA polymerases I/II/III subunit RPABC1[POLR2E],putative TAR DNA-binding protein 43 isoform X2[TARDBP],ribonucleoside-diphosphate reductase subunit M1[RRM1],putative serine/threonine-protein kinase[SMG1],transcriptional regulator[ATRX],alkylated DNA repair protein alkB homolog 6[ALKBH6],and PLAC8 motif-containing protein[PLAC8])may facilitate the repair of DNA damage induced by the high hydrostatic pressure,coldness,and high concentration of cadmium in the upper Mariana Trench.展开更多
Ulvophytes are attractive model systems for understanding the evolution of growth,development,and environmental stress responses.They are untapped resources for food,fuel,and high-value compounds.The rapid and abundan...Ulvophytes are attractive model systems for understanding the evolution of growth,development,and environmental stress responses.They are untapped resources for food,fuel,and high-value compounds.The rapid and abundant growth of Ulva species makes them key contributors to coastal biogeochemical cycles,which can cause significant environmental problems in the form of green tides and biofouling.Until now,the Ulva mutabilis genome is the only Ulva genome to have been sequenced.To obtain further insights into the evolutionary forces driving divergence in Ulva species,we analyzed 3905 single copy ortholog family from U.mutabilis,Chlamydomonas reinhardtii and Volvox carteri to identify genes under positive selection(GUPS)in U.mutabilis.We detected 63 orthologs in U.mutabilis that were considered to be under positive selection.Functional analyses revealed that several adaptive modifications in photosynthesis,amino acid and protein synthesis,signal transduction and stress-related processes might explain why this alga has evolved the ability to grow very rapidly and cope with the variable coastal ecosystem environments.展开更多
The ataxin-2 （ATXN2） gene is located on human chromo-some 12q24.1. In normal individuals, the coding region in exon 1 of this gene has fewer than 31 CAG repeats （Yu et al., 2005： Laffita-Mesa et al., 2012）. Howev...The ataxin-2 （ATXN2） gene is located on human chromo-some 12q24.1. In normal individuals, the coding region in exon 1 of this gene has fewer than 31 CAG repeats （Yu et al., 2005： Laffita-Mesa et al., 2012）. However, an abnormal expansion of CAG trinucleotide repeats results in the aggre-gation of polyglutamine （polyQ）, which causes spinocer-ebellar ataxia type 2 （SCA2） （Pulst et al., 1996）. The expanded alleles have more than 32 repeats in the affected individuals, and generally there is an inverse correlation between CAG repeat length and age of onset （Pulst et al., 1996）. SCA2 is an autosomal dominant inheritance neurodegenerative disease, whose major clinical feature is progressive cerebellar ataxia. Atrophies of the brainstem and frontal lobe have been frequently detected by magnetic resonance imaging （MRI） （Yamamoto-Watanabe et al., 2010）. This disease has the strong effect on sensory and motor control.展开更多
Vegetative insecticidal proteins （VIPs）, produced during the vegetative stage of their growth in Bacillus thuringiensis, are a group of insecticidal proteins and represent the second generation of insecticidal trans...Vegetative insecticidal proteins （VIPs）, produced during the vegetative stage of their growth in Bacillus thuringiensis, are a group of insecticidal proteins and represent the second generation of insecticidal trans-genes that will complement the novel δendotoxins in future. Fewer structural and functional relationships of Vip proteins are known in comparison with those of δ-endotoxins. In this study, both the maximum-likelihood methods and the maximum parsimony based sliding window analysis were used to evaluate the molecular evolution of Vip proteins. As a result, strong evidence was found that Vip proteins are subject to the high rates of positive selection, and 16 sites are identified to be under positive selection using the Bayes Empirical Bayesian method. Interestingly, all these positively selected sites are located from site-705 to site-809 in the C-terminus of the Vip proteins. Most of these sites are exposed and clustered in the loop regions when mapped onto its computational predicted secondary tertiary and a part of the tertiary structure. It has been postulated that the high divergence in the C-terminal of Vip proteins may not result from the lack of functional constraints, but rather from the rapid mutation to adapt their targeted insects, driven by positive selection. The potential positive selection pressures may be an attempt to adapt for the ＂arm race＂ between Vip proteins and the targeted insects, or to enlarge their target＇s host range. Sites identified to be under positive selection may be related to the insect host range, which may shed a light on the investigation of the Vip proteins＇ structural and functional relationships.展开更多
The surface glycoprotein hemagglutinin （HA） helps the influenza A virus to evade the host immune system by antigenic variation and is a major driving force for viral evolution. In this study, the selection pressure ...The surface glycoprotein hemagglutinin （HA） helps the influenza A virus to evade the host immune system by antigenic variation and is a major driving force for viral evolution. In this study, the selection pressure on HA of H5N1 influenza A virus was analyzed using bioinformatics algorithms. Most of the identified positive selection （PS） sites were found to be within or adjacent to epitope sites. Some of the identified PS sites are consistent with previous experimental studies, providing further support to the biological significance of our findings. The highest frequency of PS sites was observed in recent strains isolated during 2005-2007. Phylogenetic analysis was also conducted on HA sequences from various hosts. Viral drift is almost similar in both avian and human species with a progressive trend over the years. Our study reports new mutations in functional regions of HA that might provide markers for vaccine design or can be used to predict isolates of pandemic potential.展开更多
There is increasing interest in studying the molecular mechanisms of recent adaptations caused by positive selection in the genomics era. Such endeavors to detect recent positive selection, however, have been severely...There is increasing interest in studying the molecular mechanisms of recent adaptations caused by positive selection in the genomics era. Such endeavors to detect recent positive selection, however, have been severely handicapped by false positives due to the confounding impact of demography and the population structure. To reduce false positives, it is critical to conduct a functional analysis to identify the true candidate genes/mutations from those that are filtered through neutrality tests. However, the extremely high cost of such functional analysis may restrict studies within a small number of model species. In particular, when the false positive rate of neutrality tests is high, the efficiency of the functional analysis will also be very low. Therefore, although the recent improvements have been made in the （joint） inference of demography and selection, our ultimate goal, which is to understand the mechanism of adaptation generally in a wide variety of natural populations, may not be achieved using the currently available approaches. More attention should thus be spent on the development of more reliable tests that could not only free themselves from the confounding impact of demography and the population structure but also have reasonable power to detect selection.展开更多
HIV-1 co-receptor tropism is central for understanding the transmission and pathogenesis of HIV-1 infection. We performed a genome-wide comparison between the adaptive evolution of R5 and X4 variants from HIV-1 subtyp...HIV-1 co-receptor tropism is central for understanding the transmission and pathogenesis of HIV-1 infection. We performed a genome-wide comparison between the adaptive evolution of R5 and X4 variants from HIV-1 subtypes B and C. The results showed that R5 and X4 variants experienced differential evolutionary patterns and different HIV-1 genes encountered various positive selection pressures, suggesting that complex selection pressures are driving HIV-1 evolution. Compared with other hypervariable regions of Gp120, significantly more positively selected sites were detected in the V3 region of subtype B X4 variants, V2 region of subtype B R5 variants, and V1 and V4 regions of subtype C X4 variants, indicating an association of positive selection with co-receptor recognition/binding. Intriguingly, a significantly higher proportion (33.3% and 55.6%, P【0.05) of positively selected sites were identified in the C3 region than other conserved regions of Gp120 in all the analyzed HIV-1 variants, indicating that the C3 region might be more important to HIV-1 adaptation than previously thought. Approximately half of the positively selected sites identified in the env gene were identical between R5 and X4 variants. There were three common positively selected sites (96, 113 and 281) identified in Gp41 of all X4 and R5 variants from subtypes B and C. These sites might not only suggest a functional importance in viral survival and adaptation, but also imply a potential cross-immunogenicity between HIV-1 R5 and X4 variants, which has important implications for AIDS vaccine development.展开更多
Eight intact LTR retrotransposons （Nbr1-Nbr8） have been previously characterized from the genome of Nosema bombycis, a eu- karyotic parasite with a compact and reduced genome. Here we describe six novel transcribed ...Eight intact LTR retrotransposons （Nbr1-Nbr8） have been previously characterized from the genome of Nosema bombycis, a eu- karyotic parasite with a compact and reduced genome. Here we describe six novel transcribed Nbr elements （Nbr9-Nbr14） identified through either cDNA library or RT-PCR. Like previously determined ones, all of them belong to the Ty3/Gypsy superfamily. Retrotransposon diversity and incomplete domains with insertions （Nbr12）, deletions （Nbrll） and in-frame stop codons in coding regions （Nbr9） were detected, suggesting that both defective and loss events of LTR retrotransposon have happened in N. bornbycis genome. Analysis of selection showed that strong purifying selection acts on all elements except Nbr11. This implies that selective pressure keeps both these Nbrs and their functions in genome. Interestingly, Nbrll is under positive selection and some positively selected codons were identified, indicating that new functionality might have evolved in the Nbrll retrotransposon. Unlike other transposable elements, Nbrll has integrated into a conserved syntenic block and probably resulted in the inversion of both flanking regions. This demonstrates that transposable element is an important factor for the reshuffling and evolution of their host genomes, and may be maintained under natural selection.展开更多
Manganese superoxide dismutase(MnSOD)is an antioxidant that exists in mitochondria and can effectively remove superoxide anions in mitochondria.In a dark,high-pressure,and low-temperature deep-sea environment,MnSOD is...Manganese superoxide dismutase(MnSOD)is an antioxidant that exists in mitochondria and can effectively remove superoxide anions in mitochondria.In a dark,high-pressure,and low-temperature deep-sea environment,MnSOD is essential for the survival of sea cucumbers.Six MnSODs were identified from the transcriptomes of deep and shallow-sea sea cucumbers.To explore their environmental adaptation mechanism,we conducted environmental selection pressure analysis through the branching site model of PAML software.We obtained night positive selection sites,and two of them were significant(97F→H,134K→V):97F→H located in a highly conservative characteristic sequence,and its polarity c hange might have a great impact on the function of MnSOD;134K→V had a change in piezophilic a bility,which might help MnSOD adapt to the environment of high hydrostatic pressure in the deepsea.To further study the effect of these two positive selection sites on MnSOD,we predicted the point mutations of F97H and K134V on shallow-sea sea cucumber by using MAESTROweb and PyMOL.Results show that 97F→H,134K→V might improve MnSOD’s efficiency of scavenging superoxide a nion and its ability to resist high hydrostatic pressure by moderately reducing its stability.The above results indicated that MnSODs of deep-sea sea cucumber adapted to deep-sea environments through their amino acid changes in polarity,piezophilic behavior,and local stability.This study revealed the correlation between MnSOD and extreme environment,and will help improve our understanding of the organism’s adaptation mechanisms in deep sea.展开更多
While the recent release of the Chinese tree shrew （Tupaia belangeri chinensis） genome has made the tree shrew an increasingly viable experimental animal model for biomedical research, further study of the genome ma...While the recent release of the Chinese tree shrew （Tupaia belangeri chinensis） genome has made the tree shrew an increasingly viable experimental animal model for biomedical research, further study of the genome may facilitate new insights into the applicability of this model. For example, though the tree shrew has a rapid rate of speed and strong jumping ability, there are limited studies on its locomotion ability. In this study we used the available Chinese tree shrew genome information and compared the evolutionary pattern of 407 locomotion system related orthologs among five mammals （human, rhesus monkey, mouse, rat and dog） and the Chinese tree shrew. Our analyses identified 29 genes with significantly high co （Ka/Ks ratio） values and 48 amino acid sites in 14 genes showed significant evidence of positive selection in the Chinese tree shrew. Some of these positively selected genes, e.g. HOXA6 （homeobox A6） and AVP （arginine vasopressin）, play important roles in muscle contraction or skeletal morphogenesis. These results provide important clues in understanding the genetic bases of locomotor adaptation in the Chinese tree shrew.展开更多
[Objective] The aim was to study adaptive evolution of the large subunits of RubisCO in Magnoliophyta crops. [Method] Taking Magnoliophyta crops such as corn and rice as research materials, the analysis on molecular a...[Objective] The aim was to study adaptive evolution of the large subunits of RubisCO in Magnoliophyta crops. [Method] Taking Magnoliophyta crops such as corn and rice as research materials, the analysis on molecular adaptive evolution was carded out by using codon replacement and maximum likelihood methods. [ Result] The RubisCO suffered positive selection effect and six amino acid sites were identified. [ Conclusion] The six amino acid sites are of important guiding significance for studying catalytic activity of RubisCO large subunits and crop improvement.展开更多
The high-affinity K＋ （HAK） transporter gene family is the largest family in plant that functions as potassium transporter and is important for various aspects of plant life. In the present study, we identified 27 m...The high-affinity K＋ （HAK） transporter gene family is the largest family in plant that functions as potassium transporter and is important for various aspects of plant life. In the present study, we identified 27 members of this family in rice genome. The phylogenetic tree divided the land plant HAK transporter proteins into 6 distinct groups. Although the main characteristic of this family was established before the origin of seed plants, they also showed some differences between the members of non-seed and seed plants. The HAK genes in rice were found to have expanded in lineage-specific manner after the split of monocots and dicots, and both segmental duplication events and tandem duplication events contributed to the expansion of this family. Functional divergence analysis for this family provided statistical evidence for shifted evolutionary rate after gene duplication. Further analysis indicated that both point mutant with positive selection and gene conversion events contributed to the evolution of this family in rice.展开更多
Tibetans are welt adapted to high-altitude hypoxia. Previous genome-wide scans have reported many candidate genes for this adaptation, but only a few have been studied. Here we report on a hypoxia gene （GCH1, GTP-cyc...Tibetans are welt adapted to high-altitude hypoxia. Previous genome-wide scans have reported many candidate genes for this adaptation, but only a few have been studied. Here we report on a hypoxia gene （GCH1, GTP-cyclohydrolase I）, involved in maintaining nitric oxide synthetase （NOS） function and normal blood pressure, that harbors many potentially adaptive variants in Tibetans. We resequenced an 80.8 kb fragment covering the entire gene region of GCH1 in 50 unrelated Tibetans Combined with previously published data, we demonstrated many GCHI variants showing deep divergence between highlander Tibetans and lowlander Han Chinese. Neutrality tests confirmed a signal of positive Darwinian selection on GCH1 in Tibetans. Moreover, association analysis indicated that the Tibetan version of GCH1 was significantly associated with multiple physiological traits in Tibetans, including blood nitric oxide concentration, blood oxygen saturation and hemoglobin concentration. Taken together, we propose that GCH1 plays a role in the genetic adaptation of Tibetans to high altitude hypoxia.展开更多
Genetic transformation is an important technique for functional genomics study and genetic improvement of plants. Until now, Agrobacterium-mediated transformation methods using cotyledon as explants has been the major...Genetic transformation is an important technique for functional genomics study and genetic improvement of plants. Until now, Agrobacterium-mediated transformation methods using cotyledon as explants has been the major approach for cucumber, and its frequency has been up to 23%. For example, significantly enhancement of the transformation efficiency of this plant species was achieved from the cotyledon explants of the cultivar Poinsett 76 infected by Agrobacterium strains EHA105 with efficient positive selection system in lots of experiments. This review is to summarize some key factors influencing cucumber regeneration and genetic transformation, including target genes, selection systems and the ways of transgene introduction, and then to put forward some strategies for the increasing of cucumber transformation efficiency. In the future, it is high possible for cucumber to be potential bioreactor to produce vaccine and biomaterials for human beings.展开更多
For developing efficient vaccines, it is essential to identify which amino acid changes are most important to the survival of the virus. We investigate the amino acid substitution features in the Avian Infectious Bron...For developing efficient vaccines, it is essential to identify which amino acid changes are most important to the survival of the virus. We investigate the amino acid substitution features in the Avian Infectious Bronchitis Virus （AIBV） antigenic domain of a vaccine serotype （DE072） and a virulent viral strain （GA98） to better understand adaptive evolution of AIBV. In addition, the SARS Coronavirus （SARS-CoV） was also analyzed in the same way. It is interesting to find that extreme comparability exists between AIBV and SARS in amino acid substitution pattern. It suggests that amino acid changes that result in overall shift of residue charge and polarity should be paid special attention to during the development of vaccines.展开更多
Seahorses have evolved many unique biological traits,including a male brood pouch,the absence of caudal and pelvic fins,and the lack of spleen and gut-associated lymphatic tissue.The mitogenactivated protein kinases(M...Seahorses have evolved many unique biological traits,including a male brood pouch,the absence of caudal and pelvic fins,and the lack of spleen and gut-associated lymphatic tissue.The mitogenactivated protein kinases(MAPKs)are known to be involved in various important biological processes including growth,differentiation,immunity,and stress responses.Therefore,we hypothesized that the adaptive evolution and expression of the MAPK gene family in seahorse may differ from those of other teleost species.We identified positive selection sites in the erk2,erk5,jnk1,and p38αMAPK genes of the lined seahorse Hippocampus erectus and tiger-tailed seahorse Hippocampus comes.A novel expression profile of MAPK cascade genes was found in seahorse larvae during the first day after birth based on the RNA-seq data of H.erectus,which refl ected vital signs of immune response to its parental immune system.The expression patterns of the four positively selected MAPK genes were analyzed following the bacterial challenge of Vibrio fortis,revealing their upregulation pattern in brood pouch and other immune tissues.This study enriched our knowledge of the evolution of the H.erectus MAPK subfamilies,and could help better understanding the functional role of MAPKs in teleosts.展开更多
文摘Human enterovirus 71 viruses have been long circulating throughout the world. In this study, we performed a positive selection analysis of the VP1 genes of capsid proteins from Enterovirus 71 viruses. Our results showed that although most sites were under negative or neutral evolution, four positions of the VP1 genes were under positive selection pressure. This might account for the spread and frequent outbreaks of the viruses and the enhanced neurovirulence. In particular, position 98 might be involved in neutralizing antibodies, modulating the virus-receptor interaction and enhancing the virulence of the viruses. Moreover, both positions 145 and 241 might correlate to determine the receptor specificity. However, these positions did not display much difference in amino acid polymorphism. In addition, no position in the VP1 genes of viruses isolated from China was under positive selection.
文摘T cells are derived from progenitor thymocytes, of which only a minority receive the appropriate TCR signal, undergo positive selection and mature. Owing to the very short lifespan of thymocytes, the prerequisite for posi- tive selection is survival. TCR signal-induced Bcl-2 expression is believed to play a dominant role in the survival of positively selecting thymocytes, but how Bcl-2 is directly regulated is unknown. Here we report that the immediate early gene （IEG） c-Fos can stimulate the expression of Bcl-2, depending on a specific AP-l-binding site in the Bcl-2 promoter. In c-Fos transgenic （Fos-Tg） mice, c-Fos binds to this site and promotes the expression of Bcl-2. As a result, Fos-Tg thymocytes exhibited enhanced survival, and more mature single-positive （SP） thymocytes were generated, even on a unique TCR background. The TCR repertoire remained normal in Fos-Tg mice. Our results identified c-Fos as the mediator of the stimulatory effect of TCR signaling on Bcl-2 expression. Therefore, c-Fos, as an IEG, because of its early response ability, can quickly rescue the survival of short-lived thymocytes during positive selection. Our results provide novel insight into the mechanism regulating the survival of positively selecting thymocytes.
文摘People living on the high plateaus of the world have long fascinated biological anthropologists and geneticists because they live in ＂thin air＂ and epitomize an extreme of human biological adaptation.
基金Supported by the National Key Research and Development Program of China(Nos.2018YFC0309804,2016YFC0304905)the Major Scientifi c and Technological Projects of Hainan Province(No.ZDKJ2019011)the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDA22040502)。
文摘The Mariana Trench,the deepest trench on the earth,is ideal for deep-sea adaptation research due to its unique characters,such as the highest hydrostatic pressure on the Earth,constant ice-cold temperature,and eternal darkness.In this study,tissues of a the hadal holothurian(Paelopatides sp.)were fi xed with RNA later in situ at~6501-m depth in the Mariana Trench,which,to our knowledge,is the deepest in-situ fi xed animal sample.A high-quality transcript was obtained by de-novo transcriptome assembly.A maximum likelihood tree was constructed based on the single copy orthologs across nine species with their available omics data.To investigate deep-sea adaptation,113 positively selected genes(PSGs)were identifi ed in Paelopatides sp.Some PSGs such as microphthalmia-associated transcription factor(MITF)may contribute to the distinct phenotype of Paelopatides sp.,including its translucent white body and degenerated ossicles.At least eight PSGs(transcription factor 7-like 2[TCF7L2],ETS-related transcription factor Elf-2-like[ELF2],PERQ amino acid-rich with GYF domain-containing protein[GIGYF],cytochrome c oxidase subunit 7a,[COX7A],type I thyroxine 5′-deiodinase[DIO1],translation factor GUF1[GUF1],SWI/SNF related-matrix-associated actin-dependent regulator of chromatin subfamily C and subfamily E,member 1[SMARCC]and[SMARCE1])might be related to cold adaptation.In addition,at least nine PSGs(cell cycle checkpoint control protein[RAD9A],replication factor A3[RPA3],DNA-directed RNA polymerases I/II/III subunit RPABC1[POLR2E],putative TAR DNA-binding protein 43 isoform X2[TARDBP],ribonucleoside-diphosphate reductase subunit M1[RRM1],putative serine/threonine-protein kinase[SMG1],transcriptional regulator[ATRX],alkylated DNA repair protein alkB homolog 6[ALKBH6],and PLAC8 motif-containing protein[PLAC8])may facilitate the repair of DNA damage induced by the high hydrostatic pressure,coldness,and high concentration of cadmium in the upper Mariana Trench.
基金Foundation item:The National Key Research and Development Program of China under contract No.2016YFC1402102the Central Public-interest Scientific Institution Basal Research Fund,CAFS under contract Nos 2020TD19 and 2020TD27+3 种基金the Major Scientific and Technological Innovation Project of Shandong Provincial Key Research and Development Program under contract No.2019JZZY020706the National Natural Science Foundation of China under contract No.31770393the Earmarked Fund for China Agriculture Research System under contract No.CARS-50the Taishan Scholars Funding of Shandong Province.
文摘Ulvophytes are attractive model systems for understanding the evolution of growth,development,and environmental stress responses.They are untapped resources for food,fuel,and high-value compounds.The rapid and abundant growth of Ulva species makes them key contributors to coastal biogeochemical cycles,which can cause significant environmental problems in the form of green tides and biofouling.Until now,the Ulva mutabilis genome is the only Ulva genome to have been sequenced.To obtain further insights into the evolutionary forces driving divergence in Ulva species,we analyzed 3905 single copy ortholog family from U.mutabilis,Chlamydomonas reinhardtii and Volvox carteri to identify genes under positive selection(GUPS)in U.mutabilis.We detected 63 orthologs in U.mutabilis that were considered to be under positive selection.Functional analyses revealed that several adaptive modifications in photosynthesis,amino acid and protein synthesis,signal transduction and stress-related processes might explain why this alga has evolved the ability to grow very rapidly and cope with the variable coastal ecosystem environments.
基金supported by the National Natural Science Foundation of China(No.30400264)the Natural Science Foundation of Yunnan Province,China(No.2008ZC068M)the Chinese National High Technology Research and Development Program(No.2012AA021802)
文摘The ataxin-2 （ATXN2） gene is located on human chromo-some 12q24.1. In normal individuals, the coding region in exon 1 of this gene has fewer than 31 CAG repeats （Yu et al., 2005： Laffita-Mesa et al., 2012）. However, an abnormal expansion of CAG trinucleotide repeats results in the aggre-gation of polyglutamine （polyQ）, which causes spinocer-ebellar ataxia type 2 （SCA2） （Pulst et al., 1996）. The expanded alleles have more than 32 repeats in the affected individuals, and generally there is an inverse correlation between CAG repeat length and age of onset （Pulst et al., 1996）. SCA2 is an autosomal dominant inheritance neurodegenerative disease, whose major clinical feature is progressive cerebellar ataxia. Atrophies of the brainstem and frontal lobe have been frequently detected by magnetic resonance imaging （MRI） （Yamamoto-Watanabe et al., 2010）. This disease has the strong effect on sensory and motor control.
基金National Natural Science Foundation of China (No. 30571009).
文摘Vegetative insecticidal proteins （VIPs）, produced during the vegetative stage of their growth in Bacillus thuringiensis, are a group of insecticidal proteins and represent the second generation of insecticidal trans-genes that will complement the novel δendotoxins in future. Fewer structural and functional relationships of Vip proteins are known in comparison with those of δ-endotoxins. In this study, both the maximum-likelihood methods and the maximum parsimony based sliding window analysis were used to evaluate the molecular evolution of Vip proteins. As a result, strong evidence was found that Vip proteins are subject to the high rates of positive selection, and 16 sites are identified to be under positive selection using the Bayes Empirical Bayesian method. Interestingly, all these positively selected sites are located from site-705 to site-809 in the C-terminus of the Vip proteins. Most of these sites are exposed and clustered in the loop regions when mapped onto its computational predicted secondary tertiary and a part of the tertiary structure. It has been postulated that the high divergence in the C-terminal of Vip proteins may not result from the lack of functional constraints, but rather from the rapid mutation to adapt their targeted insects, driven by positive selection. The potential positive selection pressures may be an attempt to adapt for the ＂arm race＂ between Vip proteins and the targeted insects, or to enlarge their target＇s host range. Sites identified to be under positive selection may be related to the insect host range, which may shed a light on the investigation of the Vip proteins＇ structural and functional relationships.
基金supported by the Natural Sciences and Engineering Research Council of Canada (NSERC)the Canadian Research Chairs Program (CRC)+1 种基金the Mathematics for Information Technology and Complex Systems (MITACS)the support from the Canadian Network of Centers of Excellence, MITACS
文摘The surface glycoprotein hemagglutinin （HA） helps the influenza A virus to evade the host immune system by antigenic variation and is a major driving force for viral evolution. In this study, the selection pressure on HA of H5N1 influenza A virus was analyzed using bioinformatics algorithms. Most of the identified positive selection （PS） sites were found to be within or adjacent to epitope sites. Some of the identified PS sites are consistent with previous experimental studies, providing further support to the biological significance of our findings. The highest frequency of PS sites was observed in recent strains isolated during 2005-2007. Phylogenetic analysis was also conducted on HA sequences from various hosts. Viral drift is almost similar in both avian and human species with a progressive trend over the years. Our study reports new mutations in functional regions of HA that might provide markers for vaccine design or can be used to predict isolates of pandemic potential.
文摘There is increasing interest in studying the molecular mechanisms of recent adaptations caused by positive selection in the genomics era. Such endeavors to detect recent positive selection, however, have been severely handicapped by false positives due to the confounding impact of demography and the population structure. To reduce false positives, it is critical to conduct a functional analysis to identify the true candidate genes/mutations from those that are filtered through neutrality tests. However, the extremely high cost of such functional analysis may restrict studies within a small number of model species. In particular, when the false positive rate of neutrality tests is high, the efficiency of the functional analysis will also be very low. Therefore, although the recent improvements have been made in the （joint） inference of demography and selection, our ultimate goal, which is to understand the mechanism of adaptation generally in a wide variety of natural populations, may not be achieved using the currently available approaches. More attention should thus be spent on the development of more reliable tests that could not only free themselves from the confounding impact of demography and the population structure but also have reasonable power to detect selection.
基金supported by the National Natural Science Foundation of China (Grant No. 30600352)the "Top-notch Personnel" Project of Ji-angsu University, the National Basic Research Program of China (Grant No. 2006CB504200)the Open Research Fund Program of the State Key Laboratory of Virology of China (Grant No. 2009008)
文摘HIV-1 co-receptor tropism is central for understanding the transmission and pathogenesis of HIV-1 infection. We performed a genome-wide comparison between the adaptive evolution of R5 and X4 variants from HIV-1 subtypes B and C. The results showed that R5 and X4 variants experienced differential evolutionary patterns and different HIV-1 genes encountered various positive selection pressures, suggesting that complex selection pressures are driving HIV-1 evolution. Compared with other hypervariable regions of Gp120, significantly more positively selected sites were detected in the V3 region of subtype B X4 variants, V2 region of subtype B R5 variants, and V1 and V4 regions of subtype C X4 variants, indicating an association of positive selection with co-receptor recognition/binding. Intriguingly, a significantly higher proportion (33.3% and 55.6%, P【0.05) of positively selected sites were identified in the C3 region than other conserved regions of Gp120 in all the analyzed HIV-1 variants, indicating that the C3 region might be more important to HIV-1 adaptation than previously thought. Approximately half of the positively selected sites identified in the env gene were identical between R5 and X4 variants. There were three common positively selected sites (96, 113 and 281) identified in Gp41 of all X4 and R5 variants from subtypes B and C. These sites might not only suggest a functional importance in viral survival and adaptation, but also imply a potential cross-immunogenicity between HIV-1 R5 and X4 variants, which has important implications for AIDS vaccine development.
基金supported by the National Basic Research Program of China(No.2005CB121000)the project of Chongqing Science & Technology Commission(CSTC,No.2006AA5019 and 2009BB1241)+1 种基金the Programme of Introducing Talents of Discipline to Universities(No.B07045)State Development Fund at Risk of Callus Silk(No.M012005-000Y-00070)
文摘Eight intact LTR retrotransposons （Nbr1-Nbr8） have been previously characterized from the genome of Nosema bombycis, a eu- karyotic parasite with a compact and reduced genome. Here we describe six novel transcribed Nbr elements （Nbr9-Nbr14） identified through either cDNA library or RT-PCR. Like previously determined ones, all of them belong to the Ty3/Gypsy superfamily. Retrotransposon diversity and incomplete domains with insertions （Nbr12）, deletions （Nbrll） and in-frame stop codons in coding regions （Nbr9） were detected, suggesting that both defective and loss events of LTR retrotransposon have happened in N. bornbycis genome. Analysis of selection showed that strong purifying selection acts on all elements except Nbr11. This implies that selective pressure keeps both these Nbrs and their functions in genome. Interestingly, Nbrll is under positive selection and some positively selected codons were identified, indicating that new functionality might have evolved in the Nbrll retrotransposon. Unlike other transposable elements, Nbrll has integrated into a conserved syntenic block and probably resulted in the inversion of both flanking regions. This demonstrates that transposable element is an important factor for the reshuffling and evolution of their host genomes, and may be maintained under natural selection.
基金Supported by the Guangdong Province Basic and Applied Basic Research Fund Project(No.2020A1515110826)the National Natural Science Foundation of China(No.42006115)the Major Scientific and Technological Projects of Hainan Province(No.ZDKJ2021036)。
文摘Manganese superoxide dismutase(MnSOD)is an antioxidant that exists in mitochondria and can effectively remove superoxide anions in mitochondria.In a dark,high-pressure,and low-temperature deep-sea environment,MnSOD is essential for the survival of sea cucumbers.Six MnSODs were identified from the transcriptomes of deep and shallow-sea sea cucumbers.To explore their environmental adaptation mechanism,we conducted environmental selection pressure analysis through the branching site model of PAML software.We obtained night positive selection sites,and two of them were significant(97F→H,134K→V):97F→H located in a highly conservative characteristic sequence,and its polarity c hange might have a great impact on the function of MnSOD;134K→V had a change in piezophilic a bility,which might help MnSOD adapt to the environment of high hydrostatic pressure in the deepsea.To further study the effect of these two positive selection sites on MnSOD,we predicted the point mutations of F97H and K134V on shallow-sea sea cucumber by using MAESTROweb and PyMOL.Results show that 97F→H,134K→V might improve MnSOD’s efficiency of scavenging superoxide a nion and its ability to resist high hydrostatic pressure by moderately reducing its stability.The above results indicated that MnSODs of deep-sea sea cucumber adapted to deep-sea environments through their amino acid changes in polarity,piezophilic behavior,and local stability.This study revealed the correlation between MnSOD and extreme environment,and will help improve our understanding of the organism’s adaptation mechanisms in deep sea.
基金Foundation items： This study was supported by the National 863 Project of China （2012AA021801, 2012AA022402） and grants from Chinese Academy of Sciences （KSCX2-EW-R-11, KSCX2-EW-J23） and Yunnan Province （2013FB071）Acknowledgements： We are grateful to Dr. Dong WANG for helpful discussion.
文摘While the recent release of the Chinese tree shrew （Tupaia belangeri chinensis） genome has made the tree shrew an increasingly viable experimental animal model for biomedical research, further study of the genome may facilitate new insights into the applicability of this model. For example, though the tree shrew has a rapid rate of speed and strong jumping ability, there are limited studies on its locomotion ability. In this study we used the available Chinese tree shrew genome information and compared the evolutionary pattern of 407 locomotion system related orthologs among five mammals （human, rhesus monkey, mouse, rat and dog） and the Chinese tree shrew. Our analyses identified 29 genes with significantly high co （Ka/Ks ratio） values and 48 amino acid sites in 14 genes showed significant evidence of positive selection in the Chinese tree shrew. Some of these positively selected genes, e.g. HOXA6 （homeobox A6） and AVP （arginine vasopressin）, play important roles in muscle contraction or skeletal morphogenesis. These results provide important clues in understanding the genetic bases of locomotor adaptation in the Chinese tree shrew.
文摘[Objective] The aim was to study adaptive evolution of the large subunits of RubisCO in Magnoliophyta crops. [Method] Taking Magnoliophyta crops such as corn and rice as research materials, the analysis on molecular adaptive evolution was carded out by using codon replacement and maximum likelihood methods. [ Result] The RubisCO suffered positive selection effect and six amino acid sites were identified. [ Conclusion] The six amino acid sites are of important guiding significance for studying catalytic activity of RubisCO large subunits and crop improvement.
基金supported by the National Basic Research Program of China (No. 2006CB101700)the National High- tech Research and Development Program (No. 2006AA10Z165)the Program for New Century Excellent Talents in Uni-versity of China (No. NCET2005-05- 0502).
文摘The high-affinity K＋ （HAK） transporter gene family is the largest family in plant that functions as potassium transporter and is important for various aspects of plant life. In the present study, we identified 27 members of this family in rice genome. The phylogenetic tree divided the land plant HAK transporter proteins into 6 distinct groups. Although the main characteristic of this family was established before the origin of seed plants, they also showed some differences between the members of non-seed and seed plants. The HAK genes in rice were found to have expanded in lineage-specific manner after the split of monocots and dicots, and both segmental duplication events and tandem duplication events contributed to the expansion of this family. Functional divergence analysis for this family provided statistical evidence for shifted evolutionary rate after gene duplication. Further analysis indicated that both point mutant with positive selection and gene conversion events contributed to the evolution of this family in rice.
基金supported by grants from the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB13010000)the National Natural Science Foundation of China(91631306 to BS,31671329 to XQ,31460287 to Ou.,31501013 to HZ and 31360032 to CC)+2 种基金the National 973 program(2012CB518202 to TW)the State Key Laboratory of Genetic Resources and Evolution(GREKF15-05,GREKF16-04)the Zhufeng Scholar Program of Tibetan University
文摘Tibetans are welt adapted to high-altitude hypoxia. Previous genome-wide scans have reported many candidate genes for this adaptation, but only a few have been studied. Here we report on a hypoxia gene （GCH1, GTP-cyclohydrolase I）, involved in maintaining nitric oxide synthetase （NOS） function and normal blood pressure, that harbors many potentially adaptive variants in Tibetans. We resequenced an 80.8 kb fragment covering the entire gene region of GCH1 in 50 unrelated Tibetans Combined with previously published data, we demonstrated many GCHI variants showing deep divergence between highlander Tibetans and lowlander Han Chinese. Neutrality tests confirmed a signal of positive Darwinian selection on GCH1 in Tibetans. Moreover, association analysis indicated that the Tibetan version of GCH1 was significantly associated with multiple physiological traits in Tibetans, including blood nitric oxide concentration, blood oxygen saturation and hemoglobin concentration. Taken together, we propose that GCH1 plays a role in the genetic adaptation of Tibetans to high altitude hypoxia.
基金financially supported by grants from the Biogreen 21 Program, RDA, Korea (PJ00810304)the Agricultural Science and Technology Innovation Program (ASTIP) of Chinese Academy of Agricultural Sciences (2014–2015)the Beijing Municipal Education Commission, China (KM200910011001)
文摘Genetic transformation is an important technique for functional genomics study and genetic improvement of plants. Until now, Agrobacterium-mediated transformation methods using cotyledon as explants has been the major approach for cucumber, and its frequency has been up to 23%. For example, significantly enhancement of the transformation efficiency of this plant species was achieved from the cotyledon explants of the cultivar Poinsett 76 infected by Agrobacterium strains EHA105 with efficient positive selection system in lots of experiments. This review is to summarize some key factors influencing cucumber regeneration and genetic transformation, including target genes, selection systems and the ways of transgene introduction, and then to put forward some strategies for the increasing of cucumber transformation efficiency. In the future, it is high possible for cucumber to be potential bioreactor to produce vaccine and biomaterials for human beings.
文摘For developing efficient vaccines, it is essential to identify which amino acid changes are most important to the survival of the virus. We investigate the amino acid substitution features in the Avian Infectious Bronchitis Virus （AIBV） antigenic domain of a vaccine serotype （DE072） and a virulent viral strain （GA98） to better understand adaptive evolution of AIBV. In addition, the SARS Coronavirus （SARS-CoV） was also analyzed in the same way. It is interesting to find that extreme comparability exists between AIBV and SARS in amino acid substitution pattern. It suggests that amino acid changes that result in overall shift of residue charge and polarity should be paid special attention to during the development of vaccines.
基金Supported by the Shandong Province Science and Technology Support Program for Outstanding Youth of Colleges and Universities(No.2020KJF007)the Shandong Province Science and Technology Research Program for Colleges and Universities(No.J18KA146)+3 种基金the Yantai Foundation for Development of Science and Technology(Nos.2020LJRC120,2019CXJJ040)the Weihai Foundation for Development of Science and Technology(No.2017GNS10)the Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou)(No.GML2019ZD0407)the Guangdong Basic and Applied Basic Research Foundation(No.2019A1515110199)。
文摘Seahorses have evolved many unique biological traits,including a male brood pouch,the absence of caudal and pelvic fins,and the lack of spleen and gut-associated lymphatic tissue.The mitogenactivated protein kinases(MAPKs)are known to be involved in various important biological processes including growth,differentiation,immunity,and stress responses.Therefore,we hypothesized that the adaptive evolution and expression of the MAPK gene family in seahorse may differ from those of other teleost species.We identified positive selection sites in the erk2,erk5,jnk1,and p38αMAPK genes of the lined seahorse Hippocampus erectus and tiger-tailed seahorse Hippocampus comes.A novel expression profile of MAPK cascade genes was found in seahorse larvae during the first day after birth based on the RNA-seq data of H.erectus,which refl ected vital signs of immune response to its parental immune system.The expression patterns of the four positively selected MAPK genes were analyzed following the bacterial challenge of Vibrio fortis,revealing their upregulation pattern in brood pouch and other immune tissues.This study enriched our knowledge of the evolution of the H.erectus MAPK subfamilies,and could help better understanding the functional role of MAPKs in teleosts.
