The genus Salix is a common component of the Northern Hemisphere dendroflora with important ecological and economic value.However,taxonomy and systematics of Salix is extremely difficult and relationships between main...The genus Salix is a common component of the Northern Hemisphere dendroflora with important ecological and economic value.However,taxonomy and systematics of Salix is extremely difficult and relationships between main lineages,especially deep phylogenies,remain largely unresolved.In this study,we used genome-skimming,plastome assembly,and single-copy orthologs(SCOs)from 66 Salix accessions,along with publicly available plastome and sequence read archive(SRA)datasets to obtain a robust backbone phylogeny of Salix,clarify relationships between its main lineages,and gain a more precise understanding of the origin and diversification of this species-rich genus.The plastome and SCO datasets resolved Salix into two robust clades,with plastome-based phylogenies lacking inner resolution and SCO offering fully resolved phylogenies.Our results support the classification of Salix into five subgenera:Salix,Urbaniana,Triandrae,Longifoliae and Vetrix.We observed a significant acceleration in the diversification rate within the Chamaetia-Vetrix clade,while Salix exhibited increased rates of diversification spanning from the early Oligocene to the late Miocene.These changes coincided with contemporaneous tectonic and climate change events.Our results provide a foundation for future systematic and evolutionary studies of Salix.Additionally,we showed that genome skimming data is an efficient,rapid,and reliable approach for obtaining extensive genomic data for phylogenomic studies,enabling the comprehensive elucidation of Salix relationships.展开更多
Human and mouse orthologs are expected to have similar biological functions; however, many discrepancies have also been reported. We systematically compared human and mouse orthologs in terms of alternative splicing p...Human and mouse orthologs are expected to have similar biological functions; however, many discrepancies have also been reported. We systematically compared human and mouse orthologs in terms of alternative splicing patterns and expression profiles. Human-mouse orthologs are divergent in alternative splicing, as human orthologs could generally encode more isoforms than their mouse orthologs. In early embryos, exon skipping is far more common with human orthologs, whereas constitutive exons are more prevalent with mouse orthologs. This may correlate with divergence in expression of splicing regulators. Orthologous expression similarities are different in distinct embryonic stages, with the highest in morula. Expression differences for orthologous transcription factor genes could play an important role in orthologous expression discordance. We further detected largely orthologous divergence in differential expression between distinct embryonic stages. Collectively, our study uncovers significant orthologous divergence from multiple aspects, which may result in functional differences and dynamics between human-mouse orthologs during embryonic development.展开更多
Rice and wheat provide nearly 40%of human calorie and protein requirements.They share a common ancestor and belong to the Poaceae(grass)family.Characterizing their genetic homology is crucial for developing new cultiv...Rice and wheat provide nearly 40%of human calorie and protein requirements.They share a common ancestor and belong to the Poaceae(grass)family.Characterizing their genetic homology is crucial for developing new cultivars with enhanced traits.Several wheat genes and gene families have been characterized based on their rice orthologs.Rice–wheat orthology can identify genetic regions that regulate similar traits in both crops.Rice–wheat comparative genomics can identify candidate wheat genes in a genomic region identified by association or QTL mapping,deduce their putative functions and biochemical pathways,and develop molecular markers for marker-assisted breeding.A knowledge of gene homology facilitates the transfer between crops of genes or genomic regions associated with desirable traits by genetic engineering,gene editing,or wide crossing.展开更多
Background Photosystem II(PSII)constitutes an intricate assembly of protein pigments,featuring extrinsic and intrinsic polypeptides within the photosynthetic membrane.The low-molecular-weight transmembrane protein Psb...Background Photosystem II(PSII)constitutes an intricate assembly of protein pigments,featuring extrinsic and intrinsic polypeptides within the photosynthetic membrane.The low-molecular-weight transmembrane protein PsbX has been identified in PSII,which is associated with the oxygen-evolving complex.The expression of PsbX gene protein is regulated by light.PsbX’s central role involves the regulation of PSII,facilitating the binding of quinone molecules to the Qb(PsbA)site,and it additionally plays a crucial role in optimizing the efficiency of photosynthesis.Despite these insights,a comprehensive understanding of the PsbX gene’s functions has remained elusive.Results In this study,we identified ten PsbX genes in Gossypium hirsutum L.The phylogenetic analysis results showed that 40 genes from nine species were classified into one clade.The resulting sequence logos exhibited substantial conservation across the N and C terminals at multiple sites among all Gossypium species.Furthermore,the ortholo-gous/paralogous,Ka/Ks ratio revealed that cotton PsbX genes subjected to positive as well as purifying selection pressure might lead to limited divergence,which resulted in the whole genome and segmental duplication.The expression patterns of GhPsbX genes exhibited variations across specific tissues,as indicated by the analysis.Moreover,the expression of GhPsbX genes could potentially be regulated in response to salt,intense light,and drought stresses.Therefore,GhPsbX genes may play a significant role in the modulation of photosynthesis under adverse abiotic conditions.Conclusion We examined the structure and function of PsbX gene family very first by using comparative genom-ics and systems biology approaches in cotton.It seems that PsbX gene family plays a vital role during the growth and development of cotton under stress conditions.Collectively,the results of this study provide basic information to unveil the molecular and physiological function of PsbX genes of cotton plants.展开更多
With the development and decreasing cost of sequencing techniques, it is possible for scientists to conduct deeper research in phylogenomics. During the procedure of phylogenomic analysis, the mostimportant and vitale...With the development and decreasing cost of sequencing techniques, it is possible for scientists to conduct deeper research in phylogenomics. During the procedure of phylogenomic analysis, the mostimportant and vitalest step is orthology prediction, for that the prerequisite to phylogenetic reconstruction is that the genes being compared are orthologous. Here we briefly review the related concept of orthology anddifferent methods for orthology prediction. We also provide recommendations to give some advice for better selection of orthology prediction methods.展开更多
The multidrug and toxic compound extrusion(MATE) family plays pivotal roles in the detoxification process in plants, while no information has been provided for this gene family in melon(Cucumis melo L.) thus far, limi...The multidrug and toxic compound extrusion(MATE) family plays pivotal roles in the detoxification process in plants, while no information has been provided for this gene family in melon(Cucumis melo L.) thus far, limiting our understanding of its functions in melon acclimation to stressful environments. In this study, a total of 39 MATEs(CmMATE1–CmMATE39) were observed in the melon genome;these were unevenly distributed in all chromosomes, with the most on Chromosome 1. Based on their orthologous relationship with those from Arabidopsis, rice, and sorghum, melon MATEs were clustered into three subfamilies of Clades Ⅰ, Ⅱ, and Ⅲ, wherein 23, 9, and 7 members were included, respectively.Variable exon number was observed in CmMATEs, and the most were harbored by CmMATE8. Gene ontology(GO) term and cis-regulatory element(CRE) analyses pointed to the potential roles of CmMATEs in both the regulation of melon development and acclimation to various abiotic and biotic stressors. The RNA-seq and qRT-PCR(quantitative real-time PCR) results demonstrated that under normal growth conditions, CmMATEs were expressed in a tissue-and development-specific manner, while their abundance apparently varied in a stress-dependent manner when melon plants were exposed to unfavorable environmental conditions. Altogether, these observations could expand our knowledge about the plant MATE family and benefit functional genomics analysis for CmMATEs in the future.展开更多
Comparative analyses of genome structure and sequence of closely related species have yielded insights into the evolution and function of plant genomes. A total of 103,844 BAC end sequences delegated -73.8 Mb of O. of...Comparative analyses of genome structure and sequence of closely related species have yielded insights into the evolution and function of plant genomes. A total of 103,844 BAC end sequences delegated -73.8 Mb of O. officinalis that belongs to the CC genome type of the rice genus Oryza were obtained and compared with the genome sequences office cultivar, O. sativa ssp.japonica cv. Nipponbare. We found that more than 45% of O. officinalis genome consists of repeat sequences, which is higher than that of Nipponbare cultivar. To further investigate the evolutionary divergence of AA and CC genomes, two BAC-contigs of O. officinalis were compared with the collinear genomic regions of Nipponbare. Of 57 genes predicted in the AA genome orthologous regions, 39 had orthologs in the regions of the CC genome. Alignment of the orthologous regions indicated that the CC genome has undergone expansion in both genic and intergenic regions through primarily retroelement insertion. Particularly, the density of RNA transposable elements was 17.95% and 1.78% in O. officinalis and O. sativa, respectively. This explains why the orthologous region is about 100 kb longer in the CC genome in comparison to the AA genome.展开更多
AIM: To identify alkyl hydroperoxide reductase subunit C(AhpC) homologs in Bacillus subtilis(B. subtilis) and to characterize their structural and biochemical properties. AhpC is responsible for the detoxification of ...AIM: To identify alkyl hydroperoxide reductase subunit C(AhpC) homologs in Bacillus subtilis(B. subtilis) and to characterize their structural and biochemical properties. AhpC is responsible for the detoxification of reactive oxygen species in bacteria.METHODS: Two AhpC homologs(AhpC_H1 and AhpC_H2) were identified by searching the B. subtilis database; these were then cloned and expressed in Escherichia coli. AhpC mutants carrying substitutions of catalytically important Cys residues(C37S, C47 S, C166 S, C37/47 S, C37/166 S, C47/166 S, and C37/47/166 S for AhpC_H1; C52 S, C169 S, and C52/169 S for AhpC_H2) were obtained by site-directed mutagenesis and purified, and their structure-function relationship was analyzed. The B. subtilis ahp C genes were disrupted by the short flanking homology method, and the phenotypes of the resulting AhpC-deficient bacteria were examined.RESULTS: Comparative characterization of AhpC homologs indicates that AhpC_H1 contains an extra C37, which forms a disulfide bond with the peroxidatic C47, and behaves like an atypical 2-Cys AhpC, while AhpC_H2 functions like a typical 2-Cys AhpC. Tryptic digestion analysis demonstrated the presence of intramolecular Cys37-Cys47 linkage, which could be reduced by thioredoxin, resulting in the association of the dimer into higher-molecular-mass complexes. Peroxidase activity analysis of Cys→Ser mutants indicated that three Cys residues were involved in the catalysis. AhpC_H1 was resistant to inactivation by peroxide substrates, but had lower activity at physiological H2O2 concentrations compared to AhpC_H2, suggesting that in B. subtilis, the enzymes may be physiologically functional at different substrate concentrations. The exposure to organic peroxides induced AhpC_H1 expression, while AhpC_H1-deficient mutants exhibited growth retardation in the stationary phase, suggesting the role of AhpC_H1 as an antioxidant scavenger of lipid hydroperoxides and a stress-response factor in B. subtilis. CONCLUSION: AhpC_H1, a novel atypical 2-Cys AhpC, is functionally distinct from AhpC_H2, a typical 2-Cys AhpC.展开更多
Microorganisms plays an important role in the growth of Pyropia haitanensis.To understand the structural and functional diversity of the microorganism community of P.haitanensis(PH40),the associated metabolic pathway ...Microorganisms plays an important role in the growth of Pyropia haitanensis.To understand the structural and functional diversity of the microorganism community of P.haitanensis(PH40),the associated metabolic pathway network in cluster of orthologous groups(COG)and Kyoto Encyclopedia of Genes and Genomes(KEGG),and carbohydrate-active enzymes(CAZymes)were explored in metagenomic analysis.DNA extraction from gametophytes of P.haitanensis was performed first,followed by library construction,sequencing,preprocessing of sequencing data,taxonomy assignment,gene prediction,and functional annotation.The results show that the predominant microorganisms of P.haitanensis were bacteria(98.98%),and the phylum with the highest abundance was Proteobacteria(54.64%),followed by Bacteroidetes(37.92%).Erythrobacter(3.98%)and Hyunsoonleella jejuensis(1.56%)were the genera and species with the highest abundance of bacteria,respectively.The COG annotation demonstrated that genes associated with microbial metabolism was the predominant category.The results of metabolic pathway annotation show that the ABC transport system and two-component system were the main pathways in the microbial community.Plant growth hormone biosynthesis pathway and multi-vitamin biosynthesis functional units(modules)were the other important pathways.The CAZyme annotation revealed that the starch might be an important carbon source for microorganisms.Glycosyl transferase family 2(GT2)and glycosyl transferase family 3(GT3)were the highly abundant families in glucoside transferase superfamily.Six metagenome-assembled genomes containing enzymes involved in the biosynthesis of cobalamin(vitamin B 12)and indole-3-acetic acid were obtained by binning method.They were confirmed to belong to Rhodobacterales and Rhizobiales,respectively.Our findings provide comprehensive insights into the microorganism community of Pyropia.展开更多
Understanding the genetic architecture of indi-vidual taxa of medical importance is the first step for designing disease preventive strategies. To understand the genetic details and evolu-tionary perspective of the mo...Understanding the genetic architecture of indi-vidual taxa of medical importance is the first step for designing disease preventive strategies. To understand the genetic details and evolu-tionary perspective of the model malaria vector, Anopheles gambiae and to use the information in other species of local importance, we scanned the published X-chromosome se-quence for detail characterization and obtain evolutionary status of different genes. The te-locentric X-chromosome contains 106 genes of known functions and 982 novel genes. Majori-ties of both the known and novel genes are with introns. The known genes are strictly biased towards less number of introns;about half of the total known genes have only one or two in-trons. The extreme sized (either long or short) genes were found to be most prevalent (58% short and 23% large). Statistically significant positive correlations between gene length and intron length as well as with intron number and intron length were obtained signifying the role of introns in contributing to the overall size of the known genes of X-chromosome in An. gam-biae. We compared each individual gene of An. gambiae with 33 other taxa having whole ge-nome sequence information. In general, the mosquito Aedes aegypti was found to be ge-netically closest and the yeast Saccharomyces cerevisiae as most distant taxa to An. gambiae. Further, only about a quarter of the known genes of X-chromosome were unique to An. gambiae and majorities have orthologs in dif-ferent taxa. A phylogenetic tree was constructed based on a single gene found to be highly orthologous across all the 34 taxa. Evolutionary relationships among 13 different taxa were in-ferred which corroborate the previous and pre-sent findings on genetic relationships across various taxa.展开更多
<i>Bacillus thuringiensis</i> (Bt) parasporal crystal proteins were well known to be toxic to certain insects and cytocidal activity against various human cancer cells. Bt serovar <i>coreanensis</...<i>Bacillus thuringiensis</i> (Bt) parasporal crystal proteins were well known to be toxic to certain insects and cytocidal activity against various human cancer cells. Bt serovar <i>coreanensis</i> ST7, non-pathogenic to insects and non-hemolytic, has an important parasporin, PS4Aa1 (Cry45Aa1), with potential toxicity to human cancer cells. In this study, we reported the feature of complete genome sequence and the cluster of orthologous groups of proteins function classification of ST7. Meanwhile, the evolutionary of ST7 was also studied. The genome data of ST7 will strongly contribute to a better understanding of the genomic diversity and evolution, and enrich the Bt genome database.展开更多
Dear Editor,In dynamic environments,the memory system of the brain must be able to perceive and process conflicting experiences to reach an adaptive decision.In Drosophila,in contrast to consistent experiences,conflic...Dear Editor,In dynamic environments,the memory system of the brain must be able to perceive and process conflicting experiences to reach an adaptive decision.In Drosophila,in contrast to consistent experiences,conflicting experiences trigger significantly increased Rac1 activity which mediates active forgetting [1].The ability to cope with conflicting experiences but not simple learning experiences is impaired in mutants of multiple autism-risk genes [2].展开更多
Genome-wide identification and comparative gene-famiy analyses have commonly been performed to investigate spedesspecif ic evolution Inked to various traits and molecular pathways.However,most previous studies have be...Genome-wide identification and comparative gene-famiy analyses have commonly been performed to investigate spedesspecif ic evolution Inked to various traits and molecular pathways.However,most previous studies have been Smited to gene screening h a single reference genome,faiing to account for the gene presence/absence variations(gPAVs)in a species.Here,we propose an innovative pangenome-based approach for gene-family analyses based on orthologous gene groups(OGGs).Usng the basic heix-bop-helix(bH_H)transcription factor family in barley as an example,we identified 161-176 bHLHs in 20 barley genomes,which can be classified into 201 OGGs.These 201 OGGs were further dassif jed into 140 core,12 softcore,29 shell,and 20 Ihe-spedfic/cloud bHLHs,reveaing the complete profile of bHLH genes in barley.Using a genome-scanning approach,we overcame the genome annotation bias and identified an average of 15 un-amotated core bHLHs per barley genome We found that whole-genome/segmental duplicates are predominant mechanisms contrixiting to the expansion of most core/softcore bHLHs,whereas dispensable bHLHs are more Ikely to result from small-scale dupication events.Interestingly,we noticed that the dispensable bHLHs tend to be enriched in the specific subfamiSes SF13,SF27,and SF28,rn plying the potentially based expansion of specific bHLHs h barley.We found that 50%of the bHLHs con tan at least 1 intact transposon element(TE)within the 2-kb upstream-to-downstream region.bHLHs with copy-number variations(CWs)have 1.48 TEs on average,sigrif icantiy more than core bhLHs without CNVs(1.36),supporting a potential role ofTEs in bHLH expansion.Analyses of selection pressure showed that dispensablebHLHs have experienced dearrelaxation of selection compared with core bHLHs,consistent with their conservation patterns.We also integrated the pangenome data with recently avaiable barley pantranscrip-tome data from 5 tissues and discovered apparent transcriptional divergence within and across bHLH sifofamiies.We conclude that pangenome-based gene-family analyses can better describe the previously untapped,genu'ne evolutionary status of bHLHs and provide novel insights into bHLH evolution in barley.We expect that this study wil inspire similar analyses in many other gene famiies and species.展开更多
A recent study published in Cell by Chen et al.,highlighted by Nature journal,identified the HKU5-CoV-2 lineage,a coronavirus detected in bats with the potential to interact with the human ACE2 receptor.1:2 Experiment...A recent study published in Cell by Chen et al.,highlighted by Nature journal,identified the HKU5-CoV-2 lineage,a coronavirus detected in bats with the potential to interact with the human ACE2 receptor.1:2 Experiments conducted in intestinal and airway cells indicated that HkU5-CoV-2 binds to the receptor less efficiently than SARS-CoV-2.However,the broad ACE2 ortholog tropism suggests a potential risk of adaptation to the human host.展开更多
TNNI3K(troponin-I interacting kinase)encodes a duo tyrosine and serine/threonine kinase implicated in cardiomyopathy,arrhythmias,and cardiac conduction disease(CCD).1 However,no direct downstream phosphorylation targe...TNNI3K(troponin-I interacting kinase)encodes a duo tyrosine and serine/threonine kinase implicated in cardiomyopathy,arrhythmias,and cardiac conduction disease(CCD).1 However,no direct downstream phosphorylation targets of TNNI3K have been identified yet.2 Here,we employed the CRISPR/Cas9 gene-editing technique to generate a splicing mutation in the 4th exon of zebrafish tnni3k ortholog gene that mimics a TNNI3K splicing variant identified from a patient family with cardiomyopathy and CCD.展开更多
Glycosyltransferases （GTs; EC 2.4.x.y） constitute a large group of enzymes that form glycosidic bonds through transfer of sugars from activated donor molecules to acceptor molecules. GTs are critical to the biosynth...Glycosyltransferases （GTs; EC 2.4.x.y） constitute a large group of enzymes that form glycosidic bonds through transfer of sugars from activated donor molecules to acceptor molecules. GTs are critical to the biosynthesis of plant cell walls, among other diverse functions. Based on the Carbohydrate-Active enZymes （CAZy） database and sequence similarity.searches, we have identified 609 potential GT genes （loci） corresponding to 769 transcripts （gene models） in rice （Oryza sativa）, the reference monocotyledonous species. Using domain composition and sequence similarity, these rice GTs were classified into 40 CAZy families plus an additional unknown class. We found that two Pfam domains of unknown function, PF04577 and PF04646, are associated with GT families GT61 and GT31, respectively. To facilitate functional analysis of this important and large gene family, we created a phylogenomic Rice GT Database （http：//ricephylogenomics. ucdavis.edu/cellwalls/gtJ）. Through the database, several classes of functional genomic data, including mutant lines and gene expression data, can be displayed for each rice GT in the context of a phylogenetic tree, allowing for comparative analysis both within and between GT families. Comprehensive digital expression analysis of public gene expression data revealed that most （-80%） rice GTs are expressed. Based on analysis with Inparanoid, we identified 282 ‘rice-diverged＇ GTs that lack orthologs in sequenced dicots （Arabidopsis thaliana, Populus tricocarpa, Medicago truncatula, and Ricinus communis）. Combining these analyses, we identified 33 rice-diverged GT genes （45 gene models） that are highly expressed in above-ground, vegetative tissues. From the literature and this analysis, 21 of these loci are excellent targets for functional examination toward understanding and manipulating grass cell wall qualities. Study of the remainder may reveal aspects of hormone and protein metabolism that are critical for rice biology. This list of 33 genes and the Rice GT Database will facilitate the study of GTs and cell wall synthesis in rice and other plants.展开更多
基金supported by NSFC(32070226,32360065)the Key Projects of the Joint Fund of the National Natural Science Foundation of China(U23A20149)+3 种基金the Second Tibetan Plateau Scientific Expedition and Research(STEP)program(2024QZKK0200)Yunnan Fundamental Research Projects(202101AS070032)the CAS“Light ofWest China”Program(xbzg-zdsys-202110)the Yunnan Innovation Team Project(202305AS350004,with LD/NY/SB/CJG/CJH as the core member).
文摘The genus Salix is a common component of the Northern Hemisphere dendroflora with important ecological and economic value.However,taxonomy and systematics of Salix is extremely difficult and relationships between main lineages,especially deep phylogenies,remain largely unresolved.In this study,we used genome-skimming,plastome assembly,and single-copy orthologs(SCOs)from 66 Salix accessions,along with publicly available plastome and sequence read archive(SRA)datasets to obtain a robust backbone phylogeny of Salix,clarify relationships between its main lineages,and gain a more precise understanding of the origin and diversification of this species-rich genus.The plastome and SCO datasets resolved Salix into two robust clades,with plastome-based phylogenies lacking inner resolution and SCO offering fully resolved phylogenies.Our results support the classification of Salix into five subgenera:Salix,Urbaniana,Triandrae,Longifoliae and Vetrix.We observed a significant acceleration in the diversification rate within the Chamaetia-Vetrix clade,while Salix exhibited increased rates of diversification spanning from the early Oligocene to the late Miocene.These changes coincided with contemporaneous tectonic and climate change events.Our results provide a foundation for future systematic and evolutionary studies of Salix.Additionally,we showed that genome skimming data is an efficient,rapid,and reliable approach for obtaining extensive genomic data for phylogenomic studies,enabling the comprehensive elucidation of Salix relationships.
基金supported by the China Human Proteomics Project (2014DFB30010)the National High Technology Research and Development Program of China (2015AA020104)+1 种基金the National Natural Science Foundation of China (31071162)the Graduate School of East China Normal University
文摘Human and mouse orthologs are expected to have similar biological functions; however, many discrepancies have also been reported. We systematically compared human and mouse orthologs in terms of alternative splicing patterns and expression profiles. Human-mouse orthologs are divergent in alternative splicing, as human orthologs could generally encode more isoforms than their mouse orthologs. In early embryos, exon skipping is far more common with human orthologs, whereas constitutive exons are more prevalent with mouse orthologs. This may correlate with divergence in expression of splicing regulators. Orthologous expression similarities are different in distinct embryonic stages, with the highest in morula. Expression differences for orthologous transcription factor genes could play an important role in orthologous expression discordance. We further detected largely orthologous divergence in differential expression between distinct embryonic stages. Collectively, our study uncovers significant orthologous divergence from multiple aspects, which may result in functional differences and dynamics between human-mouse orthologs during embryonic development.
文摘Rice and wheat provide nearly 40%of human calorie and protein requirements.They share a common ancestor and belong to the Poaceae(grass)family.Characterizing their genetic homology is crucial for developing new cultivars with enhanced traits.Several wheat genes and gene families have been characterized based on their rice orthologs.Rice–wheat orthology can identify genetic regions that regulate similar traits in both crops.Rice–wheat comparative genomics can identify candidate wheat genes in a genomic region identified by association or QTL mapping,deduce their putative functions and biochemical pathways,and develop molecular markers for marker-assisted breeding.A knowledge of gene homology facilitates the transfer between crops of genes or genomic regions associated with desirable traits by genetic engineering,gene editing,or wide crossing.
基金supported by National Natural Science Foundation of China(32060466)Chinese Academy of Agricultural Sciences。
文摘Background Photosystem II(PSII)constitutes an intricate assembly of protein pigments,featuring extrinsic and intrinsic polypeptides within the photosynthetic membrane.The low-molecular-weight transmembrane protein PsbX has been identified in PSII,which is associated with the oxygen-evolving complex.The expression of PsbX gene protein is regulated by light.PsbX’s central role involves the regulation of PSII,facilitating the binding of quinone molecules to the Qb(PsbA)site,and it additionally plays a crucial role in optimizing the efficiency of photosynthesis.Despite these insights,a comprehensive understanding of the PsbX gene’s functions has remained elusive.Results In this study,we identified ten PsbX genes in Gossypium hirsutum L.The phylogenetic analysis results showed that 40 genes from nine species were classified into one clade.The resulting sequence logos exhibited substantial conservation across the N and C terminals at multiple sites among all Gossypium species.Furthermore,the ortholo-gous/paralogous,Ka/Ks ratio revealed that cotton PsbX genes subjected to positive as well as purifying selection pressure might lead to limited divergence,which resulted in the whole genome and segmental duplication.The expression patterns of GhPsbX genes exhibited variations across specific tissues,as indicated by the analysis.Moreover,the expression of GhPsbX genes could potentially be regulated in response to salt,intense light,and drought stresses.Therefore,GhPsbX genes may play a significant role in the modulation of photosynthesis under adverse abiotic conditions.Conclusion We examined the structure and function of PsbX gene family very first by using comparative genom-ics and systems biology approaches in cotton.It seems that PsbX gene family plays a vital role during the growth and development of cotton under stress conditions.Collectively,the results of this study provide basic information to unveil the molecular and physiological function of PsbX genes of cotton plants.
基金supported by the National Natural Science Foundation of China (J0930005,30970350,31071959)
文摘With the development and decreasing cost of sequencing techniques, it is possible for scientists to conduct deeper research in phylogenomics. During the procedure of phylogenomic analysis, the mostimportant and vitalest step is orthology prediction, for that the prerequisite to phylogenetic reconstruction is that the genes being compared are orthologous. Here we briefly review the related concept of orthology anddifferent methods for orthology prediction. We also provide recommendations to give some advice for better selection of orthology prediction methods.
基金supported by National Key Research and Development Program of China (Grant No. 2018YFD1000)Shandong Vegetable Research System (Grant No. SDAIT-05–05)+1 种基金Major Agricultural Application Technology Innovation Project of Shandong Province (2018)The Key Research and Development Program of Shandong and Chongqing Cooperation (Grant No. 2020LYXZ001)
文摘The multidrug and toxic compound extrusion(MATE) family plays pivotal roles in the detoxification process in plants, while no information has been provided for this gene family in melon(Cucumis melo L.) thus far, limiting our understanding of its functions in melon acclimation to stressful environments. In this study, a total of 39 MATEs(CmMATE1–CmMATE39) were observed in the melon genome;these were unevenly distributed in all chromosomes, with the most on Chromosome 1. Based on their orthologous relationship with those from Arabidopsis, rice, and sorghum, melon MATEs were clustered into three subfamilies of Clades Ⅰ, Ⅱ, and Ⅲ, wherein 23, 9, and 7 members were included, respectively.Variable exon number was observed in CmMATEs, and the most were harbored by CmMATE8. Gene ontology(GO) term and cis-regulatory element(CRE) analyses pointed to the potential roles of CmMATEs in both the regulation of melon development and acclimation to various abiotic and biotic stressors. The RNA-seq and qRT-PCR(quantitative real-time PCR) results demonstrated that under normal growth conditions, CmMATEs were expressed in a tissue-and development-specific manner, while their abundance apparently varied in a stress-dependent manner when melon plants were exposed to unfavorable environmental conditions. Altogether, these observations could expand our knowledge about the plant MATE family and benefit functional genomics analysis for CmMATEs in the future.
基金supported by the grants from the Ministry of Science and Technology of China (the China Rice Functional Genomics Programs, No. 2006AA10A102 and 2005CB120805)the Chinese Academy of Sciences (No. KSCX2-YWN-024)the Shanghai Municipal Commission of Science and Technology
文摘Comparative analyses of genome structure and sequence of closely related species have yielded insights into the evolution and function of plant genomes. A total of 103,844 BAC end sequences delegated -73.8 Mb of O. officinalis that belongs to the CC genome type of the rice genus Oryza were obtained and compared with the genome sequences office cultivar, O. sativa ssp.japonica cv. Nipponbare. We found that more than 45% of O. officinalis genome consists of repeat sequences, which is higher than that of Nipponbare cultivar. To further investigate the evolutionary divergence of AA and CC genomes, two BAC-contigs of O. officinalis were compared with the collinear genomic regions of Nipponbare. Of 57 genes predicted in the AA genome orthologous regions, 39 had orthologs in the regions of the CC genome. Alignment of the orthologous regions indicated that the CC genome has undergone expansion in both genic and intergenic regions through primarily retroelement insertion. Particularly, the density of RNA transposable elements was 17.95% and 1.78% in O. officinalis and O. sativa, respectively. This explains why the orthologous region is about 100 kb longer in the CC genome in comparison to the AA genome.
基金Supported by The Basic Science Research Program through the Korea Research Foundation Grant funded by the Ministry of Education,Science,and Technology(NRF-2011-0008913)Kim IH and Cha MK performed this work during their research sabbatical supported by Paichai University(2014-2015)
文摘AIM: To identify alkyl hydroperoxide reductase subunit C(AhpC) homologs in Bacillus subtilis(B. subtilis) and to characterize their structural and biochemical properties. AhpC is responsible for the detoxification of reactive oxygen species in bacteria.METHODS: Two AhpC homologs(AhpC_H1 and AhpC_H2) were identified by searching the B. subtilis database; these were then cloned and expressed in Escherichia coli. AhpC mutants carrying substitutions of catalytically important Cys residues(C37S, C47 S, C166 S, C37/47 S, C37/166 S, C47/166 S, and C37/47/166 S for AhpC_H1; C52 S, C169 S, and C52/169 S for AhpC_H2) were obtained by site-directed mutagenesis and purified, and their structure-function relationship was analyzed. The B. subtilis ahp C genes were disrupted by the short flanking homology method, and the phenotypes of the resulting AhpC-deficient bacteria were examined.RESULTS: Comparative characterization of AhpC homologs indicates that AhpC_H1 contains an extra C37, which forms a disulfide bond with the peroxidatic C47, and behaves like an atypical 2-Cys AhpC, while AhpC_H2 functions like a typical 2-Cys AhpC. Tryptic digestion analysis demonstrated the presence of intramolecular Cys37-Cys47 linkage, which could be reduced by thioredoxin, resulting in the association of the dimer into higher-molecular-mass complexes. Peroxidase activity analysis of Cys→Ser mutants indicated that three Cys residues were involved in the catalysis. AhpC_H1 was resistant to inactivation by peroxide substrates, but had lower activity at physiological H2O2 concentrations compared to AhpC_H2, suggesting that in B. subtilis, the enzymes may be physiologically functional at different substrate concentrations. The exposure to organic peroxides induced AhpC_H1 expression, while AhpC_H1-deficient mutants exhibited growth retardation in the stationary phase, suggesting the role of AhpC_H1 as an antioxidant scavenger of lipid hydroperoxides and a stress-response factor in B. subtilis. CONCLUSION: AhpC_H1, a novel atypical 2-Cys AhpC, is functionally distinct from AhpC_H2, a typical 2-Cys AhpC.
基金Supported by the National Key R&D Program of China(Nos.2018YFC1406704,2018YFD0900106,2018YFC1406700)the Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology(Qingdao)(No.2018SDKJ0302-4)the MOA Modern Agricultural Talents Support Project。
文摘Microorganisms plays an important role in the growth of Pyropia haitanensis.To understand the structural and functional diversity of the microorganism community of P.haitanensis(PH40),the associated metabolic pathway network in cluster of orthologous groups(COG)and Kyoto Encyclopedia of Genes and Genomes(KEGG),and carbohydrate-active enzymes(CAZymes)were explored in metagenomic analysis.DNA extraction from gametophytes of P.haitanensis was performed first,followed by library construction,sequencing,preprocessing of sequencing data,taxonomy assignment,gene prediction,and functional annotation.The results show that the predominant microorganisms of P.haitanensis were bacteria(98.98%),and the phylum with the highest abundance was Proteobacteria(54.64%),followed by Bacteroidetes(37.92%).Erythrobacter(3.98%)and Hyunsoonleella jejuensis(1.56%)were the genera and species with the highest abundance of bacteria,respectively.The COG annotation demonstrated that genes associated with microbial metabolism was the predominant category.The results of metabolic pathway annotation show that the ABC transport system and two-component system were the main pathways in the microbial community.Plant growth hormone biosynthesis pathway and multi-vitamin biosynthesis functional units(modules)were the other important pathways.The CAZyme annotation revealed that the starch might be an important carbon source for microorganisms.Glycosyl transferase family 2(GT2)and glycosyl transferase family 3(GT3)were the highly abundant families in glucoside transferase superfamily.Six metagenome-assembled genomes containing enzymes involved in the biosynthesis of cobalamin(vitamin B 12)and indole-3-acetic acid were obtained by binning method.They were confirmed to belong to Rhodobacterales and Rhizobiales,respectively.Our findings provide comprehensive insights into the microorganism community of Pyropia.
文摘Understanding the genetic architecture of indi-vidual taxa of medical importance is the first step for designing disease preventive strategies. To understand the genetic details and evolu-tionary perspective of the model malaria vector, Anopheles gambiae and to use the information in other species of local importance, we scanned the published X-chromosome se-quence for detail characterization and obtain evolutionary status of different genes. The te-locentric X-chromosome contains 106 genes of known functions and 982 novel genes. Majori-ties of both the known and novel genes are with introns. The known genes are strictly biased towards less number of introns;about half of the total known genes have only one or two in-trons. The extreme sized (either long or short) genes were found to be most prevalent (58% short and 23% large). Statistically significant positive correlations between gene length and intron length as well as with intron number and intron length were obtained signifying the role of introns in contributing to the overall size of the known genes of X-chromosome in An. gam-biae. We compared each individual gene of An. gambiae with 33 other taxa having whole ge-nome sequence information. In general, the mosquito Aedes aegypti was found to be ge-netically closest and the yeast Saccharomyces cerevisiae as most distant taxa to An. gambiae. Further, only about a quarter of the known genes of X-chromosome were unique to An. gambiae and majorities have orthologs in dif-ferent taxa. A phylogenetic tree was constructed based on a single gene found to be highly orthologous across all the 34 taxa. Evolutionary relationships among 13 different taxa were in-ferred which corroborate the previous and pre-sent findings on genetic relationships across various taxa.
文摘<i>Bacillus thuringiensis</i> (Bt) parasporal crystal proteins were well known to be toxic to certain insects and cytocidal activity against various human cancer cells. Bt serovar <i>coreanensis</i> ST7, non-pathogenic to insects and non-hemolytic, has an important parasporin, PS4Aa1 (Cry45Aa1), with potential toxicity to human cancer cells. In this study, we reported the feature of complete genome sequence and the cluster of orthologous groups of proteins function classification of ST7. Meanwhile, the evolutionary of ST7 was also studied. The genome data of ST7 will strongly contribute to a better understanding of the genomic diversity and evolution, and enrich the Bt genome database.
基金supported by grants from the National Natural Science Foundation of China (31970955 and 31700912)。
文摘Dear Editor,In dynamic environments,the memory system of the brain must be able to perceive and process conflicting experiences to reach an adaptive decision.In Drosophila,in contrast to consistent experiences,conflicting experiences trigger significantly increased Rac1 activity which mediates active forgetting [1].The ability to cope with conflicting experiences but not simple learning experiences is impaired in mutants of multiple autism-risk genes [2].
基金supported by the Australia Grain Research and Development Corporation(9176507).
文摘Genome-wide identification and comparative gene-famiy analyses have commonly been performed to investigate spedesspecif ic evolution Inked to various traits and molecular pathways.However,most previous studies have been Smited to gene screening h a single reference genome,faiing to account for the gene presence/absence variations(gPAVs)in a species.Here,we propose an innovative pangenome-based approach for gene-family analyses based on orthologous gene groups(OGGs).Usng the basic heix-bop-helix(bH_H)transcription factor family in barley as an example,we identified 161-176 bHLHs in 20 barley genomes,which can be classified into 201 OGGs.These 201 OGGs were further dassif jed into 140 core,12 softcore,29 shell,and 20 Ihe-spedfic/cloud bHLHs,reveaing the complete profile of bHLH genes in barley.Using a genome-scanning approach,we overcame the genome annotation bias and identified an average of 15 un-amotated core bHLHs per barley genome We found that whole-genome/segmental duplicates are predominant mechanisms contrixiting to the expansion of most core/softcore bHLHs,whereas dispensable bHLHs are more Ikely to result from small-scale dupication events.Interestingly,we noticed that the dispensable bHLHs tend to be enriched in the specific subfamiSes SF13,SF27,and SF28,rn plying the potentially based expansion of specific bHLHs h barley.We found that 50%of the bHLHs con tan at least 1 intact transposon element(TE)within the 2-kb upstream-to-downstream region.bHLHs with copy-number variations(CWs)have 1.48 TEs on average,sigrif icantiy more than core bhLHs without CNVs(1.36),supporting a potential role ofTEs in bHLH expansion.Analyses of selection pressure showed that dispensablebHLHs have experienced dearrelaxation of selection compared with core bHLHs,consistent with their conservation patterns.We also integrated the pangenome data with recently avaiable barley pantranscrip-tome data from 5 tissues and discovered apparent transcriptional divergence within and across bHLH sifofamiies.We conclude that pangenome-based gene-family analyses can better describe the previously untapped,genu'ne evolutionary status of bHLHs and provide novel insights into bHLH evolution in barley.We expect that this study wil inspire similar analyses in many other gene famiies and species.
基金supported in part by the Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior(CAPES)(Grant/Award Number:001)Conselho Nacional de Desenvolvimento Cientifico e Tecnologico,and Fundacao de Amparo a Pesquisa do Estado de Minas Gerais(CNPq/FAPEMIG)(Grant/Award Number:BPD-00626-22 andAPQ-01297-23).
文摘A recent study published in Cell by Chen et al.,highlighted by Nature journal,identified the HKU5-CoV-2 lineage,a coronavirus detected in bats with the potential to interact with the human ACE2 receptor.1:2 Experiments conducted in intestinal and airway cells indicated that HkU5-CoV-2 binds to the receptor less efficiently than SARS-CoV-2.However,the broad ACE2 ortholog tropism suggests a potential risk of adaptation to the human host.
基金supported in part by the National Natural Science Foundation of China(No.31970504,31772548,82371863,82070394)the NHC Key Laboratory of Birth Defect for Research and Prevention(Hunan Provincial Maternal and Child Health Care Hospital)(No.KF2021003)the Postgraduate Scientific Innovation Fund of Hunan Province,China(No.CX2018B302).
文摘TNNI3K(troponin-I interacting kinase)encodes a duo tyrosine and serine/threonine kinase implicated in cardiomyopathy,arrhythmias,and cardiac conduction disease(CCD).1 However,no direct downstream phosphorylation targets of TNNI3K have been identified yet.2 Here,we employed the CRISPR/Cas9 gene-editing technique to generate a splicing mutation in the 4th exon of zebrafish tnni3k ortholog gene that mimics a TNNI3K splicing variant identified from a patient family with cardiomyopathy and CCD.
文摘Glycosyltransferases （GTs; EC 2.4.x.y） constitute a large group of enzymes that form glycosidic bonds through transfer of sugars from activated donor molecules to acceptor molecules. GTs are critical to the biosynthesis of plant cell walls, among other diverse functions. Based on the Carbohydrate-Active enZymes （CAZy） database and sequence similarity.searches, we have identified 609 potential GT genes （loci） corresponding to 769 transcripts （gene models） in rice （Oryza sativa）, the reference monocotyledonous species. Using domain composition and sequence similarity, these rice GTs were classified into 40 CAZy families plus an additional unknown class. We found that two Pfam domains of unknown function, PF04577 and PF04646, are associated with GT families GT61 and GT31, respectively. To facilitate functional analysis of this important and large gene family, we created a phylogenomic Rice GT Database （http：//ricephylogenomics. ucdavis.edu/cellwalls/gtJ）. Through the database, several classes of functional genomic data, including mutant lines and gene expression data, can be displayed for each rice GT in the context of a phylogenetic tree, allowing for comparative analysis both within and between GT families. Comprehensive digital expression analysis of public gene expression data revealed that most （-80%） rice GTs are expressed. Based on analysis with Inparanoid, we identified 282 ‘rice-diverged＇ GTs that lack orthologs in sequenced dicots （Arabidopsis thaliana, Populus tricocarpa, Medicago truncatula, and Ricinus communis）. Combining these analyses, we identified 33 rice-diverged GT genes （45 gene models） that are highly expressed in above-ground, vegetative tissues. From the literature and this analysis, 21 of these loci are excellent targets for functional examination toward understanding and manipulating grass cell wall qualities. Study of the remainder may reveal aspects of hormone and protein metabolism that are critical for rice biology. This list of 33 genes and the Rice GT Database will facilitate the study of GTs and cell wall synthesis in rice and other plants.
