Genomes and Genes
Experts and Doctors on multigene family in Wuhan, Hubei, China
Locale: Wuhan, Hubei, China
Topic: multigene family
- Shi T. Impact of gene family evolutionary histories on phylogenetic species tree inference by gene tree parsimony. Mol Phylogenet Evol. 2016;96:9-16 pubmed publisher..As these evolutionary properties can significantly influence species tree accuracy, I discussed the potential weighting of the duplication cost by evolutionary properties of gene families in future GTP analyses. ..
- Du C, Hu K, Xian S, Liu C, Fan J, Tu J, et al. Dynamic transcriptome analysis reveals AP2/ERF transcription factors responsible for cold stress in rapeseed (Brassica napusÂ L.). Mol Genet Genomics. 2016;291:1053-67 pubmed publisher..This study is the first dynamic analysis of the AP2/ERF TFs responsible for cold stress in rapeseed. These findings will serve as a reference for future functional research on transcription in rapeseed. ..
- Li Q, Yan W, Chen H, Tan C, Han Z, Yao W, et al. Duplication of OsHAP family genes and their association with heading date in rice. J Exp Bot. 2016;67:1759-68 pubmed publisher..Selection of HAP genes is probably caused by their diverse functions rather than regulation of heading. ..
- Zhang Y, Ding D, Liu M, Yang X, Zong B, Wang X, et al. Effect of the glycosyltransferases on the capsular polysaccharide synthesis of Streptococcus suis serotype 2. Microbiol Res. 2016;185:45-54 pubmed publisher..In summary, this study characterized four genes (cps2E, cps2G, cps2J and cps2L) involved in CPS synthesis of S. suis 2 SC19 and it revealed that these genes were all crucial for SC19 to invade and survive in the host. ..
- Xu Q, Wen X, Deng X. Genomic organization, rapid evolution and meiotic instability of nucleotide-binding-site-encoding genes in a new fruit crop, "chestnut rose". Genetics. 2008;178:2081-91 pubmed publisher..Moreover, a transposon-like element was isolated in the flanking region of NBS genes, implying a possible role for transposon in the evolutionary history of resistance genes. ..
- Zhao H, Ma H, Yu L, Wang X, Zhao J. Genome-wide survey and expression analysis of amino acid transporter gene family in rice (Oryza sativa L.). PLoS ONE. 2012;7:e49210 pubmed publisher..This study will facilitate further studies on OsAAT family and provide useful clues for functional validation of OsAATs. ..
- Gao J, Yu X, Xie Z. Draft genome sequence of high-siderophore-yielding Pseudomonas sp. strain HYS. J Bacteriol. 2012;194:4121 pubmed publisher..The 5.6-Mb draft genome sequence has a special pattern of pyoverdine synthesis clusters and contains an hmuRSTUV heme uptake cluster, which has a homolog only in some strains of the order Enterobacteriales. ..
- Liu H, Wang S, Zhang J, Dai H, Tang H, Zhou N. Patchwork assembly of nag-like nitroarene dioxygenase genes and the 3-chlorocatechol degradation cluster for evolution of the 2-chloronitrobenzene catabolism pathway in Pseudomonas stutzeri ZWLR2-1. Appl Environ Microbiol. 2011;77:4547-52 pubmed publisher..This provides another example to help elucidate the bacterial evolution of catabolic pathways in response to xenobiotic chemicals...
- Zou X, Suppanz I, Raman H, Hou J, Wang J, Long Y, et al. Comparative analysis of FLC homologues in Brassicaceae provides insight into their role in the evolution of oilseed rape. PLoS ONE. 2012;7:e45751 pubmed publisher..This cluster of flowering-time genes might have conferred a selective advantage to Brassica species in terms of increased adaptability to diverse environments during their evolution and domestication process...
- Liu T, Xu Y, Liu H, Luo S, Yin Y, Liu S, et al. Functional characterization of a gene cluster involved in gentisate catabolism in Rhodococcus sp. strain NCIMB 12038. Appl Microbiol Biotechnol. 2011;90:671-8 pubmed publisher..Our study suggested that the gentisate degradation pathway was shared by both naphthalene and 3-hydroxybenzoate catabolism in this strain...
- Wang L, Guo K, Li Y, Tu Y, Hu H, Wang B, et al. Expression profiling and integrative analysis of the CESA/CSL superfamily in rice. BMC Plant Biol. 2010;10:282 pubmed publisher..These investigations revealed very useful clues on the major roles of CESA/CSL, their potentially functional complement and their associations for appropriate cell wall synthesis in higher plants. ..
- Chen L, Hu W, Tan S, Wang M, Ma Z, Zhou S, et al. Genome-wide identification and analysis of MAPK and MAPKK gene families in Brachypodium distachyon. PLoS ONE. 2012;7:e46744 pubmed publisher..Taken together, our data would provide a foundation for evolutionary and functional characterization of MAPK and MAPKK gene families in B. distachyon and other plant species to unravel their biological roles...
- Zhou M, Yan J, Ma Z, Zhou Y, Abbood N, Liu J, et al. Comparative and evolutionary analysis of the HES/HEY gene family reveal exon/intron loss and teleost specific duplication events. PLoS ONE. 2012;7:e40649 pubmed publisher..This study shows a model of gene family analysis with gene structure evolution and duplication. ..
- Hu Z, Bao K, Zhou X, Zhou Q, Hopwood D, Kieser T, et al. Repeated polyketide synthase modules involved in the biosynthesis of a heptaene macrolide by Streptomyces sp. FR-008. Mol Microbiol. 1994;14:163-72 pubmed..The methods developed for transformation and gene replacement in Streptomyces sp. FR-008 make it possible to genetically manipulate polyene macrolide production, and may later lead to the biosynthesis of novel polyene macrolides. ..
- Zhang Y, Liu T, Jiang J, Shi J, Liu Y, Li S, et al. Identification of a novel Gig2 gene family specific to non-amniote vertebrates. PLoS ONE. 2013;8:e60588 pubmed publisher..The specificity of this gene family to non-amniotes might contribute to a large extent to distinct physiology in non-amniote vertebrates. ..
- Huang T, Zhu M, Li X, Zhao S. Discovery of porcine microRNAs and profiling from skeletal muscle tissues during development. PLoS ONE. 2008;3:e3225 pubmed publisher..In silico analysis of the miRNA-mRNA interaction sites suggested that the potential mRNA targets of the differentially expressed miRNAs may play important roles in muscle growth and development. ..
- Munir S, Khan M, Song J, Munir S, Zhang Y, Ye Z, et al. Genome-wide identification, characterization and expression analysis of calmodulin-like (CML) proteins in tomato (Solanum lycopersicum). Plant Physiol Biochem. 2016;102:167-79 pubmed publisher..These results illustrate the complexity of the CML gene family and indicate a potential vital role for these molecules in tomato growth and development as Ca(2+) signal transducers. ..
- Luo S, Peng J, Li K, Wang M, Kuang H. Contrasting evolutionary patterns of the Rp1 resistance gene family in different species of Poaceae. Mol Biol Evol. 2011;28:313-25 pubmed publisher..The Rp1 homologues in wheat and barley were most divergent, probably due to lack of sequence exchanges among them. Our results shed more light on R-gene evolution, particularly on the differentiation of Type I and Type II R-genes. ..
- Ding X, Hou X, Xie K, Xiong L. Genome-wide identification of BURP domain-containing genes in rice reveals a gene family with diverse structures and responses to abiotic stresses. Planta. 2009;230:149-63 pubmed publisher..Promoter sequence analysis revealed an over-abundance of stress-related cis-elements in the stress-responsive genes. The data presented here provide important clues for elucidating the functions of genes of this family. ..
- Islam M, Du H, Ning J, Ye H, Xiong L. Characterization of Glossy1-homologous genes in rice involved in leaf wax accumulation and drought resistance. Plant Mol Biol. 2009;70:443-56 pubmed publisher..Compared to the over-expression and wild type plants, the osgl1-2 mutant was more sensitive to drought stress at reproductive stage, suggesting an important role of this gene in drought resistance. ..
- Feng Z, Zhou Q, Ma G, Li K, Zhao S. Mapping of porcine BTG1, BTG4, TOB2, USP2 and PEG3 using somatic cell and radiation hybrid panels. Anim Genet. 2007;38:536-7 pubmed
- Wang Y, Lechno Yossef S, Gong Y, Fan Q, Wolk C, Xu X. Predicted glycosyl transferase genes located outside the HEP island are required for formation of heterocyst envelope polysaccharide in Anabaena sp. strain PCC 7120. J Bacteriol. 2007;189:5372-8 pubmed..Mutations in the histidine kinase genes hepN and hepK appear to silence the promoter of hepB and incompletely down-regulate all4160. ..
- Lu Z, Huang X, Ouyang Y, Yao J. Genome-wide identification, phylogenetic and co-expression analysis of OsSET gene family in rice. PLoS ONE. 2013;8:e65426 pubmed publisher..This study will facilitate further studies on OsSET family and provide useful clues for functional validation of OsSETs. ..
- Liu J, Chen P, Zheng C, Huang Y. Characterization of maltocin P28, a novel phage tail-like bacteriocin from Stenotrophomonas maltophilia. Appl Environ Microbiol. 2013;79:5593-600 pubmed publisher..We found that maltocin P28 had bactericidal activity against 38 of 81 tested S. maltophilia strains. Therefore, maltocin P28 is a promising therapeutic substitute for antibiotics for S. maltophilia infections...
- Zhou R, Liu L, Guo Y, Yu H, Cheng H, Huang X, et al. Similar gene structure of two Sox9a genes and their expression patterns during gonadal differentiation in a teleost fish, rice field eel (Monopterus albus). Mol Reprod Dev. 2003;66:211-7 pubmed publisher..The closely related gene structure and expression patterns of the two sox9a genes in the rice field eel also suggest that they arose in recent gene duplication events during evolution of this fish lineage...
- Qi J, Guo A, Cui P, Chen Y, Mustafa R, Ba X, et al. Comparative geno-plasticity analysis of Mycoplasma bovis HB0801 (Chinese isolate). PLoS ONE. 2012;7:e38239 pubmed publisher..05). Compared to Hubei-1, a total of 122 SNP loci were disclosed in HB0801. In conclusion, although genomic plasticity was thought to be an evolutionary advantage, it did not apparently affect virulence of M. bovis strains in cattle...
- Li N, Zhang L, Zhang J, Liu Z, Huang B, Zhang S, et al. Type I restriction-modification system and its resistance in electroporation efficiency in Flavobacterium columnare. Vet Microbiol. 2012;160:61-8 pubmed publisher..columnare G(4). It will be of significant interest to examine the composition and diversity of R-M systems in strains of F. columnare in order to set up a suitable genetic manipulation system for the bacterium...
- Zheng L, Zhou X, Zhang H, Ji X, Li L, Huang L, et al. Structural and functional analysis of validoxylamine A 7'-phosphate synthase ValL involved in validamycin A biosynthesis. PLoS ONE. 2012;7:e32033 pubmed publisher..Furthermore, the modeling of V7P in the active site of ValL suggests that ValL might have a similar SNi-like mechanism as OtsA...
- Li X, Fan X, Wang X, Cai L, Yang W. The cotton ACTIN1 gene is functionally expressed in fibers and participates in fiber elongation. Plant Cell. 2005;17:859-75 pubmed..No defined actin network was observed in these fibers and, consequently, fiber elongation was inhibited. Our results suggested that GhACT1 plays an important role in fiber elongation but not fiber initiation. ..
- Zhang H, Cao Y, Zhao J, Li X, Xiao J, Wang S. A pair of orthologs of a leucine-rich repeat receptor kinase-like disease resistance gene family regulates rice response to raised temperature. BMC Plant Biol. 2011;11:160 pubmed publisher..The LRR domain of RKe protein appears to be important to sense increased temperature. The RKe-involved temperature-related pathway and Xa3/Xa26-mediated disease-resistance pathway may partially overlap. ..
- Zhong L, Yu X, Tong J. Sox genes in grass carp (Ctenopharyngodon idella) with their implications for genome duplication and evolution. Genet Sel Evol. 2006;38:673-87 pubmed..The potential uses of Sox genes as markers in revealing the evolutionary history of grass carp are discussed. ..
- Zhou J, Zhu T, Hu C, Li H, Chen G, Xu G, et al. Comparative genomics and function analysis on BI1 family. Comput Biol Chem. 2008;32:159-62 pubmed publisher..They share multiple motifs and transcriptional factors within the promoter and the coding regions. They may represent regulators of cell death pathways, which are concluded from structure conservation of BI1 family. ..
- Lu Y, Ouyang B, Zhang J, Wang T, Lu C, Han Q, et al. Genomic organization, phylogenetic comparison and expression profiles of annexin gene family in tomato (Solanum lycopersicum). Gene. 2012;499:14-24 pubmed publisher..Most of these annexin genes were induced by salt, drought, wounding, and heat or cold stresses. The present study provides significant information for understanding the diverse roles of annexins in tomato growth and development...
- Zhang W, Du Y, Khudyakov I, Fan Q, Gao H, Ning D, et al. A gene cluster that regulates both heterocyst differentiation and pattern formation in Anabaena sp. strain PCC 7120. Mol Microbiol. 2007;66:1429-43 pubmed..The presence of homologous clusters in filamentous genera without heterocysts is suggestive of a more general role. ..
- Ouyang Y, Chen J, Xie W, Wang L, Zhang Q. Comprehensive sequence and expression profile analysis of Hsp20 gene family in rice. Plant Mol Biol. 2009;70:341-57 pubmed publisher..Our results suggest that the expression patterns of the OsHsp20 genes are diversified not only in developmental stages but also in variety level. ..
- Wang M, Yuan D, Gao W, Li Y, Tan J, Zhang X. A comparative genome analysis of PME and PMEI families reveals the evolution of pectin metabolism in plant cell walls. PLoS ONE. 2013;8:e72082 pubmed publisher..This study will advance the evolutionary understanding of the PME and PMEI families and plant cell wall development. ..
- Li A, Xia T, Xu W, Chen T, Li X, Fan J, et al. An integrative analysis of four CESA isoforms specific for fiber cellulose production between Gossypium hirsutum and Gossypium barbadense. Planta. 2013;237:1585-97 pubmed publisher..In addition, we discussed that callose synthesis might be regulated in vivo for massive cellulose production during active secondary cell wall biosynthesis in cotton fibers...
- Chao H, Zhou N. GenR, an IclR-type regulator, activates and represses the transcription of gen genes involved in 3-hydroxybenzoate and gentisate catabolism in Corynebacterium glutamicum. J Bacteriol. 2013;195:1598-609 pubmed publisher..The results reveal a new regulatory function of the IclR family in the catabolism of aromatic compounds. ..
- Zhao X, Huang J, Yu H, Wang L, Xie W. Genomic survey, characterization and expression profile analysis of the peptide transporter family in rice (Oryza sativa L.). BMC Plant Biol. 2010;10:92 pubmed publisher..These investigations add to our understanding of the importance of OsPTR family members and provide useful reference for selecting candidate genes for functional validation studies of this family in rice. ..
- Duan X, He Z. Characterization of the specific interaction between archaeal FHA domain-containing protein and the promoter of a flagellar-like gene-cluster and its regulation by phosphorylation. Biochem Biophys Res Commun. 2011;407:242-7 pubmed publisher..These findings not only increase our knowledge about the function of an archaeal FHA domain-containing regulator but also offer important insights for further understanding the signaling mechanism of environmental adaptation in archaea...
- Ouyang Y, Huang X, Lu Z, Yao J. Genomic survey, expression profile and co-expression network analysis of OsWD40 family in rice. BMC Genomics. 2012;13:100 pubmed publisher..All of these analyses suggest that the functions of OsWD40 genes are diversified, which provide useful references for selecting candidate genes for further functional studies. ..
- Jiang Y, Xiao P, Yu G, Sano T, Pan Q, Li R. Molecular basis and phylogenetic implications of deoxycylindrospermopsin biosynthesis in the cyanobacterium Raphidiopsis curvata. Appl Environ Microbiol. 2012;78:2256-63 pubmed publisher..The transcripts of the mutated cyrI gene may result from polycistronic transcription. The high conservation of the cyr genes may be ascribed to purifying selection and horizontal gene transfer. ..
- Chen Z, Lei T, Chen X, Zhang J, Yu A, Long Q, et al. Porcine KLF gene family: Structure, mapping, and phylogenetic analysis. Genomics. 2010;95:111-9 pubmed publisher..The current work represents the first comprehensive study of KLF genes in pigs and provides a foundation for future studies concerning structural, functional, and evolutionary analyses of KLF gene family. ..
- Ye H, Du H, Tang N, Li X, Xiong L. Identification and expression profiling analysis of TIFY family genes involved in stress and phytohormone responses in rice. Plant Mol Biol. 2009;71:291-305 pubmed publisher..These results suggest that the OsTIFY family may have important roles in response to abiotic stresses. The data presented in this report provide important clues for further elucidating the functions of the genes in the OsTIFY family. ..
- Huang J, Zhao X, Yu H, Ouyang Y, Wang L, Zhang Q. The ankyrin repeat gene family in rice: genome-wide identification, classification and expression profiling. Plant Mol Biol. 2009;71:207-26 pubmed publisher..Our data provided a very useful reference for cloning and functional analysis of members of this gene family in rice...
- Liu Y, Zhang Y, Liu T, Gui J. Lineage-specific expansion of IFIT gene family: an insight into coevolution with IFN gene family. PLoS ONE. 2013;8:e66859 pubmed publisher..Our results are helpful for understanding of evolution of vertebrate IFN system...
- Cai L, Rensing C, Li X, Wang G. Novel gene clusters involved in arsenite oxidation and resistance in two arsenite oxidizers: Achromobacter sp. SY8 and Pseudomonas sp. TS44. Appl Microbiol Biotechnol. 2009;83:715-25 pubmed publisher..This study showed novel structures and arrangements of arsenic gene clusters associated with bacterial As(III) oxidation and As(V) reduction...
- Wang C, Zhou X, Ye S, Han D, Tan X, Zheng F, et al. Combined effects of apoE-CI-CII cluster and LDL-R gene polymorphisms on chromosome 19 and coronary artery disease risk. Int J Hyg Environ Health. 2006;209:265-73 pubmed..Drinking and smoking enhance the genetic predisposition to CAD. ..
- Chen X, Zhang S, Cheng Z, Cooke J, Werling D, Wathes D, et al. Polymorphisms in the selectin gene cluster are associated with fertility and survival time in a population of Holstein Friesian cows. PLoS ONE. 2017;12:e0175555 pubmed publisher..These results suggest that polymorphisms in SELP and SELE are associated with the likelihood of successful pregnancy, potentially through compromised implantation and placental development. ..
- Ma H, Zhao J. Genome-wide identification, classification, and expression analysis of the arabinogalactan protein gene family in rice (Oryza sativa L.). J Exp Bot. 2010;61:2647-68 pubmed publisher..Taken together, the genome-wide identification and expression analysis of the rice AGP gene family might facilitate further functional studies of rice AGPs. ..
- Feng L, Chang Y, Yuan D, Miao W. [Expression analysis of 5 hsp70 genes in Tetrahymena thermophila]. Dongwuxue Yanjiu. 2011;32:267-76 pubmed publisher..Blast2GO indicated that they participated in dissimilar biological processes, suggesting hsp70-3 and hsp70-5 perform different functions. ..
- Chang Y, Feng L, Xiong J, Miao W. [Function comparison and evolution analysis of metallothionein gene MTT2 and MTT4 in Tetrahymena thermophila]. Dongwuxue Yanjiu. 2011;32:476-84 pubmed publisher..The high similarities in gene structures and functions indicate that MTT2 and MTT4 were generated by recent gene duplication following the dosage balance model...