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14-3-3蛋白在植物细胞信号传导中发挥重要的作用,探索木本植物14-3-3蛋白家族的进化模式对深入理解该基因家族的功能有重要的指导意义。本文采用生物信息学的方法,在基因组水平上搜索和鉴定了12个杨树14-3-3蛋白基因,其中ε类有7个,非ε类有5个。通过对杨树14-3-3基因家族的系统进化、序列相似性、基因结构和染色体位置分析,发现杨树14-3-3基因的扩张主要是通过最近的一次全基因组加倍事件产生的。在全基因组加倍事件中共产生5对重复基因对,Ka/Ks分析显示这5对重复基因对处于较强的净化选择压力。RT-PCR分析显示在杨树12个14-3-3基因中有8个在不同组织中均表达,另外4个基因的表达部位发生了变异。因此,杨树14-3-3基因家族的分子进化及表达模式的研究结果预示着基因重复后其功能发生了分化。 相似文献
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Operons are clusters of unrelated genes with related functions that are a feature of prokaryotic genomes. Here, we report on an operon-like gene cluster in the plant Arabidopsis thaliana that is required for triterpene synthesis (the thalianol pathway). The clustered genes are coexpressed, as in bacterial operons. However, despite the resemblance to a bacterial operon, this gene cluster has been assembled from plant genes by gene duplication, neofunctionalization, and genome reorganization, rather than by horizontal gene transfer from bacteria. Furthermore, recent assembly of operon-like gene clusters for triterpene synthesis has occurred independently in divergent plant lineages (Arabidopsis and oat). Thus, selection pressure may act during the formation of certain plant metabolic pathways to drive gene clustering. 相似文献
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Dietrich FS Voegeli S Brachat S Lerch A Gates K Steiner S Mohr C Pöhlmann R Luedi P Choi S Wing RA Flavier A Gaffney TD Philippsen P 《Science (New York, N.Y.)》2004,304(5668):304-307
We have sequenced and annotated the genome of the filamentous ascomycete Ashbya gossypii. With a size of only 9.2 megabases, encoding 4718 protein-coding genes, it is the smallest genome of a free-living eukaryote yet characterized. More than 90% of A. gossypii genes show both homology and a particular pattern of synteny with Saccharomyces cerevisiae. Analysis of this pattern revealed 300 inversions and translocations that have occurred since divergence of these two species. It also provided compelling evidence that the evolution of S. cerevisiae included a whole genome duplication or fusion of two related species and showed, through inferred ancient gene orders, which of the duplicated genes lost one copy and which retained both copies. 相似文献
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基于水稻与拟南芥全基因组序列,在基因组与蛋白质组水平上对这2种模式植物的丝氨酸羧肽酶 (SCPs)基因家族进行比较分析.利用隐马可夫模型(hidden Markov models,HMM),发现水稻与拟南芥中分别存在71个与54个丝氨酸羧肽酶类(serine carboxypeptidases like,SCPL)蛋白编码基因,它们广泛分布于基因组中各条染色体上,并且存在多个基因簇聚区.基因结构分析显示,拟南芥的SCPL基因存在广泛的交替剪接方式,而这种现象在水稻SCPL基因中却不常见.蛋白结构分析表明,所有SCPL家族成员均具有α/β水解酶折叠亚族与S10家族典型的保守结构域与二级结构特征.系统进化分析表明,这125个SCPL蛋白可以分成3大类,与水稻不同,大多数拟南芥SCPL (88.9%)可归属于双链羧肽酶Ⅰ或Ⅱ. 相似文献
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应用生物信息学方法从杨树基因组数据库中筛选出19个杨树肉桂醇脱氢酶基因,它们聚为3类.序列分析表明,杨树CAD基因家族主要通过全基因组加倍和串联复制的方式进行扩张.杨树和拟南芥CAD家族共6对旁系同源基因,在较强的净化选择压力下进化.19个基因在杨树不同组织中均有表达,表达量较高的是PoptrCAD17、PoptrCA... 相似文献
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【目的】研究葡萄醛脱氢酶ALDH2基因家族中ALDH2B4、ALDH2B8和ALDH2B9 3个成员的进化关系,对其在病原菌侵染、非生物胁迫及激素处理下的表达进行分析,为揭示ALDH2基因在植物逆境胁迫下的作用机理提供理论依据。【方法】运用生物信息学方法,鉴定葡萄ALDH蛋白序列;通过葡萄和拟南芥ALDH2基因的系统发育树、基因结构及同线性分析探讨其进化关系;利用葡萄Affymetrix芯片数据,分析葡萄ALDH2（ALDH2B4、ALDH2B8和ALDH2B9）基因在病原菌侵染、非生物胁迫和激素处理下的表达谱;采用在线软件PlantCARE分析3个葡萄ALDH2基因的启动子元件组成差异。【结果】在葡萄基因组中共鉴定出23个ALDH基因,并发现了ALDH2基因的可变剪接现象。基因结构分析结果表明,3个葡萄ALDH2基因的内含子/外显子组成高度相似,且均是通过大规模基因倍增产生的;仅有ALDH2B4具有剪接变体。葡萄与拟南芥的ALDH2基因位于同线区域,表明葡萄与拟南芥的ALDH2基因具有共同的祖先,ALDH2基因先于植物分化而存在。表达分析结果表明,VvALDH2B8是一个多病原菌和非生物胁迫响应基因,VvALDH2B4是一个渗透胁迫响应基因。葡萄的3个ALDH2基因的启动子区域均含有逆境胁迫响应元件,在VvALDH2B8上还发现了病原菌侵染响应元件Box-W1。【结论】葡萄的3个ALDH2基因虽然具有共同的祖先,但其在逆境条件下的表达差异很大,VvALDH2B8和VvALDH2B4可能在植物抵抗逆境胁迫中起重要作用。 相似文献
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Ivens AC Peacock CS Worthey EA Murphy L Aggarwal G Berriman M Sisk E Rajandream MA Adlem E Aert R Anupama A Apostolou Z Attipoe P Bason N Bauser C Beck A Beverley SM Bianchettin G Borzym K Bothe G Bruschi CV Collins M Cadag E Ciarloni L Clayton C Coulson RM Cronin A Cruz AK Davies RM De Gaudenzi J Dobson DE Duesterhoeft A Fazelina G Fosker N Frasch AC Fraser A Fuchs M Gabel C Goble A Goffeau A Harris D Hertz-Fowler C Hilbert H Horn D Huang Y Klages S Knights A Kube M Larke N Litvin L Lord A 《Science (New York, N.Y.)》2005,309(5733):436-442
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薛庆中 《浙江大学学报(农业与生命科学版)》2005,31(2):119-124
本文综述了谷类作物基因组结构现状,基于水稻和拟南芥全基因组分析以及谷类作物基因组长片段的测序注释表明,谷类作物基因组存在许多嵌合结构,富基因岛重组上活性部分常被高拷贝DNA模块分隔.谷类作物基因组内,具保守的宏共线性.玉米,水稻,高梁,小麦,及大麦的Sh2/A1直向同源区域的基因顺序分析表明,Sh2和A1同系物间隔分别为20kb(在水稻和高梁)和140kb(在玉米);小麦族Sh2/A1区同线性在X1和X2基因间有一个断裂.如同其他禾本科作物,A1和X2基因在部分同源染色体保留共线性,Sh2和X1直向同源依然是共线性,但在非部分同源染色体的位置已改变.植物基因可以通过多倍体化,节段重复及局部基因扩增3种途径增加序列的数量.单个基因内,微共线性常被破坏.对基因组直向同源区段的初步比较分析暗示,植物基因组内基因局部扩增和易位也许有某些关联. 相似文献
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Synteny and collinearity in plant genomes 总被引：4，自引：0，他引：4
Correlated gene arrangements among taxa provide a valuable framework for inference of shared ancestry of genes and for the utilization of findings from model organisms to study less-well-understood systems. In angiosperms, comparisons of gene arrangements are complicated by recurring polyploidy and extensive genome rearrangement. New genome sequences and improved analytical approaches are clarifying angiosperm evolution and revealing patterns of differential gene loss after genome duplication and differential gene retention associated with evolution of some morphological complexity. Because of variability in DNA substitution rates among taxa and genes, deviation from collinearity might be a more reliable phylogenetic character. 相似文献
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Xiao H Jiang N Schaffner E Stockinger EJ van der Knaap E 《Science (New York, N.Y.)》2008,319(5869):1527-1530
Edible fruits, such as that of the tomato plant and other vegetable crops, are markedly diverse in shape and size. SUN, one of the major genes controlling the elongated fruit shape of tomato, was positionally cloned and found to encode a member of the IQ67 domain-containing family. We show that the locus arose as a result of an unusual 24.7-kilobase gene duplication event mediated by the long terminal repeat retrotransposon Rider. This event resulted in a new genomic context that increased SUN expression relative to that of the ancestral copy, culminating in an elongated fruit shape. Our discovery demonstrates that retrotransposons may be a major driving force in genome evolution and gene duplication, resulting in phenotypic change in plants. 相似文献
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温州光唇鱼线粒体基因组结构及系统发育分析 总被引：1，自引：0，他引：1
采用已公布的鱼类线粒体基因组全序列,设计8对引物扩增、测定并注释温州光唇鱼(Acrossocheilus wenchowensis)线粒体基因组(GenBank登录号:KC_495074)。序列全长16 591 bp,包括13个蛋白质基因、22个tRNA基因、2个rRNA基因和1个非编码区,各基因的位置及组成与已公布的鲤科鱼类一致;37个基因中,1个蛋白质编码基因(ND6)和8个tRNA基因(tRNAGln、tRNAAla、tRNAAsn、tRNACys、tRNATyr、tRNASer(UCN)、tRNAGlu和tRNAPro)由L链编码,其余的均由H链编码。A、T、G、C碱基组成分别为30.92%、24.86%、16.41%、27.81%;除tRNASer(AGN)外,其它21个tRNA的二级结构均具有典型的三叶草结构;13个蛋白编码基因中,除COⅠ起始密码子为GTG外,其余均以ATG为起始密码子,而COⅡ、ND4和Cytb基因的终止密码子为不完整的T,其它10个基因均具有完整的终止密码子。利用鲤科共17属18种线粒体基因组13个蛋白质基因的氨基酸序列,从线粒体基因组水平探讨了温州光唇鱼在鲤科鱼类中的系统进化地位,为光唇鱼属乃至鲤科鱼类的系统分类学研究提供基础资料。 相似文献
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Genome-wide insertional mutagenesis of Arabidopsis thaliana 总被引：2，自引：0，他引：2
Alonso JM Stepanova AN Leisse TJ Kim CJ Chen H Shinn P Stevenson DK Zimmerman J Barajas P Cheuk R Gadrinab C Heller C Jeske A Koesema E Meyers CC Parker H Prednis L Ansari Y Choy N Deen H Geralt M Hazari N Hom E Karnes M Mulholland C Ndubaku R Schmidt I Guzman P Aguilar-Henonin L Schmid M Weigel D Carter DE Marchand T Risseeuw E Brogden D Zeko A Crosby WL Berry CC Ecker JR 《Science (New York, N.Y.)》2003,301(5633):653-657
Over 225,000 independent Agrobacterium transferred DNA (T-DNA) insertion events in the genome of the reference plant Arabidopsis thaliana have been created that represent near saturation of the gene space. The precise locations were determined for more than 88,000 T-DNA insertions, which resulted in the identification of mutations in more than 21,700 of the approximately 29,454 predicted Arabidopsis genes. Genome-wide analysis of the distribution of integration events revealed the existence of a large integration site bias at both the chromosome and gene levels. Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene. 相似文献
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为了促进杨树早期开花,缩短杨树遗传育种周期,采用农杆菌AGL1介导的转化方法及热激诱导方法,进行了热激启动子HSP控制下的3类FT基因转化2种杨树无性系(353与717)诱导杨树早期开花的比较研究.结果表明:来自拟南芥的FT基因促花效果优于来自杨树的FT1和FT2基因;FT类基因与受体基因型/性别之间互作明显,开花较好... 相似文献
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Khaitovich P Hellmann I Enard W Nowick K Leinweber M Franz H Weiss G Lachmann M Pääbo S 《Science (New York, N.Y.)》2005,309(5742):1850-1854
The determination of the chimpanzee genome sequence provides a means to study both structural and functional aspects of the evolution of the human genome. Here we compare humans and chimpanzees with respect to differences in expression levels and protein-coding sequences for genes active in brain, heart, liver, kidney, and testis. We find that the patterns of differences in gene expression and gene sequences are markedly similar. In particular, there is a gradation of selective constraints among the tissues so that the brain shows the least differences between the species whereas liver shows the most. Furthermore, expression levels as well as amino acid sequences of genes active in more tissues have diverged less between the species than have genes active in fewer tissues. In general, these patterns are consistent with a model of neutral evolution with negative selection. However, for X-chromosomal genes expressed in testis, patterns suggestive of positive selection on sequence changes as well as expression changes are seen. Furthermore, although genes expressed in the brain have changed less than have genes expressed in other tissues, in agreement with previous work we find that genes active in brain have accumulated more changes on the human than on the chimpanzee lineage. 相似文献
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Colbourne JK Pfrender ME Gilbert D Thomas WK Tucker A Oakley TH Tokishita S Aerts A Arnold GJ Basu MK Bauer DJ Cáceres CE Carmel L Casola C Choi JH Detter JC Dong Q Dusheyko S Eads BD Fröhlich T Geiler-Samerotte KA Gerlach D Hatcher P Jogdeo S Krijgsveld J Kriventseva EV Kültz D Laforsch C Lindquist E Lopez J Manak JR Muller J Pangilinan J Patwardhan RP Pitluck S Pritham EJ Rechtsteiner A Rho M Rogozin IB Sakarya O Salamov A Schaack S Shapiro H Shiga Y Skalitzky C Smith Z Souvorov A Sung W 《Science (New York, N.Y.)》2011,331(6017):555-561
We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges. 相似文献
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通过相关网站及生物信息软件对Poptr:CYCD3;3基因启动子序列进行详细分析,从小黑杨(Populus)叶片总DNA中克隆到2 000 bp的目的片段,构建植物表达载体(p CAMBIA1301-Promoter:CYCD3;3),并利用浸花法转化野生型拟南芥(Arabidopsis thaliana);通过抗性筛选和分子检测结果显示,p CAMBIA1301-Promoter:CYCD3;3基因已经整合到拟南芥基因组中。同时对获得的转基因幼苗进行GUS染色并观察,其基因表达模式主要集中在植物分生组织中,由此表明Poptr:CYCD3;3调控CYCD3;3基因在细胞分裂中发挥作用。 相似文献
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为了对已测序杨树Populus trichocarpa Torr.Gray中磷酸肌醇特异性磷脂酶C(phosphoinositidespecific phospholipase C,PI-PLC)家族基因进行系统分析,利用杨树基因组数据库,通过生物信息学手段,鉴定杨树PI-PLC家族基因的基因结构、染色体定位和编码蛋白,通过蛋白序列比对进行进化和分类分析。结果表明,杨树中含有7个PI-PLC家族基因,含有8~10个外显子,分布于杨树的4条染色体上。MEME和Pfam保守结构域分析显示,杨树PI-PLC蛋白均含有4个保守的EF、X、Y和C2结构域。蛋白质进化树分析结果表明PI-PLC可分为2个亚家族。 相似文献