The evolution of resistance gene in plants

Resistance genes enable plants to fight against plant pathogens. Plant resistance genes (R gene) are organized complexly in genome. Some resistance gene sequence data enable an insight into R gene structure and gene evolution. Some sites like Leucine-Rich Repeat (LRR) are of specific interest since homologous recombination can happen. Crossing over, transposon insertion and excision and mutation can produce new specificity. Three models explaining R gene evolution were discussed. More information needed for dissection of R gene evolution though some step can be inferred from genetic and sequence analysis.     

Genome evolution following host jumps in the Irish potato famine pathogen lineage

Many plant pathogens, including those in the lineage of the Irish potato famine organism Phytophthora infestans, evolve by host jumps followed by specialization. However, how host jumps affect genome evolution remains largely unknown. To determine the patterns of sequence variation in the P. infestans lineage, we resequenced six genomes of four sister species. This revealed uneven evolutionary rates across genomes with genes in repeat-rich regions showing higher rates of structural polymorphisms and positive selection. These loci are enriched in genes induced in planta, implicating host adaptation in genome evolution. Unexpectedly, genes involved in epigenetic processes formed another class of rapidly evolving residents of the gene-sparse regions. These results demonstrate that dynamic repeat-rich genome compartments underpin accelerated gene evolution following host jumps in this pathogen lineage.     

广州地区猫泛白细胞减少症病毒分离鉴定及全基因组遗传分析

【目的】分析广州地区猫泛白细胞减少症病毒(Feline panleukopenia virus,FPLV)的自然重组、跨宿主传播以及流行变异情况。【方法】采集疑似感染猫泛白细胞减少症病毒的猫粪便样品进行细胞分离,并对阳性病料提取基因组DNA,PCR扩增获得病毒的全基因组序列,并与Gen Bank中相关的参考毒株序列进行遗传进化分析,同时对VP2基因与NS1基因的主要氨基酸位点进行差异分析。【结果】成功获得2株猫泛白细胞减少症病毒及其全基因组序列。遗传进化分析显示,广州地区分离的猫泛白细胞减少症病毒FPLV-GZ01、FPLV-GZ02与我国其他分离毒株FPLV-XJ01、FPLV-HRB属同一分支,提示FPLV-GZ01、FPLV-GZ02由FPLV-XJ1进化而来;NS1基因系统进化树显示,FPLV存在与CPV-447重组的可能。主要氨基酸位点分析显示,FPLV在VP2基因中的主要氨基酸位点上的遗传变异比CPV保守;在NS1基因上发现FPLV-GZ01、FPLV-GZ02分别存在不同程度的氨基酸位点突变。【结论】广州地区分离的猫泛白细胞减少症病毒仍在不断地重组进化。     

Cloning and Sequence Analysis of lef-3 Gene from Pieris rapae Granulovirus

To better understand the origination and evolution of lef-3 gene from baculovirus genome and determine the relationships between various viruses at molecular level, late expression factor 3 gene （lef-3） fragments of Pieris rapae granulovirus were obtained through conventional PCR method and sequenced after cloned into T-vector. Then, bioinformatics analysis on lef-3 gene and its encoding sequences were conducted by using bid-softs. Four mutations were appeared in the ORF of cloned lef-3 gene, which did not alter the characteristics of amino acids. It was inferred that PiraGV LEF-3 protein contained 399 amino acids, the molecular weight of which was 3.99 kD. Prediction of the LEF-3 advanced structure and homology comparison between other LEF-3 from various baculoviruses showed that the lef-3 gene might encode the single-stranded DNA-binding protein. The result of BLAST revealed that the lef-3 gene only existed in Lepidoptera host for the baculovirus genome, and the evolution analysis illustrated that lef-3 gene could be divided into 3 groups including one granulovirus （GV） group and 2 nucleopolyhedrovirus （NPV） groups. The selection pressure analysis of GV lef-3 gene coding region showed that the majority of lef-3 genes performed negative selection, while the Ka/Ks differed from different lef-3 gene, to some extent, which also performed positive selection. The origination analysis revealed that lef-3 gene of baculovirus might derive from bacteria. The lef-3 gene of PiraGV was cloned successfully and the possible patterns of origination and evolution were speculated through bioinformatics analysis.     

Synteny and collinearity in plant genomes

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.     

小菜粉蝶颗粒体病毒lef-3基因的克隆与分析

 【目的】研究杆状病毒lef-3基因的起源与进化,从分子水平明确病毒之间的亲缘关系。【方法】通过常规PCR方法获得小菜粉蝶颗粒体病毒晚期基因表达调控因子lef-3的基因片段,克隆后测序,然后利用软件对lef-3及编码序列进行生物信息学分析。【结果】克隆得到的PiraGV lef-3基因ORF序列中存在4个突变位点,但氨基酸性质未发生改变,推导PiraGV LEF-3蛋白含399个氨基酸残基,分子量为3.99 kD;通过高级结构预测及其编码序列与其它杆状病毒的LEF-3同源性比对表明,该基因可能编码单链DNA结合蛋白;BLAST比对发现lef-3基因只存在于鳞翅目昆虫为宿主的杆状病毒基因组;进化分析表明LEF-3可分为3组,其中GV属的LEF-3聚类为1个组,NPV属的LEF-3聚类为2个组;GV的lef-3基因编码区的选择压力分析表明,大多数lef-3基因间相比较表现为负向选择,但不同lef-3基因间的Ka/Ks不同,也有正向选择;起源分析表明,杆状病毒lef-3基因可能来源于细菌。【结论】获得了小菜粉蝶颗粒体病毒（PiraGV）lef-3基因,通过生物信息学分析推测出了lef-3基因的起源进化规律。     

多倍体植物基因组结构和基因表达的变化研究进展

杂交和多倍化是促进植物进化的重要力量。大量研究表明,植物多倍化后基因组结构和基因表达模式发生了复杂的变化,包括染色体重排、序列消除、基因沉默、基因激活等现象。鉴于此,综述了植物多倍化后基因组结构和基因表达模式变化的研究进展,以期为了解植物进化的机制提供参考。     

茄科植物比较基因组学研究进展

综述了茄科4种主要蔬菜作物番茄、马铃薯、辣椒和茄子比较基因组学的研究进展,包括其基因组大小、结构、基因重排及演化,R基因在茄科植物中的分布与共线性,花青素基因、果实相关性状QTLs的同源性比较等,并对比较基因组学的发展前景进行了展望。     

Comparative genomics of trypanosomatid parasitic protozoa

A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that-along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions-have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont.     

Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome

Many oomycete and fungal plant pathogens are obligate biotrophs, which extract nutrients only from living plant tissue and cannot grow apart from their hosts. Although these pathogens cause substantial crop losses, little is known about the molecular basis or evolution of obligate biotrophy. Here, we report the genome sequence of the oomycete Hyaloperonospora arabidopsidis (Hpa), an obligate biotroph and natural pathogen of Arabidopsis thaliana. In comparison with genomes of related, hemibiotrophic Phytophthora species, the Hpa genome exhibits dramatic reductions in genes encoding (i) RXLR effectors and other secreted pathogenicity proteins, (ii) enzymes for assimilation of inorganic nitrogen and sulfur, and (iii) proteins associated with zoospore formation and motility. These attributes comprise a genomic signature of evolution toward obligate biotrophy.     

Apoptotic molecular machinery: vastly increased complexity in vertebrates revealed by genome comparisons

A comparison of the proteins encoded in the recently (nearly) completed human genome to those from the fly and nematode genomes reveals a major increase in the complexity of the apoptotic molecular machinery in vertebrates, in terms of both the number of proteins involved and their domain architecture. Several components of the apoptotic system are shared by humans and flies, to the exclusion of nematodes, which seems to support the existence of a coelomate clade in animal evolution. A considerable repertoire of apoptotic protein domains was detected in Actinomycetes and Cyanobacteria, which suggests a major contribution of horizontal gene transfer to the early evolution of apoptosis.     

Mobile elements: drivers of genome evolution

Mobile elements within genomes have driven genome evolution in diverse ways. Particularly in plants and mammals, retrotransposons have accumulated to constitute a large fraction of the genome and have shaped both genes and the entire genome. Although the host can often control their numbers, massive expansions of retrotransposons have been tolerated during evolution. Now mobile elements are becoming useful tools for learning more about genome evolution and gene function.     

转座子在基因组和基因进化方面的研究进展

从转座子插入对基因组产生的重组、异位、倒位以及对基因产生的沉默、表达等方面阐述了转座子对基因组和基因进化的重要作用,从转座子在基因中插入位置的不同对基因表达和功能产生的影响进行了综述。     

逆转座子LINE-1在基因组中的调控作用

近年来研究发现真核生物基因组中的许多重复序列以及基因的内含子参与基因表达的调控。在这些重复序列中,有一种广泛分布于基因组中的逆转座子LINE-1,目前发现其对细胞的增殖与分化以及肿瘤的发生起着非常重要的作用,具体表现为影响基因的转录及整个基因组的稳定性、参与X染色体失活及基因组进化等。在正常细胞的分化调控中,基因的激活与沉默具有时间与空间的特异性,实现其“预定”的、有序的、不可逆转的分化过程。主要阐述了逆转座子LINE-1的结构特征和其在基因组中的调控作用及这些作用影响基因表达从而调节生物体的生命活动。研究LINE-1的调控机制对认识细胞的时空调控以及癌症的发生与发展具有重要的价值。     

转座子沉默与DNA甲基化

转座子(transposable elements,TEs)在生物体基因组可以通过转座或逆转座移动,它拷贝数的大规模增加是基因组不稳定的重要因素,因此,维持TEs沉默是宿主进化的方向。DNA甲基化被认为是沉默TEs的可遗传表观遗传修饰方式,同时也在维持基因组稳定、基因印迹、调节基因表达中发挥作用。本研究综述了TEs对生物基因组进化和基因表达的影响,重点总结了以DNA甲基化为主的转座子沉默机制的最新研究进展,归纳了环境因素通过DNA去甲基化调控转座子跳跃的机理。图4参82     

功能基因组注释探讨解淀粉芽孢杆菌的益生机制

旨在利用功能基因组注释的方法,深入挖掘解淀粉芽孢杆菌BLCC1-0238基因组中与益生作用密切相关的功能基因。结果表明,解淀粉芽孢杆菌BLCC1-0238的基因组大小约为3.88 Mb,含有3 941个编码序列,有8个基因簇参与聚酮类化物、非核糖体脂肽和芽孢杆菌素的生物合成,部分基因簇参与环状脂肽罗克霉素的合成;该菌还具有1个编码肽基脯氨酰异构酶的基因,12个与耐酸相关的基因和7个参与编码水解酶的基因。综上所述,这些基因的存在有助于动物机体对抗病原菌和胁迫因素,还有利于对营养物质的消化和 吸收。     

宁夏束颈蝗Cytb基因的Numt分析

核线粒体假基因Numt（Nuclear Mitochondrial pseudogene）的存在具有重大的进化意义,它为基因组进化和基因组间相互作用的动态研究打开了一个窗口。假基因是基因组上与编码基因序列非常相似的非功能性基因组DNA拷贝,一般情况都不被转录,且没有明确生理意义。Numts由于处于不同的突变压力下,与真正的线粒体序列相比具不同的进化模式,其进化速率比线粒体同源基因要慢的多,类似分子化石,在核苷酸序列上更接近现存mtDNA的祖先状态。本研究在前几年研究的基础上,通过PCR技术,旨在发现宁夏束颈蝗核基因组中所存在的线粒体Cytb基因的假基因（Numt）。通过对PCR产物的检测,推断宁夏束颈蝗存在Numt,在对目标片断进行测序并利用GeneBank的BLASTn序列比对后确定序列特征,进一步确定Numt的实验正在规化进行中。预期本研究的结果将为Numts来源和机制,基因组进化和基因组间相互作用、系统进化、横向基因转移和核序列突变等研究提供实验基础。     

苜蓿叶绿体DNA的提取及其Rbcl基因片段的克隆

[目的]获得高纯度的苜蓿叶绿体DNA（cpDNA）和Rbcl基因片段。[方法]采用改进的高盐低pH法分离和纯化苜蓿叶绿体DNA;利用叶绿体基因组进化中高度保守的特点,设计引物,从苜蓿叶绿体基因组中扩增Rbcl基因,利用生物学软件对测序结果进行分析。[结果]经检测分析,获得了产率较高和纯度较好的苜蓿叶绿体DNA,并用PCR方法扩增获得了1 130 bp的Rbcl基因片段。该基因片段有17个常用的限制性内切酶酶切位点,与烟草、水稻、菜豆、玉米、甘薯和甜菜中Rbcl基因核苷酸的同源性为85.6%～90.6%。[结论]为构建苜蓿叶绿体表达载体和通过叶绿体生物反应器生产药用蛋白等奠定了基础。     

Wasp gene expression supports an evolutionary link between maternal behavior and eusociality

The presence of workers that forgo reproduction and care for their siblings is a defining feature of eusociality and a major challenge for evolutionary theory. It has been proposed that worker behavior evolved from maternal care behavior. We explored this idea by studying gene expression in the primitively eusocial wasp Polistes metricus. Because little genomic information existed for this species, we used 454 sequencing to generate 391,157 brain complementary DNA reads, resulting in robust hits to 3017 genes from the honey bee genome, from which we identified and assayed orthologs of 32 honey bee behaviorally related genes. Wasp brain gene expression in workers was more similar to that in foundresses, which show maternal care, than to that in queens and gynes, which do not. Insulin-related genes were among the differentially regulated genes, suggesting that the evolution of eusociality involved major nutritional and reproductive pathways.     

苦荞VQ基因家族的全基因组鉴定及其在叶斑病原与激素处理下的表达谱分析

【目的】VQ基因家族在植物生长、发育以及对生物或非生物胁迫反应中发挥重要功能。在全基因组尺度上,全面鉴定苦荞(Fagopyrum tataricum L. Gaertn.)VQ(FtVQ)基因家族,分析其在苦荞叶斑病原——互格链格孢(Alternaria alternata)和黑孢霉(Nigrospora osmanthi)侵染和防御相关激素——水杨酸(SA)、茉莉酸(JA)、乙烯(ET)处理下的表达模式,为深入解析苦荞VQ基因家族在植物抗病防御中的功能及机理奠定基础,同时为优良基因资源发掘及抗病品种改良提供线索。【方法】基于VQ保守结构域的隐马尔可夫文件(PF05678),采用HMMER 3.0对苦荞平苦一号基因组数据库进行比对搜索,鉴定VQ基因;通过DNAMAN、Map Inspect、MEGA、MEME、Ortho Finder、PLACE等生物信息学工具分析基因结构、染色体分布、启动子顺式元件、蛋白质理化性质、蛋白质保守基序、蛋白质亚细胞定位和蛋白质系统进化关系;采用实时荧光定量PCR(qPCR)方法分析苦荞叶VQ基因在病原侵染或激素处理下的表达模式。【结果】从苦荞基因组中鉴定...