Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis

Traditionally, evolutionary biologists have viewed mutations within individual genes as the major source of phenotypic variation leading to adaptation through natural selection, and ultimately generating diversity among species. Although such processes must contribute to the initial development of gene functions and their subsequent fine-tuning, changes in genome repertoire, occurring through gene acquisition and deletion, are the major events underlying the emergence and evolution of bacterial pathogens and symbionts. Furthermore, pathogens and symbionts depend on similar mechanisms for interacting with hosts and show parallel trends in genome evolution.     

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.     

Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees

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.     

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.     

玉米自交系B73全基因组cystatin抗虫基因家族分析

半胱氨酸蛋白酶抑制剂(cystatin)基因具有cystatin结构特征的蛋白结构域,广泛存在于植物或动物体内。此类基因在植物或动物蛋白质组中具有多个功能各异的家族成员,并在抗虫中扮演重要角色。通过利用玉米B73全基因组的基因表达序列数据,对12个cystatin基因的结构组成、染色体分布、系统进化等进行了分析。鉴定了该基因家族在蛋白序列间3个高度保守基序,构建了基因家族系统进化树,为该重要基因家族的进化提供了依据的同时也为克隆和分离该类抗虫基因提供参考。     

基因组时代的植物系统发育研究进展

系统发育研究是进化生物中的基本问题,也是其他众多生物学分支学科的基础问题,其核心在于研究不同生物类群间的亲缘关系与进化命运。利用分子数据研究生物之间的进化关系是系统发育研究的重要手段。随着测序技术的提升和测序成本的持续下降,系统发育研究由早期基于单基因或联合少数片段逐步发展到现阶段利用大规模基因组数据对个体、群体、物种以及更高水平的进化关系进行探讨。讨论了目前植物体内的3套基因组(叶绿体基因组、线粒体基因组与核基因组)在系统发育研究中的代表性成果,总结了植物不同基因组的特征及其在系统发育研究中的优势与局限,探讨了系统发育树构建的主要方法,并对未来研究进行了展望。目前,植物体内的3套基因组适用于不同阶元和类群的系统发育研究,不同基因组之间的遗传特性差异使其在系统发育研究中具备不同的优势和应用：(1)叶绿体基因组结构相对简单,序列保守,不易重组,单亲遗传,是广泛应用于系统发育学和进化生物学等研究领域的理想分子数据资源;(2)植物线粒体基因组序列进化速率较慢,目前仅适用于早期植物和大尺度水平的系统发育研究;(3)核基因组为双亲遗传,可综合揭示双亲谱系及系统网状进化关系,在系统发育研究中具有巨...     

Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes

The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less than one-sixth of the sequence, and gene loci occupy about one-third of the genome. As with the human genome, gene loci are not evenly distributed, but are clustered into sparse and dense regions. Some "giant" genes were observed that had average coding sequence sizes but were spread over genomic lengths significantly larger than those of their human orthologs. Although three-quarters of predicted human proteins have a strong match to Fugu, approximately a quarter of the human proteins had highly diverged from or had no pufferfish homologs, highlighting the extent of protein evolution in the 450 million years since teleosts and mammals diverged. Conserved linkages between Fugu and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order.     

二倍体长穗偃麦草E组染色体研究进展

二倍体长穗偃麦草(Thinopyrum elongatum)E组染色体是组成偃麦草属(Thinopyrum)多倍体物种的基本染色体组,携带有对小麦遗传育种有益的基因,人们已从多方面解读了E组染色体与小麦及其他近缘种属的遗传进化关系。综述了二倍体长穗偃麦草E组染色体与比萨偃麦草和小麦的亲缘关系、生化标记、分子标记和高分子量谷蛋白研究的进展。     

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.     

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.     

乳苣叶绿体基因组特征及其系统发育分析

乳苣（Mulgedium tataricum）为菊科（Compositae）乳苣属（Mulgedium）植物,该物种含有天然黄酮类化合物,具有清热解毒、抗肿瘤、抗氧化等作用。叶绿体基因组中含有大量功能基因,在物种鉴定及系统发育中具有重要作用。采用高通量测序技术获得乳苣全长叶绿体基因组序列,并与NCBI已公布的32个菊科物种及拟南芥（Arabidopsis thaliana）的叶绿体基因组进行了系统发育分析。结果显示,乳苣叶绿体基因组大小为152 401 bp,呈现出典型的环状四分体结构,其包含有一对反向重复序列区（IRa和IRb）、大单拷贝区（LSC）和小单拷贝区（SSC）,它们的长度分别为25 010、83 833和18 548 bp。共注释得到132个基因,其中包含8个rRNA基因、37个tRNA基因和87个mRNA基因;SSR位点分析发现,基因组序列中含有21个散在重复序列和197个串联重复序列。边界分析表明,乳苣与其他5个菊苣族物种在边界基因上存在一定差异,且6个菊苣族物种在IR/SC区出现明显扩张和收缩。系统进化分析将菊科14个属的33个物种被聚为两个分支：第一分支包括乳苣属（Mulgedium）、莴苣属(Lactuca)、蒲公英属(Taraxacum)、苦苣菜属(Sonchus)、香青属(Anaphalis)、火绒草属(Leontopodium)、茼蒿属(Chrysanthemum)、蒿属(Artemisia)、紫菀属(Aster)和向日葵属(Helianthus),其中乳苣属和莴苣属的亲缘关系最近;第二分支包括蓟属（Cirsium）、红花属（Carthamus）、风毛菊属（Saussurea）和苍术属（Atractylodes）。研究结果为乳苣属植物的物种鉴定、系统进化及资源开发利用等奠定新的证据和材料基础。     

濒危红树植物莲叶桐叶绿体基因组及其系统进化

对濒危红树植物莲叶桐的叶绿体基因组及与其近缘物种之间的叶绿体基因组进行比较进化分析。结果表明,莲叶桐叶绿体基因组序列全长157 762 bp,包括1个大的单拷贝区(LSC)86 641 bp,1个小的单拷贝区(SSC)18 603 bp和2个反转重复区(IRs)26 260 bp。叶绿体基因组的GC含量为39.3%,含有133个基因,包括83个蛋白质编码基因、42个tRNA基因和8个rRNA基因。17个基因位于反转重复区,包括6个蛋白编码基因、7个tRNA和4个rRNA。登录号为:MG838431。通过最大似然法对16个双子叶植物（包含5个樟科植物、2个腊梅科植物、3个毛茛科植物、1个小檗科植物、1个报春花科植物、1个蔷薇科植物、1个桑科植物,1个安息香科植物以及莲叶桐）和1个外类群植物水稻的叶绿体基因组序列进行聚类分析,莲叶桐与樟科和腊梅科植物聚为一支。聚类结果将莲叶桐科划入樟目,更支持《中国高等植物图鉴》中分类方式。随后对莲叶桐及其近缘种叶绿体基因组进行了共线性分析,进一步验证了其叶绿体基因组之间具有高度保守性。研究结果为莲叶桐的系统进化提供了新的证据。     

Very low gene duplication rate in the yeast genome

The gene duplication rate in the yeast genome is estimated without assuming the molecular clock model to be approximately 0.01 to 0.06 per gene per billion years; this rate is two orders of magnitude lower than a previous estimate based on the molecular clock model. This difference is explained by extensive concerted evolution via gene conversion between duplicated genes, which violates the assumption of the molecular clock in the analyses of duplicated genes. The average length of the period of concerted evolution and the gene conversion rate are estimated to be approximately 25 million years and approximately 28 times the mutation rate, respectively.     

The impact of tandem duplication on gene evolution in Solanaceae species

Whole genome duplication(WGD) and tandem duplication(TD) are important modes of gene amplification and functional innovation, and they are common in plant genome evolution. We analyzed the genomes of three Solanaceae species(Solanum lycopersicum, Capsicum annuum, and Petunia inflata), which share a common distant ancestor with Vitis vinifera, Theobroma cacao, and Coffea canephora but have undergone an extra whole genome triplication(WGT) event. The analysis was used to investigate the phenomenon...     

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。     

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。     

生物固氮基因簇结构与进化研究进展

在固氮菌基因组中,固氮相关基因都是作为一个或几个基因簇存在,是细菌生物固氮的遗传基础。这其中包括固氮酶结构基因nifHDK,以及参与电子转运和铁钼辅因子合成及组装的其他相关基因。对不同菌中固氮基因簇的结构和进化进行了简要的比较分析。比较所有已测序固氮菌中的固氮基因簇,发现均至少含有六个保守基因:nifH、nifD、nifK、nifE、nifN和nifB,并且这6个基因在所有已鉴定的系统中都是固氮所必需的。尽管在不同种类的固氮微生物中,固氮基因簇的构成及组织模式有所不同,但是它们在结构、催化机制和系统进化上紧密相关。同时也对固氮基因的研究方向提出了展望。旨在为今后进一步研究生物固氮机制,了解固氮微生物的进化,扩展生物固氮多样性提供理论基础。     

基于Perl脚本的大豆核苷酸序列高通量提取

自从大豆全基因组测序完成和序列公布之后,阐明每个基因的生物学功能和调控网络成为当前的主要任务。基于Perl脚本开发了一套可以高通量、快速提取序列的程序,该程序可以批量提取大豆染色体某个区间的核苷酸序列并利用其他工具进行批量分析,还可用于某个基因在全基因组中的所有序列分析。本研究分别对大豆第4染色体Glyma04g00930.1～Glyma04g01740.1区间的基因序列和水通道蛋白基因家族成员TIP(液泡膜水通道蛋白)序列进行提取。结果发现:Glyma04g00930.1～Glyma04g01740.1区间共含有112个基因序列;大豆全基因组共有91个TIP基因,在20条染色体上均有分布,且在第12染色体上分布最多,多达10个,暗示该染色体可能对大豆的水分利用效率起着重要作用,基因所含内含子数为1～8个。序列提取所用的2个脚本程序可以从http://www.zlhyd.com/sxbi/soybean_strict.rar下载。     

Evolutionary biology. Twinned genes live life in the fast lane

On page 1151, researchers describe new insights into how genes arise and fuel evolution. By trolling through sequence data for nine very distinct organisms, they have uncovered evidence that genes are copied far more frequently--and the duplicates are lost from the genome far faster--than researchers had thought. What's more, the work suggests that some duplicate genes play a key role in the evolution of new traits and in speciation.