毛竹长末端重复序列反转录转座子的全基因组特征及进化分析

  目的   研究毛竹Phyllostachys edulis基因组中的长末端重复序列反转录转座子(long terminal repeat retrotransposons, LTR-REs)的特征,为今后利用LTR反转录转座子对毛竹基因组的功能和对竹种资源遗传多样性的研究奠定基础。   方法   通过生物信息学方法,利用LTRharvest和RepeatMakser软件对第2版毛竹基因组中的LTR反转录转座子进行全面注释与分类,并对得到的LTR反转录转座子的分布特征、进化特性和插入时间进行分析。   结果   在毛竹基因组中共注释得到1 014 565个LTR反转录转座子,1 562个家族,占毛竹基因组的54.97%。其中solo LTR反转录转座子与完整LTR反转录转座子(S/F)的比例较高(约1.77∶1.00),表明在毛竹LTR反转录转座子中可能发生了相对较高频率的非法重组和不平衡重组。毛竹LTR反转录转座子分为Ty1-copia和Ty3-gypsy超家族,Tork、Reftrofit、Sire、Oryco、Del、Reina、Crm、Tat、Galadriel、Athila等10个谱系。毛竹LTR反转录转座子的Ty1-copia和Ty3-gypsy超家族对PBS位点的偏好性呈相反趋势,较长的LTR反转录转座子具有更长的LTR序列,结构也更加完整。毛竹LTR反转录转座子的插入时间主要集中在0~2.0 Ma,且还处于不断缓慢增长的状态。   结论   第2版毛竹基因组的高质量组装,能更好地注释和分析毛竹基因组中的LTR反转录转座子。基于结构预测的LTRharvest法,能更精准地预测毛竹LTR反转录转座子。不同谱系的毛竹LTR反转录转座子在进化过程中具有不同的分化和扩增活性。毛竹LTR反转录转座子总体上处于不断扩增状态,这是导致毛竹基因组较大的主要原因之一。图3表3参52     

植物LTR类反转录转座子的研究概述

LTR类反转录转座子是植物基因组中的重要成分,对基因组的大小、结构、功能和进化都有重要影响.文中从结构特征、转座机制、分类、分离鉴定及对基因组的影响等多个方面概述了植物LTR类反转录转座子的研究进展,为进一步揭示LTR类反转录转座子在植物基因组中的功能奠定基础.     

植物着丝粒区串联重复序列的研究进展

着丝粒是细胞染色体的重要结构组成,控制姊妹染色单体的结合、动粒的组装和纺锤丝的附着,确保真核生物细胞在有丝分裂和减数分裂过程中染色体的正常分离及遗传信息的稳定传递。植物着丝粒DNA序列主要由反转录转座子和串联重复序列构成。串联重复序列在着丝粒功能实现和基因组进化过程中起重要作用。随着测序技术的成熟,近年来对串联重复序列的研究取得了很大的进展。综述了植物串联重复序列结构、分析方法及在进化中的作用,以期为相关研究提供参考。     

Genetics. L1 retrotransposons shape the mammalian genome

What are all of those retrotransposons doing buzzing about in our genome? According to Kazazian, in his Perspective this week, these mobile pieces of DNA are busy reshaping our genome, making it more diverse and enabling us to survive and thrive through the vagaries of evolution. And just how do they do this?...zip to page 1152 to find out.     

籽粒苋copia类反转录转座子的初步研究

本研究首次报道了籽粒苋中也存在 copia类反转录转座子 ,进一步验证了 copia类反转录转座子广泛存在于高等植物中 .采用 PCR方法分离鉴定了来自 4个种 2 7个基因型中的 5 3个 RT酶区序列 .序列分析表明 ,籽粒苋中的 copia类反转录转座子不但具有长度多样性、种间多样性、种内多样性 ,而且来自相同基因型的反转录转座子之间也存在高度异质性 .Southern杂交分析表明 ,籽粒苋中的 copia类反转录转座子以多拷贝形式存在 .Northern杂交分析表明 ,籽粒苋中的 copia类反转录转座子可能失去了转座活性 .本研究还对采用 PCR技术分离全长的 copia类反转录转座子进行了初步探讨 ,认为该方法可行 ,具有快速、经济等优点 ,可望在短期内分离出全长的反转录转座子     

Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome

The completion of the draft sequence of the rhesus macaque genome allowed us to study the genomic composition and evolution of transposable elements in this representative of the Old World monkey lineage, a group of diverse primates closely related to humans. The L1 family of long interspersed elements appears to have evolved as a single lineage, and Alu elements have evolved into four currently active lineages. We also found evidence of elevated horizontal transmissions of retroviruses and the absence of DNA transposon activity in the Old World monkey lineage. In addition, approximately 100 precursors of composite SVA (short interspersed element, variable number of tandem repeat, and Alu) elements were identified, with the majority being shared by the common ancestor of humans and rhesus macaques. Mobile elements compose roughly 50% of primate genomes, and our findings illustrate their diversity and strong influence on genome evolution between closely related species.     

A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit

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.     

燕麦EST数据库中Ty1-copia和Ty3-gypsy型反转录转座子的频数分析

为研究转座元件(Transposable elements,TES)在燕麦中的表达模式,以14个Ty1-copia型反转录转座子和3个Ty3-gypsy型反转录转座子序列为种子序列对燕麦属(Avena)表达序列标签(EST)数据库中的Ty1-copia和Ty3-gypsy型反转录转座子进行检索和分析。结果表明:燕麦根中反转录转座子的频率显著高于叶(P0.05);强降雨模式的胁迫环境下叶组织中反转录转座子的EST频率显著高于大气降雨下的(P0.05),约为正常条件下的(Ee-10,0.12%)2倍;Ty1-copia和Ty3-gypsy型反转录转座子在根的分蘖期频率差异极显著(P0.01)。这些结果揭示了燕麦属Ty1-copia和Ty3-gypsy型反转录转座子的转录存在组织和发育的时空特异性及环境应答现象,为预测重复元件的表达模式提供了依据。同时,检索到的反转录转座子也有助于对燕麦基因组序列的注释。     

水稻gypsy类逆转座子对不同胁迫条件的响应

LTR类逆转座子是水稻基因组中数量最多，分布最广的转座元件，其中Ty3-gypsy类的比重较大。根据Ty3-gypsy类逆转座子逆转录酶的保守区域，采用简并引物通过RT-PCR从5种胁迫处理后的水稻品种月亮谷的cDNA 进行了扩增，并测序获得了一批转录片段，分析不同胁迫条件诱导激活的Ty3-gypsy类逆转座子的特点。结果表明，5种胁迫处理都能诱导月亮谷中Ty3-gypsy类逆转座子的表达；对不同胁迫响应的逆转座子序列大部分同源性较高且呈交叉分布，仅有少部分具有胁迫响应的特异性，说明很多Ty3-gypsy类逆转座子能对不同胁迫进行响应。     

The composite genome of the legume symbiont Sinorhizobium meliloti

The scarcity of usable nitrogen frequently limits plant growth. A tight metabolic association with rhizobial bacteria allows legumes to obtain nitrogen compounds by bacterial reduction of dinitrogen (N2) to ammonium (NH4+). We present here the annotated DNA sequence of the alpha-proteobacterium Sinorhizobium meliloti, the symbiont of alfalfa. The tripartite 6.7-megabase (Mb) genome comprises a 3.65-Mb chromosome, and 1.35-Mb pSymA and 1.68-Mb pSymB megaplasmids. Genome sequence analysis indicates that all three elements contribute, in varying degrees, to symbiosis and reveals how this genome may have emerged during evolution. The genome sequence will be useful in understanding the dynamics of interkingdom associations and of life in soil environments.     

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     

多倍体在植物进化中的意义

几乎所有的开花作物都为多倍体植物,其基因组至少经历1次以上的全基因组加倍事件.随着测序技术的不断革新,人们对作物的基因组以及基因组的演化历史有了全新认识.分析了全基因组加倍在物种进化中的意义:多倍化改变基因组结构,丰富物种的遗传多样性,改变重复基因表达模式,增强物种的适应性,并展望多倍化在作物遗传育种中的应用.     

Au Elements and Their Evolution in Some Allopolyploid Genomes of Aegilops

To study the sequences of short interspersed nuclear elements (SINEs) evolution in some allopolyploid genomes of Aegilops, 108 Au element fragments (a novel kind of plant SINE) were amplified and sequenced in 10 species of Aegilops,which were clustered into three different groups (A, B and C) based on their related genome types. The sequences of these Au element fragments were heterogonous in di-, tetra-, and hexa-ploids, and the dendrograms of Au element obtained from phylogenetic analysis were very complex in each group and could be clustered into 15, 15 and 22 families,respectively. In this study, three rules about Au elements evolution have been drawn from the results: i. Most families were composed of Au element members with different host species in three groups; ii. Family 1-6 in Group A, Family 1-6 in Group B, Family 1-4 and Family 6-13 in Group C contained only one, apparently highly degenerate Au element member (a single representative element); iii. Elements generally fell into clades that were species-specific with respect to their host species. The potential mechanisms of Au element evolution in Aegilops were discussed.     

桉树葡萄糖-6-磷酸脱氢酶（G6PDH）的全基因组分析与进化研究

[目的]对桉树基因组中葡萄糖-6-磷酸脱氢酶（G6PDH）进行全基因组分析与进化研究。[方法]利用巨桉（Eucalyptus grandsis）全基因组数据,采用BLAST等生物信息学软件分析桉树G6PDH的基因特性、蛋白序列、系统进化树以及启动子特征。[结果]桉树基因组内存在6个G6PDH基因,其编码蛋白中,1个为胞质型G6PDH,5个为质体型G6PDH,而且桉树G6PDH均含有保守基序motif1、motif2、motif3、motif7、motif9和motif11。此外,桉树G6PDH启动子序列中均存在TATA框、增强子与涉及光应答、激素应答、胁迫应答等调控元件。[结论]可为下一步研究桉树G6PDH家族基因的分子功能提供参考。     

果蔗Ty3-gypsy类反转录转座子RT基因的多样性分析

【目的】分析Ty3-gypsy类反转录转座子反转录酶基因（RT）序列特征、多样性、系统进化关系及转录活性，为深入研究果蔗Ty3-gypsy类反转录转座子全长序列、转录转座活性及生物学功能提供理论参考。【方法】以果蔗品种拔地拉为试材，根据Ty3-gypsy类反转录转座子RT基因保守区设计简并引物对，利用其进行PCR扩增，将目的条带回收纯化后连接至pMD18-T载体，并转化大肠杆菌DH5α感受态细胞，挑取阳性克隆进行测序。依据测序结果对RT基因序列进行生物信息学分析。【结果】从果蔗拔地拉中扩增获得51条序列（SoRT4-1~SoRT4-51），去除重复序列和非RT基因序列后共获得44条RT基因序列，长度为423~433 bp，AT含量为56.84%~64.97%，AT:GC比值为1.32~1.85，核苷酸序列间相似性为44.4%~99.3%，其编码的氨基酸序列间相似性为10.8%~100.0%，说明氨基酸序列比核苷酸序列表现出更高异质性。44条RT基因序列被划分为4个家族，其中Ⅰ和Ⅲ为主要家族。44条RT基因编码的氨基酸序列中有20条发生了无义突变，说明其突变率较高。44条RT基因编码蛋白序列存在5种保守基序，其中，有29条序列同时包含Motif 1~Motif 4，其余15条序列的保守基序变异较大，说明保守基序存在一定异质性。4个家族代表性序列编码蛋白的三级结构在氢键和转角的数量方面差异较大；系统发育进化树分析结果显示，44条RT基因序列被分为七大类，Ⅰ类和Ⅱ类中的果蔗RT基因序列分别占序列总数的40.91%和27.27%，Ⅱ类和Ⅵ类中的部分果蔗RT基因序列与拟南芥的BAB40828.1、粳稻的BAB40824.1、菠菜的BAB40833.1和大豆的BAB40834.1亲缘关系较近，推测这些物种在进化过程中发生了Ty3-gypsy类反转录转座子的横向传递。初步发现1条Ty3-gypsy类反转录转座子（SoRT4-40）具有转录活性。【结论】获得44条果蔗Ty3-gypsy类反转录转座子RT基因序列，其中仅有1条序列具有转录活性，这些RT基因序列可用于开发基于Ty3-gypsy类反转录转座子的甘蔗分子标记。     

黄瓜AQP基因家族的鉴定与生物信息学分析

  目的  深入研究黄瓜Cucumis sativus水通道蛋白(aquaporin, AQP)基因家族(CsAQP)的相关功能。  方法  通过全基因组分析技术鉴定其家族成员,对其蛋白质理化性质、系统进化关系、选择压力、基因结构、保守基序、顺式作用元件、蛋白质互作进行分析。  结果  黄瓜基因组共有33个AQP基因,含有2~5个数量不等的外显子,在染色体上不均匀分布;根据物种进化关系将黄瓜AQP基因家族划分为5个亚家族;基因组重复序列分析表明:5号和6号染色体上各有2~3对基因串联重复;计算这些基因的同义替换(synonymous, K_s)和非同义替换(nonSynonymous, K_a)的比率,结果显示均小于1,表明其进化受纯化选择作用;顺式作用调控元件分析发现,大部分基因启动子区所含元件与激素调节、光响应、胁迫密切相关。  结论  通过黄瓜全基因组扫描,获得黄瓜基因组的33个AQP家族成员,分属于5个亚族,映射于7条染色体上。上游启动子区含逆境相关作用元件,且部分基因参与串联复制,历经纯化选择。图6表4参26     

Au Elements and Their Evolution in Some AIIopolyploid Genomes of Aegilops

To study the sequences of short interspersed nuclear elements （SINEs） evolution in some allopolyploid genomes of Aegilops, 108 Au element fragments （a novel kind of plant SINE） were amplified and sequenced in 10 species of Aegilops, which were clustered into three different groups （A, B and C） based on their related geuome types. The sequences of these Au element fragments were heterogouous in di-, tetra-, and hexa-ploids, and the deudrograms of Au element obtained from phylogenetic analysis were very complex in each group and could be clustered into 15, 15 and 22 families, respectively. In this study, three rules about Au elements evolution have been drawn from the results： i. Most families were composed of Au element members with different host species in three groups; ii. Family 1-6 in Group A, Family 1-6 in Group B, Family 1-4 and Family 6-13 in Group C contained only one, apparently highly degenerate Au dement member （a single representative elemeut）; iii. Elements generally fell into clades that were species-specific with respect to their host species. The potential mechanisms of Au element evolution in Aegilops were discussed.