苹果Ty1-copia类逆转座子家族鉴定及特性分析

根据逆转座子RT保守序列设计引物,利用PCR方法从苹果'嘎拉'中克隆了20条RT片段,分析苹果基因组内Ty1-copia类逆转座子家族特性及进化关系.结果显示,20条逆转录酶保守序列表现出了高度的异质性.结合已报道的37条苹果Ty1-copia类逆转座子RT片段,构建了系统发育树,发现家族1、3和4中具有转座活性的逆转座子的可能性较大;序列分析表明,Ty1-copia类逆转座子是苹果基因组内序列重组的热点.用RT序列为探针进行Southern杂交,发现苹果基因组内Ty1-copia类逆转座子拷贝数高、分布广泛.研究结果为进一步分离具有转座活性的苹果Ty1-copia类逆转座子及其人工诱导芽变奠定了基础.     

节瓜Ty1-copia类逆转座子逆转录酶序列的克隆及比对

对8个节瓜（Benincasa hispida var.chieh-qua How）品系基因组DNA中的Ty1-copia类逆转座子逆转录酶核苷酸序列进行扩增,并对品系A39FA的29个克隆产物的核苷酸序列及翻译的氨基酸序列的系统进化和同源性进行了分析,还对29条氨基酸序列进行了比对。扩增结果表明：8个节瓜品系的基因组DNA中均包含长度约260 bp的逆转录酶核苷酸片段;从品系A39FA中获得的29条Ty1-copia类逆转座子逆转录酶核苷酸序列（CqRt1至CqRt29）的长度为247~267 bp,同源率为46.2%~98.1%,而它们的氨基酸序列同源率为26.7%~98.8%。序列分析结果表明：节瓜Ty1-copia类逆转座子逆转录酶核苷酸序列中碱基A、T、G和C的数量分别为65~96、47~92、45~74和32~49,所有序列均富含碱基A和T,AT/GC比为1.35~2.33;缺失突变是造成节瓜Ty1-copia类逆转座子逆转录酶核苷酸序列长度差异的主要因素,在序列长度和碱基组成方面的明显差异表明节瓜Ty1-copia类逆转座子逆转录酶核苷酸序列具有高度异质性。翻译后的氨基酸序列中有21条序列存在终止密码子突变、12条序列存在移框突变,表明Ty1-copia类逆转座子是节瓜基因组内序列重组的热点。通过聚类分析可将29个逆转录酶核苷酸序列分为5个家族（Family）,分别包括16、4、4、4和1条序列,其中Family 1可能是具有转座活性的逆转座子家族,但存在转录活性的逆转录酶序列仅占全部序列数量的20.69%。将每一家族中的1~2条序列与其他15种植物的Ty1-copia类逆转座子逆转录酶的氨基酸序列进行比对,显示出较高的同源性。研究结果表明：节瓜与其他植物的Ty1-copia类逆转座子可能有相同起源,而且Ty1-copia类逆转座子可在不同类群间横向传递。     

BB染色体组野生种花生LTR反转录转座子RT基因的多样性分析

利用简并PCR技术从野生花生种(Arachis ipaensis Krapov.et W.C.Greg.)的基因组中扩增分离Ty1-copia类(1类)和Ty3-gypsy类(2类)反转录转座子RT基因,并对其序列特征、多样性、系统进化关系及转录活性进行分析.结果显示:对于1和2类RT基因,目的条带分别约为260和43...     

水稻逆转录转座子RIRE10拷贝数与LTR区转录活性的鉴定

在水稻第四号染色体的长臂上鉴定了一个结构完整的Ty3型逆转录转座子RIRE10。RIRE10两LTR间的中间区域在gag pol的上游还包含另一个开放阅读框。通过RT PCR与Northern印迹杂交检测到来自LTR区的转录产物 ;根据点杂交结果 ,鉴定出包含中间区域的RIRE10成员的个数以及LTR区的拷贝数。除了 6 5个完整的逆转录转座子所具备的两个LTR外 ,水稻基因组还含有近 90 0个RIRE10的solo LTR。LTR区的转录以及导致solo LTR产生的同源重组可能影响了RIRE10成员在水稻基因组中的转座活性     

Isolation of two novel complete Ty1<Emphasis Type="Italic">-copia</Emphasis> retrotransposons from apple and demonstration of use of derived S-SAP markers for distinguishing bud sports of <Emphasis Type="BoldItalic">Malus domestica</Emphasis> cv. Fuji

Retrotransposon-based molecular markers are a powerful tool for mapping and diversity studies. The scarcity of retrotransposon long terminal repeat (LTR) sequences limits the application of retrotransposon-based molecular marker systems. Here, we isolated two novel complete Ty1-copia retrotransposons (CTcrm1 and CTcrm2) in apple using a genome walking strategy. The CTcrm retrotransposons are nearly 5 kb long, and they have all the features of Ty1-copia retrotransposons. The differences in gene organization and nucleotide sequence length between the CTcrm retrotransposons and other reported complete retrotransposons in apple showed that CTcrm1 and CTcrm2 are the first two distinct complete Ty1-copia retrotransposons in the apple genome. To investigate the potential utility of the two retrotransposons as molecular markers, primers complementary to the CTcrm LTRs were designed to develop sequence-specific amplification polymorphism markers for discriminating bud sports of Fuji apple. Multiple polymorphisms corresponding to CTcrm1 and CTcrm2 were detected and could easily be used to discriminate bud sports from their Fuji progenitor, as well as from each other.     

A Ty1-copia group retrotransposon sequence in a vertebrate.

Summary We have used the polymerase chain reaction (PCR) to isolate a sequence characteristic of aTy1-copia group retrotransposon from the genome of the herring (Clupea harengus). This is the firstTy1-copia group retrotransposon sequence described in a vertebrate. Phylogenetic comparison of this sequence with other members of this group of retrotransposons shows that it resembles more closely some Tyl-copia group members fromDrosophila melanogaster than other group members in plants and fungi. These observations provide further evidence that theTy1-copia group LTR retrotransposons span many of the major eukaryote species boundaries, suggesting that horizontal transmission between different species has played a role in the evolution of this retrotransposon group.     

A computational study of the dynamics of LTR retrotransposons in the Populus trichocarpa genome

Retrotransposons are an ubiquitous component of plant genomes, especially abundant in species with large genomes. Populus trichocarpa has a relatively small genome, which was entirely sequenced; however, studies focused on poplar retrotransposons dynamics are rare. With the aim to study the retrotransposon component of the poplar genome, we have scanned the complete genome sequence searching full-length long-terminal repeat (LTR) retrotransposons, i.e., characterised by two long terminal repeats at the 5′ and 3′ ends. A computational approach based on detection of conserved structural features, on building multiple alignments, and on similarity searches was used to identify 1,479 putative full-length LTR retrotransposons. Ty1-copia elements were more numerous than Ty3-gypsy. However, many LTR retroelements were not assigned to any superfamily because lacking of diagnostic features and non-autonomous. LTR retrotransposon remnants were by far more numerous than full-length elements, indicating that during the evolution of poplar, large amplification of these elements was followed by DNA loss. Within superfamilies, Ty3-gypsy families are made of more members than Ty1-copia ones. Retrotransposition occurred with increasing frequency following the separation of Populus sections, with different waves of retrotransposition activity between Ty3-gypsy and Ty1-copia elements. Recently inserted elements appear more frequently expressed than older ones. Finally, different levels of activity of retrotransposons were observed according to their position and their density in the linkage groups. On the whole, the results support the view of retrotransposons as a community of different organisms in the genome, whose activity (both retrotransposition and DNA loss) has heavily impacted and probably continues to impact poplar genome structure and size.     

Unearthing LTR Retrotransposon gag Genes Co-opted in the Deep Evolution of Eukaryotes

LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here, we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely co-option occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and Bel-Pao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes.