植物LTR类反转录转座子序列分析识别方法

LTR类反转录转座子(Long terminal repeat retrotransponson)是真核生物中的一类重要转座元件,具有分布广泛、异质性高等特点,在真核生物基因组进化中起着重要作用,现广泛应用于植物的基因功能分析和遗传多样性研究等方面。LTR类反转录转座子的序列识别是其应用的前提条件,因此对LTR类反转录转座子的序列鉴定和分析方法的研究具有重要的理论意义和实际应用价值。LTR类反转录转座子序列的生物信息学分析软件按原理可大致分为序列比对分析和相关序列保守区域识别鉴定两类。比对软件如BLAST、DNAstar等,是一种序列相似性搜索程序,通过与已知的反转录转座子序列比对后的序列相似性来判断未知序列是否是反转录转座子序列,但这类软件不能直接获得具体的LTR等特征序列的相关信息,不能对反转录转座子序列的全长进行识别。识别鉴定软件按原理可分为从头算起法、比较基因组法、同源搜索法和结构基础法4种,如LTR-Finder等基于从头算起法的识别鉴定软件,可对LTR类反转录转座子全序列进行较准确地预测和注释,RepeatMasker等基于同源搜索法的软件,通过与数据库中的序列的相似性比对后发现可能存在的LTR类反转录转座子。文章对不同的LTR类反转录转座子预测方法进行了比较和分析,在此基础上归纳总结出一套分析LTR类反转录转座子序列的操作流程,旨在为LTR类反转录转座子序列的分析提供参考。     

植物LTR反转录转座子的研究进展

反转录转座子是真核生物基因组中普遍存在的一类可移动的遗传因子,它们以RNA为媒介,在基因组中不断自我复制。在高等植物中,反转录转座子是基因组的重要成分之一。反转录转座子可以分为5大类型,其中以长末端重复（LTR）类型报道较多。LTR类型由于其首尾具有长末端重复序列,内部含有PBS、PPT、GAG和POL开放阅读框、TSD等结构,可以采用生物信息学软件进行预测。LTR反转录转座子的活性受到自身甲基化和环境因素的影响,DNA甲基化抑制反转录转座子转座,而外界环境的刺激能够激活转座子,从而影响插入位点周边基因的表达。同时由于LTR反转录转座子在植物中普遍存在,丰富的拷贝数以及多态性为新型分子标记（RBIP、SSAP、IRAP、REMAP）的开发提供了良好的素材。该文对近年来国内外有关植物反转录转座子的类型、结构特征、 LTR反转录转座子的活性及其影响因素、 LTR反转录转座子的预测以及标记开发等方面的研究进展进行综述。     

植物基因组中的非LTR反转录转座子SINEs和LINEs

反转录转座子是基因组进化的推动者之一。分为LTR和非LTR两种类型。前者是真核基因组的主要组分,结构和转座方式与逆转录病毒类似。后者是最初发现于动物基因组新近发现在植物基因组中也广泛存在的新型重复序列,包括LINEs(long interspersed nuclear elements)和SINEs(short interspersed nuclear elements)两个亚型。它们大多因自身或受宿主基因组的调控而失去转座活性。其转座机理目前还不十分清楚,推测LINEs可以自主转座,SINEs依赖其他转座子被动转座。种系分析认为LINEs可能是最古老的反转录转座子,SINEs的起源未知。文章对以上内容进行了归纳和讨论。     

利用iPBS技术克隆牡丹反转录转座子LTR序列

利用iPBS方法从西北牡丹(Paeonia suffruticosa)品种红绣球和中原牡丹品种洛阳红中扩增出相应片段,经回收、克隆及测序,获得了12条来自牡丹LTR类反转录转座子的LTR序列,并用相关生物信息学软件对序列进行分析。结果表明,这些核苷酸序列表现出较高的异质性,主要表现为缺失突变,序列长度变化范围为313–894 bp,同源性从31.1%–65.8%不等。将其氨基酸序列与已登录的不同植物LTR类反转录转座子LTR氨基酸序列进行聚类分析,结果显示与某些植物相应序列具有较高的同源性,表明可能存在LTR类反转录转座子的横向传递关系。根据克隆出的LTR序列设计SSAP引物,对牡丹29个品种进行了SSAP分子标记分析,结果显示具丰富的多态性。实验验证了用iPBS技术分离牡丹LTR序列的适用性,并为牡丹种质资源评价提供了新的技术手段。     

高等植物基因组中的反转录转座子

高等植物基因组中的反转录转座子王石平张启发（华中农业大学作物遗传改良国家重点实验室武汉４３００７０）关键词植物,反转录转座子,遗传多样性,转座ＲＥＴＲＯＴＲＡＮＳＰＯＳＯＮＳＩＮＴＨＥＧＥＮＯＭＥＳＯＦＨＩＧＨＥＲＰＬＡＮＴＳＷＡＮＧＳｈｉＰｉｎ...     

Copia 类型反转录转座子在籽粒苋中的表现

利用籽粒苋为材料 ,通过PCR扩增、克隆研究了copia类型反转录转座子的反转录酶序列在籽粒苋中的表现 ,结果表明 :(1)反转录转座子在苋属的 30个品系中同时检测到 ,说明反转录转座子在籽粒苋的不同种中普遍存在 ;(2 )对野生苋 (A .quitensis)中克隆、序列分析 2 8个反转录转座子的反转录酶序列 ,碱基分析表明 ,它们存在高度异质性 ,不同的反转录酶序列均存在不同程度的碱基缺失突变和终止密码子的突变 ;(3)对 2 8个序列与已发表的一些不同物种 (如水稻、矮牵牛和果蝇等 )的同一类型序列聚类分析表明 ,存在于野生苋中的反转录转座子与来源于双子叶或单子叶植物的反转录转座子关系密切 ,它们与果蝇的copia因子和 1731因子可能具有相同的起源     

植物活性长末端重复序列反转录转座子研究进展

长末端重复序列(Long terminal repeat,LTR)反转录转座子是真核生物基因组中普遍存在的一类可移动的DNA序列,它们以RNA为媒介,通过"复制粘贴"机制在基因组中不断自我复制。在高等植物中,许多活性的LTR反转录转座子已被详尽研究并应用于分子标记技术、基因标签、插入型突变及基因功能等分析。本文对植物活性LTR反转录转座子进行全面的调查,并对其结构、拷贝数和分布以及转座特性进行系统的归纳,分析了植物活性LTR反转录转座子的gag(种属特异抗原)和pol(聚合酶)序列特征,以及LTR序列中顺式调控元件的分布。研究发现自主有活性的LTR反转录转座子必须具备LTR区域以及编码Gag、Pr、Int、Rt和Rh蛋白的基因区。其中两端LTR区域具有高度同源性且富含顺式调控元件;Rt蛋白必备RVT结构域;Rh蛋白必备RNase_H1_RT结构域。这些结果为后续植物活性LTR反转录转座子的鉴定和功能分析奠定了重要基础。     

植物反转录转座子的研究进展

反转录转座子是生物界中存在的一类可移动的遗传因子,其转座功能通过RNA介导反转录来实现.它在植物界中普遍存在,并在植物基因和基因组进化中扮演了一个极其重要的角色.概述了植物反转录转座子的类型结构及作为遗传工具在生物学中的作用.     

An element with long terminal repeats and its variant arrangements in the genome of Lilium henryi

Summary A 9.35 kbp element with long terminal direct repeats (LTRs) of 2.4 kbp has been characterized from the large genome of Lilium henryi. The organization of the element, named del, was examined in 20 fragments from a genomic DNA library constructed using phage EMBL3. Five fragments apparently contained full 9.35 kbp elements while in 11 del was recovered in part. Two clones carried tandem arrangements of del, with single LTRs and internal sequences alternating, and one insert contained a solo LTR. Evidence suggests that these arrangements, which can arise by unequal crossing over, have a genomic rather than a cloning origin. Finally, one cloned fragment had a complex del arrangement yet to be fully defined. Limited sequencing of five LTRs (from a full del, a tandem arrangement and a solo LTR) indicates that the consensus termini are 5TGT ... ACA 3, with del sequences flanked by a 5 bp tandem repeat. Thus del shares properties with retrotransposons such as the copia family of Drosophila and Ty of yeast. However with more than 13000 copies per genome it seems del has been amplified more than is usual for such elements.     

Proliferation and copy number variation of BEL-like long terminal repeat retrotransposons within the Diabrotica virgifera virgifera genome

The proliferation of retrotransposons within a genome can contribute to increased size and affect the function of eukaryotic genes. BEL/Pao-like long-terminal repeat (LTR) retrotransposons were annotated from the highly adaptable insect species Diabrotica virgifera virgifera, the Western corn rootworm, using survey sequences from bacterial artificial chromosome (BAC) inserts and contigs derived from a low coverage next-generation genome sequence assembly. Eleven unique D. v. virgifera BEL elements were identified that contained full-length gag–pol coding sequences, whereas 88 different partial coding regions were characterized from partially assembled elements. Estimated genome copy number for full and partial BEL-like elements ranged from ~ 8 to 1582 among individual contigs using a normalized depth of coverage (DOC) among Illumina HiSeq reads (total genome copy number ~ 8821). BEL element copy number was correlated among different D. v. virgifera populations (R² = 0.9846), but individual element numbers varied ≤ 1.68-fold and the total number varied by ~ 527 copies. These data indicate that BEL element proliferation likely contributed to a large genome size, and suggest that differences in copy number are a source of genetic variability among D. v. virgifera.     

Major repeat components covering one‐third of the ginseng (Panax ginseng C.A. Meyer) genome and evidence for allotetraploidy

Ginseng (Panax ginseng) is a famous medicinal herb, but the composition and structure of its genome are largely unknown. Here we characterized the major repeat components and inspected their distribution in the ginseng genome. By analyzing three repeat‐rich bacterial artificial chromosome (BAC) sequences from ginseng, we identified complex insertion patterns of 34 long terminal repeat retrotransposons (LTR‐RTs) and 11 LTR‐RT derivatives accounting for more than 80% of the BAC sequences. The LTR‐RTs were classified into three Ty3/gypsy (PgDel, PgTat and PgAthila) and two Ty1/Copia (PgTork and PgOryco) families. Mapping of 30‐Gbp Illumina whole‐genome shotgun reads to the BAC sequences revealed that these five LTR‐RT families occupy at least 34% of the ginseng genome. The Ty3/Gypsy families were predominant, comprising 74 and 33% of the BAC sequences and the genome, respectively. In particular, the PgDel family accounted for 29% of the genome and presumably played major roles in enlargement of the size of the ginseng genome. Fluorescence in situ hybridization (FISH) revealed that the PgDel1 elements are distributed throughout the chromosomes along dispersed heterochromatic regions except for ribosomal DNA blocks. The intensity of the PgDel2 FISH signals was biased toward 24 out of 48 chromosomes. Unique gene probes showed two pairs of signals with different locations, one pair in subtelomeric regions on PgDel2‐rich chromosomes and the other in interstitial regions on PgDel2‐poor chromosomes, demonstrating allotetraploidy in ginseng. Our findings promote understanding of the evolution of the ginseng genome and of that of related species in the Araliaceae.