Diversity, origin, and distribution of retrotransposons (gypsy and copia) in conifers
Diversity, origin, and distribution of retrotransposons (gypsy and copia) in conifers
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DOI：
10.1093/oxfordjournals.molbev.a003905
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发表时间：
2001-07-01
影响因子：
10.7
通讯作者：
Heslop-Harrison, JS
中科院分区：
文献类型：
--
作者：
Friesen, N;Brandes, A;Heslop-Harrison, JS
我们研究了广泛的裸子植物中逆转录成分的多样性、进化和基因组组织。利用新设计的吉普赛类反转录转座子和已知的CopiA类反转录转座子引物，对胎儿逆转录酶(RT)基因结构域165个片段进行了测序，并发现了较长的穿插分布的核素(线)反转录基因。Gypsy和Copia样反转录元件是裸子植物基因组的主要组成部分，原位杂交表明单个元件家族广泛存在于染色体上，与通过RNA中间体进行扩散和扩增一致。在裸子植物中广泛分布着大部分的逆转录成分家族，包括与南北半球在分类上有较大分离的物种。当裸子植物序列与其他物种的逆转录元件一起分析时，很好地支持了植物Copia、Gypsy和Line群的单系起源，另外还有一个分支包括巴特那病毒和其他可能与病毒相关的植物序列：以及动物和真菌吉普赛分子。植物逆转录元件在Copia和Gypsy RT结构域的系统发育树中都显示出高度的多样性，例如，来自拟南芥的逆转录元件序列存在于许多支持的类群中。没有初级枝划分主要的分类分支，如被子植物、单子叶植物、裸子植物或针叶植物或(基于较小的样本)蕨类、Gnetales或Shenopsida(木贼属)，这表明许多现有的多样性存在于植物进化的早期，或者可能已经发生了序列的水平转移。在吉普赛和黄柏的系统发育树中，发现了两个明显的单系裸子植物/针叶树枝，为反对最近的水平转移提供了证据。这些结果将裸子植物大而相对保守的基因组结构的进化放在了其他植物群多样性的背景下。
We examined the diversity, evolution, and genomic organization of retroelements in a wide range of gymnosperms. In fetal, 165 fragments of the reverse transcriptase (RT) gene domain were sequenced from PCR products using newly designed primers for gypsy-like retrotransposons and well-known primers for copia-like retrotransposons; representatives of long interspersed nuclear element (LINE) retroposons were also found. Gypsy and copia-like retroelements are a major component of the gymnosperm genome, and in situ hybridization showed that individual element families were widespread across the chromosomes, consistent with dispersion and amplification via an RNA intermediate. Most of the retroelement families were widely distributed among the gymnosperms, including species with wide taxonomic separation from the Northern and Southern Hemispheres. When the,gymnosperm sequences were analyzed together with retroelements from other species, the monophyletic origin of plant copia, gypsy, and LINE groups was well supported, with an additional clade including badnaviral and other, probably virus-related, plant sequences: as well as animal and fungal gypsy elements. Plant retroelements showed high diversity within the phylogenetic trees of both copia and gypsy RT domains, with, for example, retroelement sequences from Arabidopsis thaliana being present in many supported groupings. No primary branches divided major taxonomic clades such as angiosperms, monocotyledons, gymnosperms, or conifers or (based on smaller samples) ferns, Gnetales, or Sphenopsida (Equisetum), suggesting that much of the existing diversity was present early in plant evolution, or perhaps that horizontal transfer of sequences has occurred. Within the phylogenetic trees for both gypsy and copia, two clearly monophyletic gymnosperm/conifer clades were revealed, providing evidence against recent horizontal transfer. The, results put the evolution of the large and relatively conserved genome structure of gymnosperms into the context of the diversity of other groups of plants.