Wawrzynski Adam, Ashfield Tom, Chen Nicolas W G, Mammadov Jafar, Nguyen Ashley, Podicheti Ram, Cannon Steven B, Thareau Vincent, Ameline-Torregrosa Carine, Cannon Ethalinda, Chacko Ben, Couloux Arnaud, Dalwani Anita, Denny Roxanne, Deshpande Shweta, Egan Ashley N, Glover Natasha, Howell Stacy, Ilut Dan, Lai Hongshing, Del Campo Sara Martin, Metcalf Michelle, O'Bleness Majesta, Pfeil Bernard E, Ratnaparkhe Milind B, Samain Sylvie, Sanders Iryna, Ségurens Béatrice, Sévignac Mireille, Sherman-Broyles Sue, Tucker Dominic M, Yi Jing, Doyle Jeff J, Geffroy Valérie, Roe Bruce A, Maroof M A Saghai, Young Nevin D, Innes Roger W
Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
Plant Physiol. 2008 Dec;148(4):1760-71. doi: 10.1104/pp.108.127910. Epub 2008 Oct 24.
Retrotransposons and their remnants often constitute more than 50% of higher plant genomes. Although extensively studied in monocot crops such as maize (Zea mays) and rice (Oryza sativa), the impact of retrotransposons on dicot crop genomes is not well documented. Here, we present an analysis of retrotransposons in soybean (Glycine max). Analysis of approximately 3.7 megabases (Mb) of genomic sequence, including 0.87 Mb of pericentromeric sequence, uncovered 45 intact long terminal repeat (LTR)-retrotransposons. The ratio of intact elements to solo LTRs was 8:1, one of the highest reported to date in plants, suggesting that removal of retrotransposons by homologous recombination between LTRs is occurring more slowly in soybean than in previously characterized plant species. Analysis of paired LTR sequences uncovered a low frequency of deletions relative to base substitutions, indicating that removal of retrotransposon sequences by illegitimate recombination is also operating more slowly. Significantly, we identified three subfamilies of nonautonomous elements that have replicated in the recent past, suggesting that retrotransposition can be catalyzed in trans by autonomous elements elsewhere in the genome. Analysis of 1.6 Mb of sequence from Glycine tomentella, a wild perennial relative of soybean, uncovered 23 intact retroelements, two of which had accumulated no mutations in their LTRs, indicating very recent insertion. A similar pattern was found in 0.94 Mb of sequence from Phaseolus vulgaris (common bean). Thus, autonomous and nonautonomous retrotransposons appear to be both abundant and active in Glycine and Phaseolus. The impact of nonautonomous retrotransposon replication on genome size appears to be much greater than previously appreciated.
逆转座子及其残余序列通常占高等植物基因组的50%以上。尽管在玉米（Zea mays）和水稻（Oryza sativa）等单子叶作物中对其进行了广泛研究，但逆转座子对双子叶作物基因组的影响尚无充分文献记载。在此，我们对大豆（Glycine max）中的逆转座子进行了分析。对约3.7兆碱基（Mb）的基因组序列（包括0.87 Mb的着丝粒周围序列）进行分析，发现了45个完整的长末端重复序列（LTR）逆转座子。完整元件与单独LTR的比例为8:1，这是迄今为止植物中报道的最高比例之一，表明大豆中通过LTR之间的同源重组去除逆转座子的速度比之前研究的植物物种要慢。对配对LTR序列的分析发现，相对于碱基替换，缺失频率较低，这表明通过异常重组去除逆转座子序列的速度也较慢。值得注意的是，我们鉴定出了三个非自主元件亚家族，它们在最近进行了复制，这表明逆转座作用可由基因组中其他位置的自主元件反式催化。对大豆野生多年生近缘种绒毛大豆（Glycine tomentella）1.6 Mb序列的分析发现了23个完整的逆转元件，其中两个元件的LTR未积累任何突变，表明它们是最近插入的。在菜豆（Phaseolus vulgaris，普通菜豆）0.94 Mb的序列中也发现了类似模式。因此，自主和非自主逆转座子在大豆属和菜豆属中似乎都很丰富且活跃。非自主逆转座子复制对基因组大小的影响似乎比之前认为的要大得多。
