Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes
Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes
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DOI：
10.1073/pnas.0603228103
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发表时间：
2006-10-03
影响因子：
11.1
通讯作者：
Young, Nevin D.
中科院分区：
文献类型：
--
作者：
Cannon, Steven B.;Sterck, Lieven;Young, Nevin D.
模式豆科植物紫花苜蓿和莲花的基因组测序为同一植物家族的两个基因组的大规模基于序列的比较提供了机会。在这里，我们报告了这些物种之间的共性比较，包括关于染色体关系的细节，大规模的共性区块，区块内的微共性，以及缺乏明确对应的基因组区域。莲花和紫花苜蓿基因组共享至少10个大规模的同步性区块，每个都具有相当大的共线性，并且经常延长整个染色体臂的长度。每个共线块内共线和共线基因的比例相对均一。Medicago-Lotus的比较还表明，mt的基因密度相似且基本相同，尽管mt的包含基因的区域比Lj对应的区域占据了20%-30%的空间，主要是因为mt反转录转座子的数量更多。由于基因组比较的解释因大规模的基因组复制而变得复杂，我们描述了同义替换、同义替换和系统发育分析来识别和确定可能的全基因组复制事件的日期。没有直接证据表明最近在Medicago或莲花中有任何大规模的基因组复制，而是在物种形成之前的复制。系统发育比较将这种重复放在Rosid I分支中，显然是在豆科和杨柳科(杨树)分裂之后。
Genome sequencing of the model legumes, Medicago truncatula and Lotus japonicus, provides an opportunity for large-scale sequence-based comparison of two genomes in the same plant family. Here we report synteny comparisons between these species, including details about chromosome relationships, large-scale synteny blocks, microsynteny within blocks, and genome regions lacking clear correspondence. The Lotus and Medicago genomes share a minimum of 10 large-scale synteny blocks, each with substantial collinearity and frequently extending the length of whole chromosome arms. The proportion of genes syntenic and collinear within each synteny block is relatively homogeneous. Medicago-Lotus comparisons also indicate similar and largely homogeneous gene densities, although gene-containing regions in Mt occupy 20-30% more space than Lj counterparts, primarily because of larger numbers of Mt retrotransposons. Because the interpretation of genome comparisons is complicated by large-scale genome duplications, we describe synteny, synonymous substitutions and phylogenetic analyses to identify and date a probable whole-genome duplication event. There is no direct evidence for any recent large-scale genome duplication in either Medicago or Lotus but instead a duplication predating speciation. Phylogenetic comparisons place this duplication within the Rosid I clade, clearly after the split between legumes and Salicaceae (poplar).