comparison of homoeolocus organisation in paired bac clones from white clover (trifolium repens l.) and microcolinearity with model legume species比较homoeolocus组织的bac克隆从白色三叶草(三叶草被l .)和microcolinearity模型豆科物种.pdfVIP

Hand et al. BMC Plant Biology 2010, 10:94 /1471-2229/10/94 R E S E A R C H A R T I C L E Open Access Research article Comparison of homoeolocus organisation in paired BAC clones from white clover (Trifolium repens L.) and microcolinearity with model legume species 1,2,3 1,2 1,2,3 1,2,3 1,2,3 Melanie L Hand , Noel OI Cogan , Timothy I Sawbridge , German C Spangenberg and John W Forster* Abstract Background: White clover (Trifolium repens L.) is an outbreeding allotetraploid species and an important forage legume in temperate grassland agriculture. Comparison of sub-genome architecture and study of nucleotide sequence diversity within allopolyploids provides insight into evolutionary divergence mechanisms, and is also necessary for the development of whole-genome sequencing strategies. This study aimed to evaluate the degree of divergence between the O and P sub-genomes of white clover through sequencing of BAC clones containing paired homoeoloci. The microsyntenic relationships between the genomes of white clover and the model legumes Lotus japonicus and Medicago truncatula as well as Arabidopsis thaliana were also characterised. Results: A total of four paired homoeologous BACs were selected and sequenced to generate 173 kb of overlapping sequence between the O and P sub-genomes. Equivalent gene content was generally observed, apart from small- scale deletions, in contrast to conservation of intergenic sequences, which varied between the four selected regions. Measurement of the number of synonymous substitutions between homoeologous genes led to estimation of a 4.2 million year divergence time between the two sub-genomes. Microsynteny was observed between the genomes of w