Comparative analysis of the Brassica oleracea genetic map and the Arabidopsis thaliana genome
Comparative analysis of the Brassica oleracea genetic map and the Arabidopsis thaliana genome
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DOI：
10.1139/g09-035
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发表时间：
2009-07-01
期刊：
影响因子：
3.1
通讯作者：
Sadowski, Jan
中科院分区：
文献类型：
--
作者：
Kaczmarek, Malgorzata;Koczyk, Grzegorz;Sadowski, Jan
我们进一步研究了芸苔属物种和拟南芥的基因组宏同线性。这项工作的目的是比较地图建设的B。oleracea和A. thaliana染色体的基础上，160已知A.拟南芥探针：147个表达序列标签（EST）和13个全长cDNA克隆。基于对A.在拟南芥基因组中，大多数（83%）的EST代表独特或低拷贝基因。我们确定了保守的片段通过视觉检查的比较数据与先验假设，并建立了他们的意义与排队算法。评估B的数量。oleracea基因拷贝数。拟南芥EST呈上升趋势。我们建立了一个分离畸变模式的所有遗传位点，特别考虑的选择类型（配子或合子），并讨论其可能的影响遗传图谱的构建。与以前的报告一致，我们发现了大量的染色体重排和基因组片段复制的B的证据。这是两个物种分化后发生的事情。此外，我们发现，超过54%的B。oleracea基因组由24个与A.拟南芥基因组在B区平均保守片段由5个位点组成，覆盖19.3cM。oleracea的遗传图谱，A. thaliana physical map.我们还试图使用一个统一的系统的保守块（如前所述），以验证我们的结果，并进行全面的比较与其他芸苔属物种。
We further investigated genome macrosynteny for Brassica species and Arabidopsis thaliana. This work aimed at comparative map construction for B. oleracea and A. thaliana chromosomes based on 160 known A. thaliana probes: 147 expressed sequence tags (ESTs) and 13 full-length cDNA clones. Based on an in silico study of the A. thaliana genome, most of the selected ESTs (83%) represented unique or low-copy genes. We identified conserved segments by the visual inspection of comparative data with a priori assumptions, and established their significance with the LineUp algorithm. Evaluation of the number of B. oleracea gene copies per A. thaliana EST revealed a fixed upward trend. We established a segregation distortion pattern for all genetic loci, with particular consideration of the type of selection (gametic or zygotic), and discuss its possible impact on genetic map construction. Consistent with previous reports, we found evidence for numerous chromosome rearrangements and the genome fragment replication of B. oleracea that have taken place since the divergence of the two species. Also, we found that over 54% of the B. oleracea genome is covered by 24 segments conserved with the A. thaliana genome. The average conserved segment is composed of 5 loci covering 19.3 cM in the B. oleracea genetic map and 2.42 Mb in the A. thaliana physical map. We have also attempted to use a unified system of conserved blocks (previously described) to verify our results and per-form a comprehensive comparison with other Brassica species.