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首页> 外文期刊>Journal of Crop Science and Biotechnology >In silico-selection of Brassica rapa organelle genome-derived BACs using their end sequences and sequence level comparative analysis of the 124 kb mitochondrial genome sequences in the family Brassicaceae
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In silico-selection of Brassica rapa organelle genome-derived BACs using their end sequences and sequence level comparative analysis of the 124 kb mitochondrial genome sequences in the family Brassicaceae

机译：利用芸苔属植物的末端序列进行计算机筛选，并对其芸苔科中124 kb线粒体基因组序列进行序列水平比较分析

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摘要

We identified BAC clones which harbor DNAs derived from the B. rapa organelle genomes by in silico mapping of 80,292 B. rapa BAC end sequences on the Arabidopsis organelle genomes and subsequent insert size estimation and fingerprinting. A total of 1,048 putative chloroplast genome-derived BAC clones (2.6%) were identified. Fingerprinting and sequencing revealed that many of them represented the entire chloroplast genome (about 150 kb). Meanwhile, only 59 putative mitochondrial genome-derived BACs (0.15%) were identified and most of them showed rare agreement between the in silico map and fingerprinting. We sequenced BAC clone KBrB042G11 (42G11) and compared it to the mitochondrial genome of B. napus and A. thaliana which showed dynamic rearrangement events. The order of 33 orthologous genes was collinear between the 42G11 BAC and its counterpart in B. napus. Five distinctive rearrangements and two InDels were identified between these two closely related species and the rearrangements were related to the occurrence of small tandem repeat sequences. Sequences of the 33 orthologous genes in the homoeologous regions of B. napus and B. rapa were almost 100% identical. Gene orders showed no colinearity between Arabidopsis and Brassica even though 31 orthologous genes shared high sequence similarity with p-values over 1E-32. FISH analysis using the identified BAC revealed a large chloroplast genome insertion in the pericentromeric region of chromosome (chr.) 4 of B. rapa.
机译：我们通过在拟南芥细胞器基因组上对80,292个B. rapa BAC BAC末端序列进行了计算机绘图，并通过随后的插入片段大小估计和指纹鉴定，鉴定出了BAC克隆，这些克隆具有源自B. rapa细胞器基因组的DNA。总共鉴定了1,048个假定的叶绿体基因组来源的BAC克隆（2.6％）。指纹图谱和测序表明，它们中的许多代表了整个叶绿体基因组（约150 kb）。同时，仅鉴定出59个假定的线粒体基因组来源的BAC（0.15％），并且大多数在计算机谱图和指纹图谱之间显示出罕见的一致性。我们对BAC克隆KBrB042G11（42G11）进行了测序，并将其与显示动态重排事件的甘蓝型油菜和拟南芥的线粒体基因组进行了比较。 42G11 BAC及其在甘蓝型油菜中的对应基因在33个直系同源基因的顺序上是共线的。在这两个密切相关的物种之间鉴定出五个独特的重排和两个InDel，并且该重排与小串联重复序列的发生有关。甘蓝型油菜和芜菁型油菜同源区域中的33个直系同源基因的序列几乎100％相同。基因顺序显示拟南芥和芸苔属之间没有共线性，即使31个直系同源基因在p值超过1E-32时也具有很高的序列相似性。使用鉴定出的BAC进行的FISH分析表明，在B. rapa染色体（chr。）4的着丝粒区中有大量叶绿体基因组插入。

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  • 来源
    《Journal of Crop Science and Biotechnology》 |2009年第4期|207-215|共9页
  • 作者

    Jee Young Park; Soo-Jin Kwon; Beom-Soon Choi; Ki-Byung Lim; Yoon Jung Hwang; Jin-A Kim; Yong Pyo Lim; Beom-Seok Park; Tae-Jin Yang;

  • 作者单位

    Department of Plant Science Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences College of Agriculture and Life Sciences Seoul National University Seoul 151-921 Korea;

    School of Applied Biosciences College of Agriculture and Life Sciences Kyungpook National University Daegu 702-701 Korea;

    School of Applied Biosciences College of Agriculture and Life Sciences Kyungpook National University Daegu 702-701 Korea;

    Department of Horticulture Chungnam National University Daejeon 305-764 Korea;

    Department of Plant Science Plant Genomics and Breeding Institute and Research Institute for Agriculture and Life Sciences College of Agriculture and Life Sciences Seoul National University Seoul 151-921 Korea;

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  • 正文语种 eng
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  • 关键词

    Brassica rapa; BAC-end sequence; chloroplast; mitochondrial genome;

    机译：小白菜;BAC末端序列;叶绿体;线粒体基因组;

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