Comparative sequence analysis of Solanum and Arabidopsis in a hot spot for pathogen resistance on potato chromosome V reveals a patchwork of conserved and rapidly evolving genome segments.
Comparative sequence analysis of Solanum and Arabidopsis in a hot spot for pathogen resistance on potato chromosome V reveals a patchwork of conserved and rapidly evolving genome segments.
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DOI：
10.1186/1471-2164-8-112
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发表时间：
2007-05-02
期刊：
影响因子：
4.4
通讯作者：
Gebhardt C
中科院分区：
文献类型：
--
作者：
Ballvora A;Jöcker A;Viehöver P;Ishihara H;Paal J;Meksem K;Bruggmann R;Schoof H;Weisshaar B;Gebhardt C
作物农艺性状的数量表型变异受环境和遗传因素控制（数量性状位点= QTL）。为了理解这样的QTL的分子基础，鉴定潜在的基因是主要的兴趣和DNA序列分析的基因组区域窝藏QTL是一个先决条件。马铃薯（Solanum tuberosum）的QTL定位已经在染色体V上确定了由DNA标记GP 21和GP 179标记的区域，该区域包含许多重要的QTL，其中包括抗由卵菌Phytophthora infestans引起的晚疫病和根胞囊线虫的QTL。为了获得染色体V上靶向区域的基因组序列，构建了两个局部BAC（细菌人工染色体）重叠群并进行测序，其对应于二倍体杂合基因型P6/210的同源染色体的部分。组装并注释了417，445和202，781个碱基对的两个连续序列。逆转录转座子元件的非等位基因插入、分叉的基因间序列的延伸、基因内容和基因顺序的差异破坏了基因间的共线性。后者是由70 kbp的基因组片段倒位引起的。这些功能也被发现在比较的正向序列重叠群从三个同源染色体的Solanum demissum，野生块茎轴承物种。序列的功能注释在一个重叠群中鉴定出48个推定的开放阅读框（ORF），在另一个重叠群中鉴定出22个，平均每9 kbp一个ORF。10个ORF被归类为类抗性基因，11个为含F盒基因，13个为转座因子，3个为转录因子。比较马铃薯和拟南芥注释的蛋白质，揭示了五个微同线块的3至7个ORF，A。拟南芥染色体1、3和5。比较序列分析显示高度保守的共线区域，侧翼区域显示高变异性和串联重复基因。序列注释表明，大部分的ORF是多基因家族的成员。比较马铃薯和拟南芥注释的蛋白质，表明这些远亲植物物种之间存在片段化的结构保守性。
Quantitative phenotypic variation of agronomic characters in crop plants is controlled by environmental and genetic factors (quantitative trait loci = QTL). To understand the molecular basis of such QTL, the identification of the underlying genes is of primary interest and DNA sequence analysis of the genomic regions harboring QTL is a prerequisite for that. QTL mapping in potato (Solanum tuberosum) has identified a region on chromosome V tagged by DNA markers GP21 and GP179, which contains a number of important QTL, among others QTL for resistance to late blight caused by the oomycete Phytophthora infestans and to root cyst nematodes. To obtain genomic sequence for the targeted region on chromosome V, two local BAC (bacterial artificial chromosome) contigs were constructed and sequenced, which corresponded to parts of the homologous chromosomes of the diploid, heterozygous genotype P6/210. Two contiguous sequences of 417,445 and 202,781 base pairs were assembled and annotated. Gene-by-gene co-linearity was disrupted by non-allelic insertions of retrotransposon elements, stretches of diverged intergenic sequences, differences in gene content and gene order. The latter was caused by inversion of a 70 kbp genomic fragment. These features were also found in comparison to orthologous sequence contigs from three homeologous chromosomes of Solanum demissum, a wild tuber bearing species. Functional annotation of the sequence identified 48 putative open reading frames (ORF) in one contig and 22 in the other, with an average of one ORF every 9 kbp. Ten ORFs were classified as resistance-gene-like, 11 as F-box-containing genes, 13 as transposable elements and three as transcription factors. Comparing potato to Arabidopsis thaliana annotated proteins revealed five micro-syntenic blocks of three to seven ORFs with A. thaliana chromosomes 1, 3 and 5. Comparative sequence analysis revealed highly conserved collinear regions that flank regions showing high variability and tandem duplicated genes. Sequence annotation revealed that the majority of the ORFs were members of multiple gene families. Comparing potato to Arabidopsis thaliana annotated proteins suggested fragmented structural conservation between these distantly related plant species.
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DOI：
10.1073/pnas.132259199
发表时间：
2002-07-09
影响因子：
11.1
作者：
Fu, HH;Dooner, HK
通讯作者：
Dooner, HK
影响因子：
7.2
作者：
Bendahmane, A;Querci, M;Baulcombe, DC
通讯作者：
Baulcombe, DC
影响因子：
3.1
作者：
Collins, A;Milbourne, D;Waugh, R
通讯作者：
Waugh, R
影响因子：
7.2
作者：
Ballvora, A;Ercolano, MR;Gebhardt, C
通讯作者：
Gebhardt, C
影响因子：
5.4
作者：
KREIKE, CM;DEKONING, JRA;STIEKEMA, WJ
通讯作者：
STIEKEMA, WJ