High presence/absence gene variability in defense-related gene clusters of Cucumis melo.
High presence/absence gene variability in defense-related gene clusters of Cucumis melo.
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DOI：
10.1186/1471-2164-14-782
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发表时间：
2013-11-12
期刊：
影响因子：
4.4
通讯作者：
Puigdomènech P
中科院分区：
文献类型：
--
作者：
González VM;Aventín N;Centeno E;Puigdomènech P
DNA序列拷贝数的变化是真核生物基因组变异的主要机制之一。这些变化通常与表型效应有关，如遗传疾病或新的病原体抗性。通过应用下一代大规模测序技术，基因组序列的可用性日益增加，这使得在种间和种内水平上研究基因组多态性成为可能，从而有助于了解物种如何通过基因组变异性适应不断变化的环境。甜瓜基因存在/不存在变异（PAV）的数据是通过对栽培品种和一个古老的甜瓜品种进行重测序获得的，并使用先前从其他三个甜瓜品种获得的重测序数据，其中包括DHL 92，目前的甜瓜基因组序列草案是基于该数据。共检测到1，697个PAV事件，涉及预测甜瓜基因互补的4.4%。总的来说，与DHL 92参考基因组相比，平均1.5%的基因在每个分析的栽培品种中缺失。在已知功能的304个PAV基因中，最常见的功能类别是应激反应蛋白（占所有分类PAV的30%）。我们的研究结果表明，来自多拷贝家族的基因比单拷贝基因受PAV影响的可能性高5倍。此外，存在于串联阵列中的基因组中的基因受PAV影响的机会是孤立基因的两倍，PAV基因倾向于在更长的簇中。在甜瓜基因组中检测到的PAV事件的最高浓度被发现在连锁群V的1.1 Mb区域中，这也显示甜瓜胁迫应答基因的最高密度。特别是，该区域包含迄今为止在甜瓜中鉴定的最长的连续含基因PAV序列。本文首次报道了PAV在几个甜瓜品种中的全基因组变异。多拷贝和聚集的基因，特别是那些假定的压力反应功能，被发现特别受PAV多态性的影响。由于葫芦科植物的防御相关基因数量明显低于其他植物，因此PAV变异可能在亚种水平上产生新的病原体抗性方面发挥重要作用。此外，这些结果显示了单一参考基因组序列作为表征和克隆抗性基因的唯一基础的局限性。
Changes in the copy number of DNA sequences are one of the main mechanisms generating genome variability in eukaryotes. These changes are often related to phenotypic effects such as genetic disorders or novel pathogen resistance. The increasing availability of genome sequences through the application of next-generation massive sequencing technologies has allowed the study of genomic polymorphisms at both the interspecific and intraspecific levels, thus helping to understand how species adapt to changing environments through genome variability. Data on gene presence/absence variation (PAV) in melon was obtained by resequencing a cultivated accession and an old-relative melon variety, and using previously obtained resequencing data from three other melon cultivars, among them DHL92, on which the current draft melon genome sequence is based. A total of 1,697 PAV events were detected, involving 4.4% of the predicted melon gene complement. In all, an average 1.5% of genes were absent from each analyzed cultivar as compared to the DHL92 reference genome. The most populated functional category among the 304 PAV genes of known function was that of stress response proteins (30% of all classified PAVs). Our results suggest that genes from multi-copy families are five times more likely to be affected by PAV than singleton genes. Also, the chance of genes present in the genome in tandem arrays being affected by PAV is double that of isolated genes, with PAV genes tending to be in longer clusters. The highest concentration of PAV events detected in the melon genome was found in a 1.1 Mb region of linkage group V, which also shows the highest density of melon stress-response genes. In particular, this region contains the longest continuous gene-containing PAV sequence so far identified in melon. The first genome-wide report of PAV variation among several melon cultivars is presented here. Multi-copy and clustered genes, especially those with putative stress-response functions, were found to be particularly affected by PAV polymorphisms. As cucurbits are known to possess a significantly lower number of defense-related genes compared to other plant species, PAV variation may play an important role in generating new pathogen resistances at the subspecies level. In addition, these results show the limitations of single reference genome sequences as the only basis for characterization and cloning of resistance genes.
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影响因子：
7.4
作者：
Cobbett, CS
通讯作者：
Cobbett, CS
影响因子：
56.9
作者：
Sebat, J;Lakshmi, B;Wigler, M
通讯作者：
Wigler, M
影响因子：
30.8
作者：
Lai, Jinsheng;Li, Ruiqiang;Wang, Jun
通讯作者：
Wang, Jun
影响因子：
5.2
作者：
Garcia-Mas, J;van Leeuwen, H;Arús, P
通讯作者：
Arús, P
DOI：
10.1111/j.1095-8339.1980.tb01676.x
发表时间：
1980-01-01
影响因子：
2.4
作者：
JEFFREY, C
通讯作者：
JEFFREY, C