Genome analysis and avirulence gene cloning using a high-density RADseq linkage map of the flax rust fungus, Melampsora lini.
Genome analysis and avirulence gene cloning using a high-density RADseq linkage map of the flax rust fungus, Melampsora lini.
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DOI：
10.1186/s12864-016-3011-9
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发表时间：
2016-08-22
期刊：
影响因子：
4.4
通讯作者：
Jones DA
中科院分区：
文献类型：
--
作者：
Anderson C;Khan MA;Catanzariti AM;Jack CA;Nemri A;Lawrence GJ;Upadhyaya NM;Hardham AR;Ellis JG;Dodds PN;Jones DA
锈菌是一类重要的植物病原体，对农业、林业和自然生态系统造成毁灭性损失。植物可以通过编码受体的抗性基因免受锈病的侵害，这些受体在识别特定的病原体无毒蛋白时触发高度有效的防御反应。鉴定无毒基因对于了解该领域的毒力如何演变至关重要。为了方便亚麻锈病真菌Melampsora lini的无毒基因克隆，我们利用限制性内切位点相关DNA测序（RADseq）数据检测到的单核苷酸多态性构建了高密度遗传连锁图谱。该图谱包含27个连锁组中的13412个RADseq标记，总长度为5860 cM，包含2756个重组箱。这些标记序列被用于将68.9%的基因组组装锚定到遗传图谱上。利用该图谱和锚定组装结果表明：1)林氏僵菌总体减数分裂重组率较高，但重组分布不均匀，存在较大的冷点；2)表明在自发性毒性丧失突变体中发生了大量的基因组重排；3)定位克隆AvrL2和AvrM14毒力基因。AvrM14是一种双特异性无毒基因，可编码一种预测的裸水解酶。AvrL2位于M. lini基因组重组率最低的区域，编码一个小的、高电荷的富含脯氨酸的蛋白。通过提供基因组变异性的新见解和鉴定两种新的无毒基因，lini高密度连锁图谱极大地促进了我们对该病原体毒力机制的理解。本文的在线版本（doi:10.1186/s12864-016-3011-9）包含补充材料，可供授权用户使用。
Rust fungi are an important group of plant pathogens that cause devastating losses in agricultural, silvicultural and natural ecosystems. Plants can be protected from rust disease by resistance genes encoding receptors that trigger a highly effective defence response upon recognition of specific pathogen avirulence proteins. Identifying avirulence genes is crucial for understanding how virulence evolves in the field. To facilitate avirulence gene cloning in the flax rust fungus, Melampsora lini, we constructed a high-density genetic linkage map using single nucleotide polymorphisms detected in restriction site-associated DNA sequencing (RADseq) data. The map comprises 13,412 RADseq markers in 27 linkage groups that together span 5860 cM and contain 2756 recombination bins. The marker sequences were used to anchor 68.9 % of the M. lini genome assembly onto the genetic map. The map and anchored assembly were then used to: 1) show that M. lini has a high overall meiotic recombination rate, but recombination distribution is uneven and large coldspots exist; 2) show that substantial genome rearrangements have occurred in spontaneous loss-of-avirulence mutants; and 3) identify the AvrL2 and AvrM14 avirulence genes by map-based cloning. AvrM14 is a dual-specificity avirulence gene that encodes a predicted nudix hydrolase. AvrL2 is located in the region of the M. lini genome with the lowest recombination rate and encodes a small, highly-charged proline-rich protein. The M. lini high-density linkage map has greatly advanced our understanding of virulence mechanisms in this pathogen by providing novel insights into genome variability and enabling identification of two new avirulence genes. The online version of this article (doi:10.1186/s12864-016-3011-9) contains supplementary material, which is available to authorized users.