Comparative and population genomic landscape of Phellinus noxius: A hypervariable fungus causing root rot in trees
Comparative and population genomic landscape of Phellinus noxius: A hypervariable fungus causing root rot in trees
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DOI：
10.1111/mec.14359
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发表时间：
2017-11-01
影响因子：
4.9
通讯作者：
Tsai, Isheng J.
中科院分区：
文献类型：
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作者：
Chung, Chia-Lin;Lee, Tracy J.;Tsai, Isheng J.
白色腐真菌的膜壳目含有一些最具侵略性的木材腐朽菌，导致世界各地的树木死亡。尽管它们在生态上具有重要意义，并对它们引起的疾病产生影响，但人们对这些病原体的进化和传播模式知之甚少。在这里，我们测序和进行比较基因组分析的膜壳目基因组使用棕色根腐病菌noxius，木材分解真菌noxlinus lamaensis，层积根腐病菌sulphurascens和树干病原体Porodaedalea松。从这些真菌中鉴定出许多木质素降解酶基因家族，反映了它们作为白色腐菌的能力。与远缘真菌的比较突出了在P.noxius中1，3-β-葡聚糖糖苷酶的扩增，这可能是其快速生长属性的原因。我们确定了13个连锁群保守的伞菌，表明进化的稳定核型。本研究确定了毒蛾的异宗配合系统为双极异宗配合系统，其异常高度扩展的类似于60 kb的A位点，这是积累基因转位的结果。我们调查了亚太地区多个岛屿的60株P.noxius分离株的群体基因组学。全基因组测序结果显示，该多核物种含有丰富的多等位基因单核苷酸多态性，具有非典型等位基因频率。不同的模式内分离多态性反映单/杂合状态，这两者都是普遍的性质。我们已经展示了两个遗传上分离的谱系，其中一个跨越许多岛屿，尽管有地理障碍。这两个种群都具有非凡的遗传多样性，并显示出截然不同的进化情景。这些结果为进一步研究白色腐菌适合度和毒力的遗传基础提供了框架。
The order Hymenochaetales of white rot fungi contain some of the most aggressive wood decayers causing tree deaths around the world. Despite their ecological importance and the impact of diseases they cause, little is known about the evolution and transmission patterns of these pathogens. Here, we sequenced and undertook comparative genomic analyses of Hymenochaetales genomes using brown root rot fungus Phellinus noxius, wood-decomposing fungus Phellinus lamaensis, laminated root rot fungus Phellinus sulphurascens and trunk pathogen Porodaedalea pini. Many gene families of lignin-degrading enzymes were identified from these fungi, reflecting their ability as white rot fungi. Comparing against distant fungi highlighted the expansion of 1,3-beta-glucan synthases in P.noxius, which may account for its fast-growing attribute. We identified 13 linkage groups conserved within Agaricomycetes, suggesting the evolution of stable karyotypes. We determined that P.noxius has a bipolar heterothallic mating system, with unusual highly expanded similar to 60kb A locus as a result of accumulating gene transposition. We investigated the population genomics of 60 P.noxius isolates across multiple islands of the Asia Pacific region. Whole-genome sequencing showed this multinucleate species contains abundant poly-allelic single nucleotide polymorphisms with atypical allele frequencies. Different patterns of intra-isolate polymorphism reflect mono-/heterokaryotic states which are both prevalent in nature. We have shown two genetically separated lineages with one spanning across many islands despite the geographical barriers. Both populations possess extraordinary genetic diversity and show contrasting evolutionary scenarios. These results provide a framework to further investigate the genetic basis underlying the fitness and virulence of white rot fungi.