...
  • 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>MBio >A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity
【24h】

A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity

机译：真核小麦条锈病真菌 Puccinia striiformis 的近完整单倍型定基因组。 sp。 tritici 揭示了较高的单体间多样性

获取原文
           
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

ABSTRACT A long-standing biological question is how evolution has shaped the genomic architecture of dikaryotic fungi. To answer this, high-quality genomic resources that enable haplotype comparisons are essential. Short-read genome assemblies for dikaryotic fungi are highly fragmented and lack haplotype-specific information due to the high heterozygosity and repeat content of these genomes. Here, we present a diploid-aware assembly of the wheat stripe rust fungus Puccinia striiformis f. sp. tritici based on long reads using the FALCON-Unzip assembler. Transcriptome sequencing data sets were used to infer high-quality gene models and identify virulence genes involved in plant infection referred to as effectors. This represents the most complete Puccinia striiformis f. sp. tritici genome assembly to date (83?Mb, 156 contigs, N _(50)of 1.5?Mb) and provides phased haplotype information for over 92% of the genome. Comparisons of the phase blocks revealed high interhaplotype diversity of over 6%. More than 25% of all genes lack a clear allelic counterpart. When we investigated genome features that potentially promote the rapid evolution of virulence, we found that candidate effector genes are spatially associated with conserved genes commonly found in basidiomycetes. Yet, candidate effectors that lack an allelic counterpart are more distant from conserved genes than allelic candidate effectors and are less likely to be evolutionarily conserved within the P.?striiformis species complex and Pucciniales . In summary, this haplotype-phased assembly enabled us to discover novel genome features of a dikaryotic plant-pathogenic fungus previously hidden in collapsed and fragmented genome assemblies. IMPORTANCE Current representations of eukaryotic microbial genomes are haploid, hiding the genomic diversity intrinsic to diploid and polyploid life forms. This hidden diversity contributes to the organism’s evolutionary potential and ability to adapt to stress conditions. Yet, it is challenging to provide haplotype-specific information at a whole-genome level. Here, we take advantage of long-read DNA sequencing technology and a tailored-assembly algorithm to disentangle the two haploid genomes of a dikaryotic pathogenic wheat rust fungus. The two genomes display high levels of nucleotide and structural variations, which lead to allelic variation and the presence of genes lacking allelic counterparts. Nonallelic candidate effector genes, which likely encode important pathogenicity factors, display distinct genome localization patterns and are less likely to be evolutionary conserved than those which are present as allelic pairs. This genomic diversity may promote rapid host adaptation and/or be related to the age of the sequenced isolate since last meiosis.
机译：摘要一个长期存在的生物学问题是进化如何塑造了双核真菌的基因组结构。为了解决这个问题，实现单倍型比较的高质量基因组资源至关重要。由于这些基因组的高度杂合性和重复含量，用于双核生物的短读基因组装配高度碎片化，并且缺乏单倍型特异性信息。在这里，我们介绍了小麦条纹锈菌Puccinia striiformis f的二倍体感知组件。 sp。 tritici基于使用FALCON-Unzip汇编程序的长时间读取。转录组测序数据集可用于推断高质量的基因模型并鉴定参与植物感染的毒力基因，称为效应子。这代表最完整的Puccinia striiformis f。 sp。迄今为止的小麦基因组组装（83？Mb，156个重叠群，N_（50）为1.5？Mb），并提供了超过92％的基因组的分阶段单倍型信息。相块的比较显示了超过6％的高单倍型多样性。所有基因中超过25％的基因缺少清晰的等位基因。当我们调查可能促进毒力快速进化的基因组特征时，我们发现候选效应基因与在担子菌中常见的保守基因在空间上相关。然而，与等位基因候选效应子相比，缺少等位基因对应物的候选效应子与保守基因的距离更远，并且在条纹假单胞菌物种复合体和丘疹内更不可能在进化上保守。总而言之，这种单倍型分步装配使我们能够发现原先隐藏在折叠和破碎的基因组装配中的双核植物致病真菌的新基因组特征。重要信息真核微生物基因组的当前表示是单倍体，隐藏了二倍体和多倍体生命形式固有的基因组多样性。这种隐藏的多样性有助于有机体的进化潜力和适应压力条件的能力。然而，在全基因组水平上提供单倍型特异性信息是一项挑战。在这里，我们利用长期阅读的DNA测序技术和量身定制的组装算法来解开双核病原性小麦锈病真菌的两个单倍体基因组。这两个基因组显示出高水平的核苷酸和结构变异，这导致等位基因变异和缺少等位基因对应物的基因的存在。非等位基因候选效应基因可能编码重要的致病性因子，显示出独特的基因组定位模式，与那些等位基因对相比，其进化保守性更低。自上次减数分裂以来，这种基因组多样性可以促进宿主的快速适应和/或与测序分离株的年龄有关。

著录项

相似文献

  • 外文文献
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号