Comparative Analysis of Host-Associated Variation in Phytophthora cactorum.
Comparative Analysis of Host-Associated Variation in Phytophthora cactorum.
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DOI：
10.3389/fmicb.2021.679936
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发表时间：
2021
影响因子：
5.2
通讯作者：
Harrison RJ
中科院分区：
文献类型：
--
作者：
Nellist CF;Armitage AD;Bates HJ;Sobczyk MK;Luberti M;Lewis LA;Harrison RJ
恶疫霉（Phytophthora cactorum）通常被描述为一种多面手病原体，其分离物在一系列植物物种中引起疾病。它是栽培草莓中两种病害的病原体，即冠腐病（CR;导致整个植株倒塌）和革腐病（LR;影响果实）。在栽培苹果中，恶腐霉引起接穗（颈腐）和砧木（冠腐）上的环剥树皮腐烂，以及细根系的坏死（根腐）和果实腐烂。我们通过对18个分离株的比较基因组分析，研究了恶疫霉内宿主专化的证据。全基因组系统发育分析为P. cactorum内的离散谱系提供了基因组支持，草莓CR和苹果感染分离株的非重组分支得到了很好的支持，这些分离株专门用于草莓冠和苹果组织。草莓CR的分离物在全球范围内遗传相似，而苹果感染分离物的多样性更大。我们试图确定宿主专化的遗传基础，证明在P. cactorum寄生发生中效应互补物的获得和损失，代表宿主边界的假定决定因素。转录组学分析强调，那些被发现是特定于一个单一的主机或扩大在草莓谱系中的效应是其中最高度表达的草莓感染过程中，并提供了更广泛的洞察到草莓感染过程中活跃的关键效应。在其他Phytophthoras中具有同源物的许多效应子被表征为无毒基因，但在我们的测试分离株中不表达。我们的研究结果突出了几个RxLR含有效应，值得进一步调查，以确定它们是否确实是草莓和苹果的毒力因子和宿主特异性决定因素。此外，需要额外的工作来确定这些效应子是否是未来抗性育种工作的合适目标。
Phytophthora cactorum is often described as a generalist pathogen, with isolates causing disease in a range of plant species. It is the causative agent of two diseases in the cultivated strawberry, crown rot (CR; causing whole plant collapse) and leather rot (LR; affecting the fruit). In the cultivated apple, P. cactorum causes girdling bark rots on the scion (collar rot) and rootstock (crown rot), as well as necrosis of the fine root system (root rot) and fruit rots. We investigated evidence for host specialisation within P. cactorum through comparative genomic analysis of 18 isolates. Whole genome phylogenetic analysis provided genomic support for discrete lineages within P. cactorum, with well-supported non-recombining clades for strawberry CR and apple infecting isolates specialised to strawberry crowns and apple tissue. Isolates of strawberry CR are genetically similar globally, while there is more diversity in apple-infecting isolates. We sought to identify the genetic basis of host specialisation, demonstrating gain and loss of effector complements within the P. cactorum phylogeny, representing putative determinants of host boundaries. Transcriptomic analysis highlighted that those effectors found to be specific to a single host or expanded in the strawberry lineage are amongst those most highly expressed during infection of strawberry and give a wider insight into the key effectors active during strawberry infection. Many effectors that had homologues in other Phytophthoras that have been characterised as avirulence genes were present but not expressed in our tested isolate. Our results highlight several RxLR-containing effectors that warrant further investigation to determine whether they are indeed virulence factors and host-specificity determinants for strawberry and apple. Furthermore, additional work is required to determine whether these effectors are suitable targets to focus attention on for future resistance breeding efforts.
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影响因子：
12.3
作者：
Chen H;Shu H;Wang L;Zhang F;Li X;Ochola SO;Mao F;Ma H;Ye W;Gu T;Jiang L;Wu Y;Wang Y;Kamoun S;Dong S
通讯作者：
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影响因子：
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通讯作者：
Vetukuri RR
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
--
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T