Mind the gap; seven reasons to close fragmented genome assemblies

BPHJ Thomma, MF Seidl, X Shi-Kunne… - Fungal Genetics and …, 2016 - Elsevier
Like other domains of life, research into the biology of filamentous microbes has greatly
benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) …

Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen

L Faino, MF Seidl, X Shi-Kunne, M Pauper… - Genome …, 2016 - genome.cshlp.org
Genomic plasticity enables adaptation to changing environments, which is especially relevant
for pathogens that engage in “arms races” with their hosts. In many pathogens, genes …

The Genome of the Saprophytic Fungus Verticillium tricorpus Reveals a Complex Effector Repertoire Resembling That of Its Pathogenic Relatives

MF Seidl, L Faino, X Shi-Kunne… - Molecular Plant …, 2015 - Am Phytopath Society
Vascular wilts caused by Verticillium spp. are destructive plant diseases affecting hundreds
of hosts. Only a few Verticillium spp. are causal agents of vascular wilt diseases, of which V. …

Verticillium dahliae LysM effectors differentially contribute to virulence on plant hosts

A Kombrink, H Rovenich, X ShiKunne… - Molecular plant …, 2017 - Wiley Online Library
Chitin‐binding lysin motif (LysM) effectors contribute to the virulence of various plant‐pathogenic
fungi that are causal agents of foliar diseases. Here, we report the LysM effectors of the …

Molecular characterization reveals no functional evidence for naturally occurring cross‐kingdom RNA interference in the early stages of Botrytis cinerea–tomato …

…, T Bosman, G Puccetti, X ShiKunne… - Molecular Plant …, 2023 - Wiley Online Library
Plant immune responses are triggered during the interaction with pathogens. The fungus
Botrytis cinerea has previously been reported to use small RNAs (sRNAs) as effector …

Evolution within the fungal genus Verticillium is characterized by chromosomal rearrangement and gene loss

X ShiKunne, L Faino… - Environmental …, 2018 - Wiley Online Library
The fungal genus Verticillium contains ten species, some of which are notorious plant
pathogens causing vascular wilt diseases in host plants, while others are known as saprophytes …

Dynamics in Secondary Metabolite Gene Clusters in Otherwise Highly Syntenic and Stable Genomes in the Fungal Genus Botrytis

…, MBF Steentjes, JC Slot, X Shi-Kunne… - Genome biology and …, 2020 - academic.oup.com
Fungi of the genus Botrytis infect >1,400 plant species and cause losses in many crops.
Besides the broad host range pathogen Botrytis cinerea, most other species are restricted to a …

Dynamic virulence‐related regions of the plant pathogenic fungus Verticillium dahliae display enhanced sequence conservation

JRL Depotter, X ShiKunne, H Missonnier… - Molecular …, 2019 - Wiley Online Library
… ; Shi-Kunne et al., 2018), except for V. isaacii strain PD660 that was annotated with the
Maker2 pipeline in this study according to Shi-Kunne et al. (2018) and Holt and Yandell (2011). …

The Genome of the Fungal Pathogen Verticillium dahliae Reveals Extensive Bacterial to Fungal Gene Transfer

X Shi-Kunne, M van Kooten… - Genome biology and …, 2019 - academic.oup.com
Horizontal gene transfer (HGT) involves the transmission of genetic material between distinct
evolutionary lineages and can be an important source of biological innovation. Reports of …

[HTML][HTML] Analysis of plant cell death-inducing proteins of the necrotrophic fungal pathogens Botrytis squamosa and Botrytis elliptica

…, S Boeren, JAL van Kan, X Shi-Kunne - Frontiers in Plant …, 2022 - frontiersin.org
Fungal plant pathogens secrete proteins that manipulate the host in order to facilitate colonization.
Necrotrophs have evolved specialized proteins that actively induce plant cell death by …