African yam bean, Colletotrichum

Ogunsanya, Olaide, Afolabi, Clement, Colgan, Richard ORCID: https://orcid.org/0000-0002-0653-5845, Armitage, Andrew ORCID: https://orcid.org/0000-0002-0610-763X, Thompson, Elinor ORCID: https://orcid.org/0000-0002-6434-9290, Ortega-beltran, Alejandro and Abberton, Michael (2023) Polyphasic identification of causative pathogens responsible for foliar and pod diseases of African Yam Bean in Nigeria. In: Microbiology Society Annual Conference 2023, 17th - 20th April 2023, Birmingham International Convention Centre. (Unpublished)

Alternaria mali, Dothideomycete, fungal barcoding, pathotype, section, species complex

Armitage, Andrew D. ORCID: https://orcid.org/0000-0002-0610-763X, Barbara, Dez J., Harrison, Richard J., Lane, Charles R., Sreenivasaprasad, Surapareddy, Woodhall, James W. and Clarkson, John P. (2015) Discrete lineages within Alternaria alternata species group: identification using new highly variable loci and support from morphological characters. Fungal Biology, 119 (11). pp. 994-1006. ISSN 1878-6146 (doi:10.1016/j.funbio.2015.06.012)

Alternarialeafblotch,Alternariafruitspot,Alternariaarborescensspeciescomplex, Alternaria alternata, Alternaria section Alternaria, Small-spored Alternaria, Plant pathology, Pathogenic fungi, Molecular biology, Pathogenicity of plant pathogens

Fontaine, Kévin, Fourrier-Jeandel, Céline, Armitage, Andrew ORCID: https://orcid.org/0000-0002-0610-763X, Boutigny, Anne-Laure, Crépet, Manuela, Caffier, Valérie, Gnide, Dossi Carine, Shiller, Jason, Le Cam, Bruno, Giraud, Michel, Ioos, Renaud and Aguayo, Jaime (2021) Identification and pathogenicity of Alternaria species associated with leaf blotch disease and premature defoliation in French apple orchards. PeerJ, 9:e12496. ISSN 2376-5992 (Print), 2167-8359 (Online) (doi:10.7717/peerj.12496)

Bayoud disease; Fusarium oxysporum; diversity; mitogenome; date palm

Khayi, Slimane ORCID: https://orcid.org/0000-0001-8033-2117, Armitage, Andrew ORCID: https://orcid.org/0000-0002-0610-763X, El Guilli, Mohammed, Meftah Kadmiri, Issam ORCID: https://orcid.org/0000-0003-1067-1652, Lahlali, Rachid, Fokar, Mohamed and Mentag, Rachid ORCID: https://orcid.org/0000-0002-2040-637X (2021) Complete mitochondrial genome and phylogeny of the causal agent of Bayoud disease on date palm, Fusarium oxysporum f. sp. albedinis. Mitochondrial DNA Part B, 6 (10). pp. 3059-3061. ISSN 2380-2359 (Print), 2380-2359 (Online) (doi:10.1080/23802359.2021.1978894)

BioProject PRJNA935342, SRA accessions SRR23476212 and SRR23476213, colletotrichum siamense, colletotrichum truncatum

Ogunsanya, Olaide M., Armitage, Andrew D. ORCID: https://orcid.org/0000-0002-0610-763X, Afolabi, Clement G., Oyatomi, Olaniyi, Thompson, Elinor P. ORCID: https://orcid.org/0000-0002-6434-9290, Ortega-Beltran, Alejandro and Abberton, Michael (2024) Whole genome sequences of Colletotrichum siamense and Colletotrichum truncatum, causal agents of pod and foliar diseases on African yam bean. Microbiology Resource Announcements. ISSN 2576-098X (Online) (doi:10.1128/mra.00722-24)

CDC, host-specific toxin, mating type, Dothideomycetes, Alternaria mali, Alternaria gaisen, nanopore

Armitage, Andrew ORCID: https://orcid.org/0000-0002-0610-763X, Cockerton, Helen M., Sreenivasaprasad, Surapareddy, Woodhall, James, Lane, Charles R., Harrison, Richard J. and Clarkson, John P. (2020) Genomics evolutionary history and diagnostics of the Alternaria alternata species group including apple and Asian pear pathotypes. Frontiers in Microbiology, 10:3124. ISSN 1664-302X (Online) (doi:10.3389/fmicb.2019.03124)

Cassava, CBSD, PAL1, resistance, induction

Kavil, Siji, Otti, Gerald, Armitage, Andrew ORCID: https://orcid.org/0000-0002-0610-763X, Bouvaine, Sophie ORCID: https://orcid.org/0000-0002-0788-3243 and Maruthi, M.N. ORCID: https://orcid.org/0000-0002-8060-866X (2021) PAL1 gene of the phenylpropanoid pathway increases resistance to the Cassava brown streak virus in cassava. Virology Journal, 18:184. ISSN 1743-422X (Print), 1743-422X (Online) (doi:10.1186/s12985-021-01649-2)

Colletrotrichum; African yam bean; anthracnose; integrated management; orphan crop; polyphasic approach

Ogunsanya, Olaide Mary, Adebisi, Moruf Ayodele, Popoola, Akinola Rasheed, Afolabi, Clement Gboyega, Oyatomi, Olaniyi, Colgan, Richard, Armitage, Andrew ORCID: https://orcid.org/0000-0002-0610-763X, Thompson, Elinor ORCID: https://orcid.org/0000-0002-6434-9290, Abberton, Michael and Ortega-Beltran, Alejandro (2024) Morphological, pathological and phylogenetic analyses identify a diverse group of Colletotrichum spp. causing leaf, pod, and flower diseases on the orphan legume African yam bean. Plant Pathology. pp. 1-15. ISSN 0032-0862 (Print), 1365-3059 (Online) (doi:10.1111/ppa.13995)

Crown rot; Colletotrichum gloeosporiodes; Genome; Gibberella; Fragaria

Armitage, Andrew D. ORCID: https://orcid.org/0000-0002-0610-763X, Nellist, Charlotte F. ORCID: https://orcid.org/0000-0002-7453-3710, Bates, Helen J. ORCID: https://orcid.org/0000-0002-7978-9213, Zhang, Liqing, Zou, Xiaohua, Gao, Qing-Hua, Harrison, Richard J. ORCID: https://orcid.org/0000-0002-3307-3519 and Rokas, Antonis (2020) Draft genome sequence of the strawberry anthracnose pathogen colletotrichum fructicola. Microbiology Resource Announcements, 9 (12):e01598-19. ISSN 2576-098X (Online) (doi:10.1128/MRA.01598-19)

Fusarium oxysporum f. sp. lactucae, lettuce, secreted in xylem, effector, accessory genome, helitron, SIX genes, plant pathogen

Bates, Helen J., Pike, Jamie, Price, R. Jordan, Jenkins, Sascha, Connell, John, Legg, Andrew, Armitage, Andrew ORCID: https://orcid.org/0000-0002-0610-763X, Harrison, Richard J. and Clarkson, John P. (2024) Comparative genomics and transcriptomics reveal differences in effector complement and expression between races of Fusarium oxysporum f.sp. lactucae. Frontiers in Plant Science, 15:1415534. ISSN 1664-462X (Online) (doi:10.3389/fpls.2024.1415534)

Fusarium oxysporum f. sp. narcissi, Narcissus, daffodil, basal rot, pathogenicity, secreted in Xylem

Taylor, Andrew, Armitage, Andrew D. ORCID: https://orcid.org/0000-0002-0610-763X, Handy, Claire, Jackson, Alison C., Hulin, Michelle T., Harrison, Richard J. and Clarkson, John P. (2019) Basal rot of Narcissus: understanding pathogenicity in Fusarium oxysporum f. sp. narcissi. Frontiers in Microbiology, 10:2905. ISSN 1664-302X (Online) (doi:10.3389/fmicb.2019.02905)

Fusarium oxysporum f. sp. pisi, Pea, Fusarium wilt, formae speciales, race, Secreted In Xylem, gene expression, qPCR

Jenkins, Sascha, Taylor, Andrew, Jackson, Alison C., Armitage, Andrew D. ORCID: https://orcid.org/0000-0002-0610-763X, Bates, Helen J., Mead, Andrew, Harrison, Richard J. and Clarkson, John P. (2021) Identification and expression of "Secreted In Xylem" pathogenicity genes in fusarium oxysporum f. sp. pisi. Frontiers in Microbiology, 12:593140. ISSN 1664-302X (Online) (doi:10.3389/fmicb.2021.593140)

Phytophthora; Oomycete; plant-pathogen; evolution; genomics; effector

Kronmiller, Brent, Feau, Nicolas, Tabima, Javier, Ali, Shahin, Armitage, Andrew ORCID: https://orcid.org/0000-0002-0610-763X, Arrendondo, Felipe, Bailey, Bryan, Bollmann, Stephanie, Dale, Angela, Harrison, Richard, Hrywkiw, Kelly, Kasuga, Takao, McDougal, Rebecca, Nellist, Charlotte, Panda, Preeti, Tripathy, Sucheta, Williams, Nari, Ye, Wenwu, Wang, Yuanchao, Hamelin, Richard and Grunwald, Niklaus (2022) Comparative genomic analysis of 31 Phytophthora genomes reveal genome plasticity and horizontal gene transfer. Molecular Plant Microbe Interactions, 36 (1). pp. 26-46. ISSN 0894-0282 (Print), 1943-7706 (Online) (doi:10.1094/MPMI-06-22-0133-R)

QTL, Macronutrients, Symbiont, Network, Trade-off, Solidity, Rhizotron, Length distribution, AMF, Image analysis

Cockerton, Helen Maria ORCID: https://orcid.org/0000-0002-7375-1804, Li, Bo ORCID: https://orcid.org/0000-0003-0077-4383, Stavridou, Eleftheria, Johnson, Abigail, Karlström, Amanda, Armitage, Andrew Douglas ORCID: https://orcid.org/0000-0002-0610-763X, Martinez-Crucis, Ana, Galiano-Arjona, Lorena, Harrison, Nicola, Barber-Pérez, Nuria, Cobo-Medina, Magdalena and Harrison, Richard Jonathan ORCID: https://orcid.org/0000-0002-3307-3519 (2020) Genetic and phenotypic associations between root architecture, arbuscular mycorrhizal fungi colonisation and low phosphate tolerance in strawberry (Fragaria × ananassa). BMC Plant Biology, 20:154. ISSN 1471-2229 (Online) (doi:10.1186/s12870-020-02347-x)

apple black spot, apple scab, ascospore production, host mixture, super-race

Passey, Thomas A. J. ORCID: https://orcid.org/0000-0002-5678-2481, Armitage, Andrew D. ORCID: https://orcid.org/0000-0002-0610-763X, Sobczyk, Maria K., Shaw, Michael W. ORCID: https://orcid.org/0000-0002-6993-048X and Xu, Xiangming ORCID: https://orcid.org/0000-0002-4567-7117 (2020) Genomic sequencing indicates non‐random mating of Venturia inaequalis in a mixed cultivar orchard. Plant Pathology, 69 (4). pp. 669-676. ISSN 0032-0862 (Print), 1365-3059 (Online) (doi:10.1111/ppa.13150)

apple canker, NGS

Gómez-Cortecero, Antonio, Armitage, Andrew D. ORCID: https://orcid.org/0000-0002-0610-763X and Harrison, Richard J. (2015) Draft genome sequence of a European isolate of the apple canker pathogen Neonectria ditissima. Genome Announcements, 3 (6):e01243-15. ISSN 2169-8287 (Online) (doi:10.1128/genomeA.01243-15)

apple scab, apple black spot, venturia inaequalis genome

Passey, Thomas A. J. ORCID: https://orcid.org/0000-0002-5678-2481, Armitage, Andrew D. ORCID: https://orcid.org/0000-0002-0610-763X and Xu, Xiangming (2018) Annotated draft genome sequence of the apple scab pathogen Venturia inaequalis. Microbiology Resource Announcements, 7 (12):e01062-18. ISSN 2576-098X (Online) (doi:10.1128/mra.01062-18)

avirulence, VCG, wilt, octopoid, effectors, NGS

Fan, Rong, Cockerton, Helen M., Armitage, Andrew D. ORCID: https://orcid.org/0000-0002-0610-763X, Bates, Helen, Cascant-Lopez, Emma, Antanaviciute, Laima, Xu, Xiangming, Hu, Xiaoping and Harrison, Richard J. ORCID: https://orcid.org/0000-0002-3307-3519 (2018) Vegetative compatibility groups partition variation in the virulence of Verticillium dahliae on strawberry. PLOS ONE, 13 (2):e0191824. ISSN 1932-6203 (Online) (doi:10.1371/journal.pone.0191824)

avirulence, bacterial canker, comparative genomics, host specialization, prediction, Pseudomonas, toxins, type III effectors

Hulin, Michelle T., Armitage, Andrew D. ORCID: https://orcid.org/0000-0002-0610-763X, Vicente, Joana G., Holub, Eric B., Baxter, Laura, Bates, Helen J., Mansfield, John W., Jackson, Robert W. and Harrison, Richard J. ORCID: https://orcid.org/0000-0002-3307-3519 (2018) Comparative genomics of Pseudomonas syringae reveals convergent gene gain and loss associated with specialization onto cherry (Prunus avium). New Phytologist, 219 (2). pp. 672-696. ISSN 0028-646X (Print), 1469-8137 (Online) (doi:10.1111/nph.15182)

biofuels, CTG clade yeast, genome plasticity, genomic instability, transposons

Vega-Estévez, Samuel, Armitage, Andrew ORCID: https://orcid.org/0000-0002-0610-763X, Bates, Helen J., Harrison, Richard J. and Buscaino, Alessia ORCID: https://orcid.org/0000-0002-1704-3168 (2021) The genome of the CTG(Ser1) yeast Scheffersomyces stipitis is plastic. mBio, 12 (5). ISSN 2150-7511 (Print), 2150-7511 (Online) (doi:10.1128/mBio.01871-21)

biotroph; Fragaria; horticulture; mycology; Rubus; Sphaerotheca macularis

Heaven, Thomas, Cockerton, Helen M., Xu, Xiangming, Goddard, Mat and Armitage, Andrew D. ORCID: https://orcid.org/0000-0002-0610-763X (2023) A genomic resource for the strawberry powdery mildew pathogen Podosphaera aphanis. Phytopathology, 113 (2). pp. 355-359. ISSN 0031-949X (Print), 1943-7684 (Online) (doi:10.1094/PHYTO-03-22-0091-A)

crown rot, oomycete, phylogenomics, effectors, cryptic species

Armitage, Andrew ORCID: https://orcid.org/0000-0002-0610-763X, Nellist, Charlotte, Bates, Helen, Sobczyk, Maria, Luberti, Matteo, Lewis, Laura and Harrison, Richard (2021) Comparative analysis of host-associated variation in phytophthora cactorum. Frontiers in Microbiology, 12:679936. ISSN 1664-302X (Print), 1664-302X (Online) (doi:10.3389/fmicb.2021.679936)

disease resistance, Fragaria x ananassa, wilt, NDVI, NBS, breeding

Cockerton, Helen M., Li, Bo, Vickerstaff, Robert J., Eyre, Catherine A., Sargent, Daniel J., Armitage, Andrew D. ORCID: https://orcid.org/0000-0002-0610-763X, Marina-Montes, Cesar, Garcia-Cruz, Ana, Passey, Andrew J., Simpson, David W. and Harrison, Richard Jonathan (2019) Identifying Verticillium dahliae resistance in strawberry through disease screening of multiple populations and image based phenotyping. Frontiers in Plant Science, 10:924. ISSN 1664-462X (Online) (doi:10.3389/fpls.2019.00924)

effector; genome; phylogenomics; Phoenix dactylifera; pandemic; accessory chromosome; lineage specific

Khayi, Slimane, Armitage, Andrew ORCID: https://orcid.org/0000-0002-0610-763X, Gaboun, Fatima, Meftah-kadmiri, Issam, Lahlali, Rachid, Fokar, Mohamed and Mentag, Rachid (2023) Chromosome-scale assembly uncovers genomic compartmentation of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease in date palm. Frontiers in Microbiology, 14:1268051. pp. 1-14. ISSN 1664-302X (Online) (doi:10.3389/fmicb.2023.1268051)

fragaria, strawberry, diploid, polyploid, CRISPR/Cas9, phytoene desaturase

Wilson, Fiona M. ORCID: https://orcid.org/0000-0002-2073-7400, Harrison, Kate, Armitage, Andrew D. ORCID: https://orcid.org/0000-0002-0610-763X, Simkin, Andrew J. and Harrison, Richard J. (2019) CRISPR/Cas9-mediated mutagenesis of phytoene desaturase in diploid and octoploid strawberry. Plant Methods, 15:45. ISSN 1746-4811 (doi:10.1186/s13007-019-0428-6)

metabolites; entomopathogenic fungi; biopesticides; metabolomics; HPLC

Mills, Deanna, Ogunsanya, Olaide, Armitage, Andrew ORCID: https://orcid.org/0000-0002-0610-763X, Stevenson, Philip ORCID: https://orcid.org/0000-0002-0736-3619 and Harte, Steven ORCID: https://orcid.org/0000-0001-9628-7912 (2023) Mining the untapped chemical potential of entomopathogenic fungi. In: LIDo End of Rotation 1 Presentation Day, 17th Feb, 2023, Medical Sciences and Anatomy building, UCL.

nectria, basal rot, disease complex, SIX2, secreted in xylem

Armitage, Andrew D. ORCID: https://orcid.org/0000-0002-0610-763X, Taylor, Andrew, Hulin, Michelle T., Jackson, Alison C., Harrison, Richard J. and Clarkson, John P. (2019) Draft genome sequence of an onion basal rot isolate of Fusarium proliferatum. Microbiology Resource Announcements, 8 (1):e01385-18. ISSN 2576-098X (Online) (doi:10.1128/MRA.01385-18)

oomycete, effector, avirulence, fragaria x ananassa, RxLR, crinkler

Armitage, Andrew D. ORCID: https://orcid.org/0000-0002-0610-763X, Lysøe, Erik, Nellist, Charlotte F. ORCID: https://orcid.org/0000-0002-7453-3710, Lewis, Laura A., Cano, Liliana M., Harrison, Richard J. ORCID: https://orcid.org/0000-0002-3307-3519 and Brurberg, May B. (2018) Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum. PLOS ONE, 13 (10):e0202305. ISSN 1932-6203 (Online) (doi:10.1371/journal.pone.0202305)

quantitative trait loci (QTLs); plant pathogen; biotroph; linkage map; genotyping by sequencing; single nucleotide polymorphism (SNP); genome; dose response; polygenic; tebuconazole

Heaven, Thomas, Armitage, Andrew ORCID: https://orcid.org/0000-0002-0610-763X, Xu, Xiangming, Goddard, Matthew and Cockerton, Helen (2023) Dose-dependent genetic resistance to Azole fungicides found in the apple scab pathogen. Journal of Fungi, 9 (12):1136. pp. 1-18. ISSN 2309-608X (Online) (doi:10.3390/jof9121136)

red core, oomycete, RNA-Seq, host–microbe interactions, nanopore sequencing, population resequencing, race structure

Adams, Thomas M., Armitage, Andrew D. ORCID: https://orcid.org/0000-0002-0610-763X, Sobczyk, Maria K., Bates, Helen J., Tabima, Javier F., Kronmiller, Brent A., Tyler, Brett M., Grünwald, Niklaus J., Dunwell, Jim M., Nellist, Charlotte F. and Harrison, Richard J. (2020) Genomic investigation of the strawberry pathogen Phytophthora fragariae indicates pathogenicity is associated with transcriptional variation in three key races. Frontiers in Microbiology, 11:490. ISSN 1664-302X (Online) (doi:10.3389/fmicb.2020.00490)

secreted in xylem (SIX), onion, Fusarium oxysporum f. sp. cepae, effector genes, pathogenicity, Fusarium basal rot

Armitage, Andrew D. ORCID: https://orcid.org/0000-0002-0610-763X, Taylor, Andrew, Sobczyk, Maria K., Baxter, Laura ORCID: https://orcid.org/0000-0003-3287-7547, Greenfield, Bethany P. J., Bates, Helen J., Wilson, Fiona, Jackson, Alison C., Ott, Sascha, Harrison, Richard J. ORCID: https://orcid.org/0000-0002-3307-3519 and Clarkson, John P. (2018) Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae. Scientific Reports, 8:13530. ISSN 2045-2322 (Online) (doi:10.1038/s41598-018-30335-7)

yam; penicillium; dioscorea; post harvest; rot; PASET; Côte d'Ivoire

Kamara, Adjata, Camara, Brahima, Armitage, Andrew ORCID: https://orcid.org/0000-0002-0610-763X, Ogunsanya, Olaide, Gouannou, Vartinel and Koné, Daouda (2024) First report of penicillium sclerotigenum causing post-harvest rot of yam in Côte d'Ivoire. New Disease Reports, 50 (1):e12307. ISSN 2044-0588 (doi:10.1002/ndr2.12307)