avirulence

Hulin, Michelle T., Armitage, Andrew D. ORCID: 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: 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:https://doi.org/10.1111/nph.15182)

bacterial canker

Hulin, Michelle T., Armitage, Andrew D. ORCID: 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: 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:https://doi.org/10.1111/nph.15182)

biofuels

Vega-Estévez, Samuel, Armitage, Andrew ORCID: 0000-0002-0610-763X , Bates, Helen J., Harrison, Richard J. and Buscaino, Alessia ORCID: 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:https://doi.org/10.1128/mBio.01871-21)

Colletotrichum gloeosporiodes

Armitage, Andrew D. ORCID: 0000-0002-0610-763X , Nellist, Charlotte F. ORCID: 0000-0002-7453-3710 , Bates, Helen J. ORCID: 0000-0002-7978-9213 , Zhang, Liqing, Zou, Xiaohua, Gao, Qing-Hua, Harrison, Richard J. ORCID: 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:https://doi.org/10.1128/MRA.01598-19)

comparative genomics

Hulin, Michelle T., Armitage, Andrew D. ORCID: 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: 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:https://doi.org/10.1111/nph.15182)

Crown rot

Armitage, Andrew D. ORCID: 0000-0002-0610-763X , Nellist, Charlotte F. ORCID: 0000-0002-7453-3710 , Bates, Helen J. ORCID: 0000-0002-7978-9213 , Zhang, Liqing, Zou, Xiaohua, Gao, Qing-Hua, Harrison, Richard J. ORCID: 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:https://doi.org/10.1128/MRA.01598-19)

CTG clade yeast

Vega-Estévez, Samuel, Armitage, Andrew ORCID: 0000-0002-0610-763X , Bates, Helen J., Harrison, Richard J. and Buscaino, Alessia ORCID: 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:https://doi.org/10.1128/mBio.01871-21)

effector genes

Armitage, Andrew D. ORCID: 0000-0002-0610-763X , Taylor, Andrew, Sobczyk, Maria K., Baxter, Laura ORCID: 0000-0003-3287-7547 , Greenfield, Bethany P. J., Bates, Helen J., Wilson, Fiona, Jackson, Alison C., Ott, Sascha, Harrison, Richard J. ORCID: 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:https://doi.org/10.1038/s41598-018-30335-7)

formae speciales

Jenkins, Sascha, Taylor, Andrew, Jackson, Alison C., Armitage, Andrew D. ORCID: 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:https://doi.org/10.3389/fmicb.2021.593140)

Fragaria

Armitage, Andrew D. ORCID: 0000-0002-0610-763X , Nellist, Charlotte F. ORCID: 0000-0002-7453-3710 , Bates, Helen J. ORCID: 0000-0002-7978-9213 , Zhang, Liqing, Zou, Xiaohua, Gao, Qing-Hua, Harrison, Richard J. ORCID: 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:https://doi.org/10.1128/MRA.01598-19)

Fusarium basal rot

Armitage, Andrew D. ORCID: 0000-0002-0610-763X , Taylor, Andrew, Sobczyk, Maria K., Baxter, Laura ORCID: 0000-0003-3287-7547 , Greenfield, Bethany P. J., Bates, Helen J., Wilson, Fiona, Jackson, Alison C., Ott, Sascha, Harrison, Richard J. ORCID: 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:https://doi.org/10.1038/s41598-018-30335-7)

Fusarium oxysporum f. sp. cepae

Armitage, Andrew D. ORCID: 0000-0002-0610-763X , Taylor, Andrew, Sobczyk, Maria K., Baxter, Laura ORCID: 0000-0003-3287-7547 , Greenfield, Bethany P. J., Bates, Helen J., Wilson, Fiona, Jackson, Alison C., Ott, Sascha, Harrison, Richard J. ORCID: 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:https://doi.org/10.1038/s41598-018-30335-7)

Fusarium oxysporum f. sp. pisi

Jenkins, Sascha, Taylor, Andrew, Jackson, Alison C., Armitage, Andrew D. ORCID: 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:https://doi.org/10.3389/fmicb.2021.593140)

Fusarium wilt

Jenkins, Sascha, Taylor, Andrew, Jackson, Alison C., Armitage, Andrew D. ORCID: 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:https://doi.org/10.3389/fmicb.2021.593140)

gene expression

Jenkins, Sascha, Taylor, Andrew, Jackson, Alison C., Armitage, Andrew D. ORCID: 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:https://doi.org/10.3389/fmicb.2021.593140)

Genome

Armitage, Andrew D. ORCID: 0000-0002-0610-763X , Nellist, Charlotte F. ORCID: 0000-0002-7453-3710 , Bates, Helen J. ORCID: 0000-0002-7978-9213 , Zhang, Liqing, Zou, Xiaohua, Gao, Qing-Hua, Harrison, Richard J. ORCID: 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:https://doi.org/10.1128/MRA.01598-19)

genome plasticity

Vega-Estévez, Samuel, Armitage, Andrew ORCID: 0000-0002-0610-763X , Bates, Helen J., Harrison, Richard J. and Buscaino, Alessia ORCID: 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:https://doi.org/10.1128/mBio.01871-21)

genomic instability

Vega-Estévez, Samuel, Armitage, Andrew ORCID: 0000-0002-0610-763X , Bates, Helen J., Harrison, Richard J. and Buscaino, Alessia ORCID: 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:https://doi.org/10.1128/mBio.01871-21)

Gibberella

Armitage, Andrew D. ORCID: 0000-0002-0610-763X , Nellist, Charlotte F. ORCID: 0000-0002-7453-3710 , Bates, Helen J. ORCID: 0000-0002-7978-9213 , Zhang, Liqing, Zou, Xiaohua, Gao, Qing-Hua, Harrison, Richard J. ORCID: 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:https://doi.org/10.1128/MRA.01598-19)

host specialization

Hulin, Michelle T., Armitage, Andrew D. ORCID: 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: 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:https://doi.org/10.1111/nph.15182)

host–microbe interactions

Adams, Thomas M., Armitage, Andrew D. ORCID: 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:https://doi.org/10.3389/fmicb.2020.00490)

nanopore sequencing

Adams, Thomas M., Armitage, Andrew D. ORCID: 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:https://doi.org/10.3389/fmicb.2020.00490)

onion

Armitage, Andrew D. ORCID: 0000-0002-0610-763X , Taylor, Andrew, Sobczyk, Maria K., Baxter, Laura ORCID: 0000-0003-3287-7547 , Greenfield, Bethany P. J., Bates, Helen J., Wilson, Fiona, Jackson, Alison C., Ott, Sascha, Harrison, Richard J. ORCID: 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:https://doi.org/10.1038/s41598-018-30335-7)

oomycete

Adams, Thomas M., Armitage, Andrew D. ORCID: 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:https://doi.org/10.3389/fmicb.2020.00490)

pathogenicity

Armitage, Andrew D. ORCID: 0000-0002-0610-763X , Taylor, Andrew, Sobczyk, Maria K., Baxter, Laura ORCID: 0000-0003-3287-7547 , Greenfield, Bethany P. J., Bates, Helen J., Wilson, Fiona, Jackson, Alison C., Ott, Sascha, Harrison, Richard J. ORCID: 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:https://doi.org/10.1038/s41598-018-30335-7)

Pea

Jenkins, Sascha, Taylor, Andrew, Jackson, Alison C., Armitage, Andrew D. ORCID: 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:https://doi.org/10.3389/fmicb.2021.593140)

population resequencing

Adams, Thomas M., Armitage, Andrew D. ORCID: 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:https://doi.org/10.3389/fmicb.2020.00490)

prediction

Hulin, Michelle T., Armitage, Andrew D. ORCID: 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: 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:https://doi.org/10.1111/nph.15182)

Pseudomonas

Hulin, Michelle T., Armitage, Andrew D. ORCID: 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: 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:https://doi.org/10.1111/nph.15182)

qPCR

Jenkins, Sascha, Taylor, Andrew, Jackson, Alison C., Armitage, Andrew D. ORCID: 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:https://doi.org/10.3389/fmicb.2021.593140)

race

Jenkins, Sascha, Taylor, Andrew, Jackson, Alison C., Armitage, Andrew D. ORCID: 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:https://doi.org/10.3389/fmicb.2021.593140)

race structure

Adams, Thomas M., Armitage, Andrew D. ORCID: 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:https://doi.org/10.3389/fmicb.2020.00490)

red core

Adams, Thomas M., Armitage, Andrew D. ORCID: 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:https://doi.org/10.3389/fmicb.2020.00490)

RNA-Seq

Adams, Thomas M., Armitage, Andrew D. ORCID: 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:https://doi.org/10.3389/fmicb.2020.00490)

Secreted In Xylem

Jenkins, Sascha, Taylor, Andrew, Jackson, Alison C., Armitage, Andrew D. ORCID: 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:https://doi.org/10.3389/fmicb.2021.593140)

secreted in xylem (SIX)

Armitage, Andrew D. ORCID: 0000-0002-0610-763X , Taylor, Andrew, Sobczyk, Maria K., Baxter, Laura ORCID: 0000-0003-3287-7547 , Greenfield, Bethany P. J., Bates, Helen J., Wilson, Fiona, Jackson, Alison C., Ott, Sascha, Harrison, Richard J. ORCID: 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:https://doi.org/10.1038/s41598-018-30335-7)

toxins

Hulin, Michelle T., Armitage, Andrew D. ORCID: 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: 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:https://doi.org/10.1111/nph.15182)

transposons

Vega-Estévez, Samuel, Armitage, Andrew ORCID: 0000-0002-0610-763X , Bates, Helen J., Harrison, Richard J. and Buscaino, Alessia ORCID: 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:https://doi.org/10.1128/mBio.01871-21)

type III effectors

Hulin, Michelle T., Armitage, Andrew D. ORCID: 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: 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:https://doi.org/10.1111/nph.15182)