John Jones
Current research interests
- Functional analysis of effectors of plant parasitic nematodes.
- Genomics of the potato cyst nematode Globodera pallida.
- Horizontal gene transfer in plant parasitic nematodes.
John leads the Institute's Cell and Molecular Sciences group, and has a joint appointment at the University of St Andrews.
John is part of the Dundee Effector Consortium.
Past research
- Work in our group is focused on identification and characterisation of secreted effector proteins of plant parasitic nematodes, with a particular focus on effectors that suppress host defences.
- Our work uses genomics tools to identify and characterise effectors. We have been involved in projects sequencing genomes and transcriptomes of a range of plant-parasitic nematodes.
- One unexpected finding that has emerged from this work is that genes important in the parasitic process seem to have been acquired by horizontal gene transfer, from bacteria or fungi, in all groups of plant parasitic nematodes studied to date.
- Current work is aimed at functional characterisation of proteins we suspect are important in generating a susceptible response or suppressing host defences in plants.
Bibliography
- Pokhare, S.S.; Habash, S.S; Jones, J.T.; Elashry, A.; Grundler, F.M.W. (2019) In vitro life cycle of Heterodera sacchari on pluronic gel., Nematology, 21, 573-579.
- Espada, M.; Eves-van den Akker, S.; Maier, T.; Vijaypalani, P.; Baum, T.J.; Mota, M.; Jones, J.T. (2018) STATAWAARS: A promoter motif associated with spatial expression in the major effector -producing tissues of the planparasitic nematode Bursaphelenchus xylophilus. ., BMC Genomics, 19, Article No. 553.
- Mei, Y.; Wright, K.M.; Haegeman, A.; Bauters, L.; Diaz-Granados, A.; Goverse, A.; Gheysen, G.; Jones, T.J.; Mantelin, S. (2018) The Globodera pallida SPRYSEC effector GpSPRY-414-2 that suppresses plant defenses targets a regulatory component of the dynamic microtubule network., Frontiers in Plant Science, 9, Article No. 1019.
- Eves-van den Akker, S.; Jones, J.T. (2018) Sex: not all that it’s cracked up to be?, PLoS Genetics, 14, Article No. e1007160.
- Wang, X.; Xue, B.: Dai, J.; Qin, X.: Liu, L.; Chi, Y.; Jones, J.T.; Li, H. (2018) A novel Meloidogyne incognita chorismate mutase effector suppresses plant immunity by manipulating the salicylic acid pathway and functions mainly during the early stages of nematode parasitism., Plant Pathology, 67, 1436-1448.
- Perry, R.N.; Moens, M.; Jones, J.T. (eds.) (2018) Cyst nematodes., Wallingford, CABI Publishing, 488pp.
- Jones, J.T.; Mitchum, M.G. (2018) Biology of effectors., In: Perry, R.N., Moens, M. & Jones, J.T. (eds.). Cyst Nematodes. CABI Publishing, Wallingford, Chapter 4, 74-88.
- Kikuchi, T.; Eves-van den Akker, S.; Jones, J.T. (2017) Genome evolution of plant-parasitic nematodes., Annual Review of Phytopathology, 55, 333-354.
- Mantelin, S.; Thorpe, P.; Jones, J.T. (2017) Translational biology of nematode effectors. Or, to put it another way, functional analysis of effectors - what's the point?, Nematology, 19, 251-261.
- Danchin, E.G.J.; Perfus-Barbeoch, L.; Rancurel, C.; Thorpe, P.; Da Rocha, M.; Bajew, S.; Neilson, R.; Sokolova, E.; Da Silva, C.; Guy, J.; Labadie, K.; Esmenjaud, D.; Helder, J.; Jones, J.T.; Eves-van den Akker, S. (2017) The transcriptomes of xiphinema index and longidorus elongatus suggest independent acquisition of some plant parasitism genes by horizontal gene transfer in early-branching nematodes., Genes, 8, Article No. 287.
- Eves-van den Akker, S.; Laetsch, D.R.; Thorpe, P.; Lilley, C.J.; Danchin, E.G.J.; Da Rocha, M.; Rancurel, C.; Holroyd, N.E.; Cotton, J.A.; Szitenberg, A.; Grenier, E.; Montarry, J.; Mimee, B.; Duceppe, M.O.; Boyes, I.; Marvin, J.M.C.; Jones, L.M.; Yusup, H.B.; Lafond-Lapalme, J.; Esquibet, M.; Sabeh, M.; Rott, M.; Overmars, H.; Finkers-Tomczak, A.; Smant, G.; Koutsovoulos, G.; Blok, V.; Mantelin, S.; Cock, P.J.A.; Phillips, W.; Henrissat, B.; Urwin, P.E.; Blaxter, M.; Jones, J.T. (2016) The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence., Genome Biology, 17, Article No. 124.
- Espada, M.; Jones, J.T.; Mota, M. (2016) Characterization of glutathione S-transferases from the pinewood nematode, Bursaphelenchus xylophilus., Nematology, 18, 697-709.
- Eves-van den Akker, S.; Lilley, C.J.; Hazijah, B.Y.; Jones, J.T.; Urwin, P.E. (2016) Functional C-terminally encoded plant peptide (CEP) hormone domains evolved de novo in the plant parasite Rotylenchulus reniformis., Molecular Plant Pathology, 17, 1265-1275.
- Tsai, I.J.; Tanaka, R.; Kanzaki, N.; Akiba, M.; Yokoi, T.; Espada, M.; Jones, J.T.; Kikuchi, T. (2016) Transcriptional and morphological changes in the transition from mycetophagous to phytophagous phase in the plant-parasitic nematode Bursaphelenchus xylophilus., Molecular Plant Pathology, 17, 77-83.
- Espada, M.; Silva, A.C.; Eves-van den Akker, S.; Cock, P.J.A.; Mota, M.; Jones, J.T. (2016) Identification and characterization of parasitism genes from the pinewood nematode Bursaphelenchus xylophilus reveals a multilayered detoxification strategy., Molecular Plant Pathology, 17, 286-295.
- Palomares-Rius, J.E.; Hedley, P.; Cock, P.J.A.; Morris, J.A.; Jones, J.T.; Blok, V.C. (2016) Gene expression changes in diapause or quiescent potato cyst nematode, Globodera pallida, eggs after hydration or exposure to tomato root diffusate., PeerJ, 4, Article No. e1654.
- Danchin, E.G.J.; Guzeeva, E.; Mantelin, S.; Berekpiki, A.; Jones, J.T. (2016) Horizontal gene transfer from bacteria has enabled the plant-parasitic nematode Globodera pallida to feed on plant-derived sucrose., Molecular Biology and Evolution, 33, 1571-1579.
- Eves-van den Akker, S.; Lilley, C.J.; Yusup, H.B.; Jones, J.T.; Urwin, P.E. (2016) Functional C-TERMINALLY ENCODED PEPTIDE (CEP) plant hormone domains evolved de novo in the plant parasite Rotylenchulus reniformis., Molecular Plant Pathology, 17, 1265-1275.
- Eves-van den Akker, S.; Lilley, C.J.; Reid, A.; Pickup, J.; Anderson, E.; Cock, P.J.A.; Blaxter, M.; Urwin, P.E.; Jones, J.T.; Blok, V.C. (2015) A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual., Molecular Ecology, 24, 5842-5851.
- Mei, Y.; Thorpe, P.; Guzha, A.; Haegeman, A.; Blok, V.C.; MacKenzie, K.; Gheysen, G.; Jones, J.T.; Mantelin, S. (2015) Only a small subset of the SPRY domain gene family in Globodera pallida is likely to encode effectors, two of which suppress host defences induced by the potato resistance gene Gpa2., Nematology, 17, 409-424.
- Mantelin, S.; Thorpe, P.; Jones, J.T. (2015) Suppression of plant defences by plant-parasitic nematodes. Chapter thirteen of "Plant Nematode Interactions - A View on Compatible Interrelationships"., Advances in Botanical Research, 73, 325-337.
- Sarkies, P.; Selkirk, M.E.; Jones, J.T.; Blok, V.C.; Boothby, T.; Goldstein, B.; Hanelt, B.; Ardila-Garcia, A.; Fast, N.M.; Schiffer, P.M.; Kraus, C.; Schierenberg, E.; Taylor, M.J.; Koutsovoulos, G.; Blaxter, M.L.; Miska, E.A. (2015) Ancient and novel small RNA pathways compensate for the loss of piRNAs in multiple independent nematode lineages., PLoS Biology, 13, Article No. e1002061.
- Bird, D.M.; Jones, J.T.; Opperman, C.H.; Kikuchi, T.; Danchin, E.G.J. (2015) Signatures of adaptation to plant parasitism in nematode genomes., Parasitology, 142, S71-S84.
- Eves-van den Akker, S.; Lilley, C.J.; Jones, J.T.; Urwin, P.E. (2015) Plant-parasitic nematode feeding tubes and plugs: new perspectives on function., Nematology, 17, 1-9.
- Eves-van den Akker, S.; Lilley, C.J.; Danchin, E.G.J.; Rancurel, C.; Cock, P.J.A.; Urwin, P.E.; Jones, J.T. (2014) The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes., Genome Biology and Evolution, 6, 2181-2194.
- Palomares-Rius, J.E.; Hirooka, Y.; Tsai, I.J.; Masuya, H.; Hino, A.; Kanzaki, N.; Jones, J.T.; Kikuchi, T. (2014) Distribution and evolution of glycoside hydrolase family 45 cellulases in nematodes and fungi., BMC Evolutionary Biology, 14, Article No. 69.
- van Den Akker, S.E.; Lilley, C.J.; Jones, J.T.; Urwin, P.E. (2014) Identification and characterisation of a hyper-variable apoplastic effector gene family of the potato cyst nematodes., PLoS Pathogens, 10, Article No. e1004391.
- Thorpe, P.; Mantelin, S.; Cock, P.J.A.; Blok, V.C.; Coke M.C.; van Den Akker, S.E.; Guzeeva, E.; Lilley, C.J.; Smant, G.; Reid, A.J.; Wright, K.M.; Urwin, P.E.; Jones, J.T. (2014) Genomic characterisation of the effector complement of the potato cyst nematode Globodera pallida., BMC Genomics, 15, Article No. 923.
- Eves-van den Akker, S.; Lilley, C.J.; Ault, J.R.; Ashcroft, A.E.; Jones, J.T.; Urwin, P.E. (2014) The feeding tube of cyst nematodes: characterisation of protein exclusion., PLoS ONE, 9, Article No. e87289.
- Cotton, J.A.; Lilley, C.J.; Jones, L.M.; Kikuchi, T.; Reid, A.J.; Thorpe, P.; Tsai, I.J.; Beasley, H.; Blok, V.C.; Cock, P.J.A.; Eves-van den Akker, S.; Holroyd, N.; Hunt, M.; Mantelin, S.; Naghra, H.; Pain, A.; Palomares-Rius, J.E.; Zarowiecki, M.; Berriman, M.; Jones, J.T.; Urwin, P.E. (2014) The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode., Genome Biology, 15, Article No. R43.
- Kikuchi, T.; Cock, P.J.A.; Helder, J.; Jones, J.T. (2014) Characterisation of the transcriptome of Aphelenchoides besseyi and identification of a GHF 45 cellulase., Nematology, 16, 99-107.
- Reid, A.J.; Jones, J.T. (2014) Bioinformatic analysis of expression data to identify effector candidates., In: Birch, P., Jones, J.T. & Bos, J.I.B. (eds.). Plant-Pathogen Interactions: Methods and Protocols. Methods in Molecular Biology, Volume 1127. Humana Press, New York, 2nd ed. Chapter 2, 17-27.
- Elling, A.A.; Jones, J.T. (2014) Functional characterization of nematode effectors in plants., In: Birch, P., Jones, J.T. & Bos, J.I.B. (eds.). Plant-Pathogen Interactions: Methods and Protocols. Methods in Molecular Biology, Volume 1127. Humana Press, New York, 2nd ed. Chapter 9, 113-124..
- Birch, P.; Jones, J.; Bos, J.I. (eds). (2014) Plant-pathogen interactions: methods and protocols., Methods in Molecular Biology, Volume 1127. 2nd edition, Humana Press, New York, 306pp.
- Jones, J.T.; Haegeman, A.; Danchin, E.G.J.; Gaur, H.S.; Helder, J.; Jones, M.G.K.; Kikuchi, T.; Manzanilla-Lopez, R.; Palomares-Rius, J.E.; Wesemael, W.M.L.; Perry, R.N. (2013) Top 10 plant parasitic nematodes in molecular plant pathology., Molecular Plant Pathology, 14, 946-961.
- Palomares-Rius, J.E.; Jones, J.T.; Cock, P.J.; Castillo, P.; Blok, V.C. (2013) Activation of hatching in diapaused and quiescent Globodera pallida., Parasitology, 140, 445-454.
- Palomares-Rius, J.E.; Hedley, P.E.; Cock, P.J.A.; Morris, J.A.; Jones, J.T.; Vovlas, N.; Blok, V. (2012) Comparison of transcript profiles in different life stages of the nematode Globodera pallida under different host potato genotypes., Molecular Plant Pathology, 13, 1120-1134.
- Haegeman, A.; Mantelin, S.; Jones, J.T.; Gheysen, G. (2012) Functional roles of effectors of plant-parasitic nematodes., Gene, 492, 19-31.
- Tyson, T.; O'Mahony, Zamora, G.; Skelton, M.; Daly, M.B.; Jones, J.T.; Elsworth, B.; Phillips, M.; Blaxter, M.; Burnell, A.M. (2012) A molecular analysis of desiccation tolerance mechanisms in the anhydrobiotic nematode Panagrolaimus superbus using expressed sequenced tags., BMC Research Notes, 5, Article No. e68.
- Birch, P.R.J.; Bryan, G.J.; Fenton, B.; Gilroy, E.M.; Hein, I.; Jones, J.T.; Prashar, A.; Taylor, M.A.; Torrance, L.; Toth, I.K. (2012) Crops that feed the world 8: potato: are the trends of increased global production sustainable?, Food Security, 4, 477-508.
- Pokhare, S.S.; Habash, S.S; Jones, J.T.; Elashry, A.; Grundler, F.M.W. (2019) In vitro life cycle of Heterodera sacchari on pluronic gel., Nematology, 21, 573-579.
- Espada, M.; Eves-van den Akker, S.; Maier, T.; Vijaypalani, P.; Baum, T.J.; Mota, M.; Jones, J.T. (2018) STATAWAARS: A promoter motif associated with spatial expression in the major effector -producing tissues of the planparasitic nematode Bursaphelenchus xylophilus. ., BMC Genomics, 19, Article No. 553.
- Mei, Y.; Wright, K.M.; Haegeman, A.; Bauters, L.; Diaz-Granados, A.; Goverse, A.; Gheysen, G.; Jones, T.J.; Mantelin, S. (2018) The Globodera pallida SPRYSEC effector GpSPRY-414-2 that suppresses plant defenses targets a regulatory component of the dynamic microtubule network., Frontiers in Plant Science, 9, Article No. 1019.
- Eves-van den Akker, S.; Jones, J.T. (2018) Sex: not all that it’s cracked up to be?, PLoS Genetics, 14, Article No. e1007160.
- Wang, X.; Xue, B.: Dai, J.; Qin, X.: Liu, L.; Chi, Y.; Jones, J.T.; Li, H. (2018) A novel Meloidogyne incognita chorismate mutase effector suppresses plant immunity by manipulating the salicylic acid pathway and functions mainly during the early stages of nematode parasitism., Plant Pathology, 67, 1436-1448.
- Kikuchi, T.; Eves-van den Akker, S.; Jones, J.T. (2017) Genome evolution of plant-parasitic nematodes., Annual Review of Phytopathology, 55, 333-354.
- Mantelin, S.; Thorpe, P.; Jones, J.T. (2017) Translational biology of nematode effectors. Or, to put it another way, functional analysis of effectors - what's the point?, Nematology, 19, 251-261.
- Danchin, E.G.J.; Perfus-Barbeoch, L.; Rancurel, C.; Thorpe, P.; Da Rocha, M.; Bajew, S.; Neilson, R.; Sokolova, E.; Da Silva, C.; Guy, J.; Labadie, K.; Esmenjaud, D.; Helder, J.; Jones, J.T.; Eves-van den Akker, S. (2017) The transcriptomes of xiphinema index and longidorus elongatus suggest independent acquisition of some plant parasitism genes by horizontal gene transfer in early-branching nematodes., Genes, 8, Article No. 287.
- Eves-van den Akker, S.; Laetsch, D.R.; Thorpe, P.; Lilley, C.J.; Danchin, E.G.J.; Da Rocha, M.; Rancurel, C.; Holroyd, N.E.; Cotton, J.A.; Szitenberg, A.; Grenier, E.; Montarry, J.; Mimee, B.; Duceppe, M.O.; Boyes, I.; Marvin, J.M.C.; Jones, L.M.; Yusup, H.B.; Lafond-Lapalme, J.; Esquibet, M.; Sabeh, M.; Rott, M.; Overmars, H.; Finkers-Tomczak, A.; Smant, G.; Koutsovoulos, G.; Blok, V.; Mantelin, S.; Cock, P.J.A.; Phillips, W.; Henrissat, B.; Urwin, P.E.; Blaxter, M.; Jones, J.T. (2016) The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence., Genome Biology, 17, Article No. 124.
- Espada, M.; Jones, J.T.; Mota, M. (2016) Characterization of glutathione S-transferases from the pinewood nematode, Bursaphelenchus xylophilus., Nematology, 18, 697-709.
- Eves-van den Akker, S.; Lilley, C.J.; Hazijah, B.Y.; Jones, J.T.; Urwin, P.E. (2016) Functional C-terminally encoded plant peptide (CEP) hormone domains evolved de novo in the plant parasite Rotylenchulus reniformis., Molecular Plant Pathology, 17, 1265-1275.
- Tsai, I.J.; Tanaka, R.; Kanzaki, N.; Akiba, M.; Yokoi, T.; Espada, M.; Jones, J.T.; Kikuchi, T. (2016) Transcriptional and morphological changes in the transition from mycetophagous to phytophagous phase in the plant-parasitic nematode Bursaphelenchus xylophilus., Molecular Plant Pathology, 17, 77-83.
- Espada, M.; Silva, A.C.; Eves-van den Akker, S.; Cock, P.J.A.; Mota, M.; Jones, J.T. (2016) Identification and characterization of parasitism genes from the pinewood nematode Bursaphelenchus xylophilus reveals a multilayered detoxification strategy., Molecular Plant Pathology, 17, 286-295.
- Palomares-Rius, J.E.; Hedley, P.; Cock, P.J.A.; Morris, J.A.; Jones, J.T.; Blok, V.C. (2016) Gene expression changes in diapause or quiescent potato cyst nematode, Globodera pallida, eggs after hydration or exposure to tomato root diffusate., PeerJ, 4, Article No. e1654.
- Danchin, E.G.J.; Guzeeva, E.; Mantelin, S.; Berekpiki, A.; Jones, J.T. (2016) Horizontal gene transfer from bacteria has enabled the plant-parasitic nematode Globodera pallida to feed on plant-derived sucrose., Molecular Biology and Evolution, 33, 1571-1579.
- Eves-van den Akker, S.; Lilley, C.J.; Yusup, H.B.; Jones, J.T.; Urwin, P.E. (2016) Functional C-TERMINALLY ENCODED PEPTIDE (CEP) plant hormone domains evolved de novo in the plant parasite Rotylenchulus reniformis., Molecular Plant Pathology, 17, 1265-1275.
- Eves-van den Akker, S.; Lilley, C.J.; Reid, A.; Pickup, J.; Anderson, E.; Cock, P.J.A.; Blaxter, M.; Urwin, P.E.; Jones, J.T.; Blok, V.C. (2015) A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual., Molecular Ecology, 24, 5842-5851.
- Mei, Y.; Thorpe, P.; Guzha, A.; Haegeman, A.; Blok, V.C.; MacKenzie, K.; Gheysen, G.; Jones, J.T.; Mantelin, S. (2015) Only a small subset of the SPRY domain gene family in Globodera pallida is likely to encode effectors, two of which suppress host defences induced by the potato resistance gene Gpa2., Nematology, 17, 409-424.
- Mantelin, S.; Thorpe, P.; Jones, J.T. (2015) Suppression of plant defences by plant-parasitic nematodes. Chapter thirteen of "Plant Nematode Interactions - A View on Compatible Interrelationships"., Advances in Botanical Research, 73, 325-337.
- Sarkies, P.; Selkirk, M.E.; Jones, J.T.; Blok, V.C.; Boothby, T.; Goldstein, B.; Hanelt, B.; Ardila-Garcia, A.; Fast, N.M.; Schiffer, P.M.; Kraus, C.; Schierenberg, E.; Taylor, M.J.; Koutsovoulos, G.; Blaxter, M.L.; Miska, E.A. (2015) Ancient and novel small RNA pathways compensate for the loss of piRNAs in multiple independent nematode lineages., PLoS Biology, 13, Article No. e1002061.
- Bird, D.M.; Jones, J.T.; Opperman, C.H.; Kikuchi, T.; Danchin, E.G.J. (2015) Signatures of adaptation to plant parasitism in nematode genomes., Parasitology, 142, S71-S84.
- Eves-van den Akker, S.; Lilley, C.J.; Jones, J.T.; Urwin, P.E. (2015) Plant-parasitic nematode feeding tubes and plugs: new perspectives on function., Nematology, 17, 1-9.
- Eves-van den Akker, S.; Lilley, C.J.; Danchin, E.G.J.; Rancurel, C.; Cock, P.J.A.; Urwin, P.E.; Jones, J.T. (2014) The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes., Genome Biology and Evolution, 6, 2181-2194.
- Palomares-Rius, J.E.; Hirooka, Y.; Tsai, I.J.; Masuya, H.; Hino, A.; Kanzaki, N.; Jones, J.T.; Kikuchi, T. (2014) Distribution and evolution of glycoside hydrolase family 45 cellulases in nematodes and fungi., BMC Evolutionary Biology, 14, Article No. 69.
- van Den Akker, S.E.; Lilley, C.J.; Jones, J.T.; Urwin, P.E. (2014) Identification and characterisation of a hyper-variable apoplastic effector gene family of the potato cyst nematodes., PLoS Pathogens, 10, Article No. e1004391.
- Thorpe, P.; Mantelin, S.; Cock, P.J.A.; Blok, V.C.; Coke M.C.; van Den Akker, S.E.; Guzeeva, E.; Lilley, C.J.; Smant, G.; Reid, A.J.; Wright, K.M.; Urwin, P.E.; Jones, J.T. (2014) Genomic characterisation of the effector complement of the potato cyst nematode Globodera pallida., BMC Genomics, 15, Article No. 923.
- Eves-van den Akker, S.; Lilley, C.J.; Ault, J.R.; Ashcroft, A.E.; Jones, J.T.; Urwin, P.E. (2014) The feeding tube of cyst nematodes: characterisation of protein exclusion., PLoS ONE, 9, Article No. e87289.
- Cotton, J.A.; Lilley, C.J.; Jones, L.M.; Kikuchi, T.; Reid, A.J.; Thorpe, P.; Tsai, I.J.; Beasley, H.; Blok, V.C.; Cock, P.J.A.; Eves-van den Akker, S.; Holroyd, N.; Hunt, M.; Mantelin, S.; Naghra, H.; Pain, A.; Palomares-Rius, J.E.; Zarowiecki, M.; Berriman, M.; Jones, J.T.; Urwin, P.E. (2014) The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode., Genome Biology, 15, Article No. R43.
- Kikuchi, T.; Cock, P.J.A.; Helder, J.; Jones, J.T. (2014) Characterisation of the transcriptome of Aphelenchoides besseyi and identification of a GHF 45 cellulase., Nematology, 16, 99-107.
- Jones, J.T.; Haegeman, A.; Danchin, E.G.J.; Gaur, H.S.; Helder, J.; Jones, M.G.K.; Kikuchi, T.; Manzanilla-Lopez, R.; Palomares-Rius, J.E.; Wesemael, W.M.L.; Perry, R.N. (2013) Top 10 plant parasitic nematodes in molecular plant pathology., Molecular Plant Pathology, 14, 946-961.
- Palomares-Rius, J.E.; Jones, J.T.; Cock, P.J.; Castillo, P.; Blok, V.C. (2013) Activation of hatching in diapaused and quiescent Globodera pallida., Parasitology, 140, 445-454.
- Palomares-Rius, J.E.; Hedley, P.E.; Cock, P.J.A.; Morris, J.A.; Jones, J.T.; Vovlas, N.; Blok, V. (2012) Comparison of transcript profiles in different life stages of the nematode Globodera pallida under different host potato genotypes., Molecular Plant Pathology, 13, 1120-1134.
- Haegeman, A.; Mantelin, S.; Jones, J.T.; Gheysen, G. (2012) Functional roles of effectors of plant-parasitic nematodes., Gene, 492, 19-31.
- Tyson, T.; O'Mahony, Zamora, G.; Skelton, M.; Daly, M.B.; Jones, J.T.; Elsworth, B.; Phillips, M.; Blaxter, M.; Burnell, A.M. (2012) A molecular analysis of desiccation tolerance mechanisms in the anhydrobiotic nematode Panagrolaimus superbus using expressed sequenced tags., BMC Research Notes, 5, Article No. e68.
- Birch, P.R.J.; Bryan, G.J.; Fenton, B.; Gilroy, E.M.; Hein, I.; Jones, J.T.; Prashar, A.; Taylor, M.A.; Torrance, L.; Toth, I.K. (2012) Crops that feed the world 8: potato: are the trends of increased global production sustainable?, Food Security, 4, 477-508.
- Kikuchi, T.; Cotton, J.A.; Dalzell, J.J.; Hasegawa, K.; Kanzaki, N.; McVeigh, P.; Takanashi, T.; Tsai, I.J.; Assefa, S.A.; Cock, P.J.A.; Otto, T.D.; Hunt, M.; Reid, A.J.; Sanchez-Flores, A.; Tsuchihara, K.; Yokoi, T.; Larsson, M.C.; Miwa, J.; Maule, A.G.; Sahashi, N.; Jones, J.T.; Berriman, M. (2011) Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus., PLoS Pathogens, 7, Article No. e1002219.
- Haegeman, A.; Jones, J.T.; Danchin, E.G.J. (2011) Horizontal gene transfer in nematodes: a catalyst for plant parasitism?, Molecular Plant-Microbe Interactions, 24, 879-887.
- Yan, X.; De Clercq, P.; Han, R.; Jones, J.T.; Chen, S.; Moens, M. (2011) Osmotic responses of different strains of Steinernema carpocapsae., Nematology, 13, 845-851.
- Veronico, P.; Melillo, M.T.; Saponaro, C.; Leonetti, P.; Picardi, E.; Jones, J.T. (2011) A polygalacturonase-inhibiting protein with a role in pea defence against the cyst nematode Heterodera goettingianna., Molecular Plant Pathology, 12, 275-287.
- Rosso, M.N.; Jones, J.T.; Abad, P. (2009) RNAi and functional genomics in plant parasitic nematodes., Annual Review of Phytopathology, 47, 207-232.
- Perry, R.N.; Moens, M.; Jones, J.T. (eds.) (2018) Cyst nematodes., Wallingford, CABI Publishing, 488pp.
- Jones, J.T.; Mitchum, M.G. (2018) Biology of effectors., In: Perry, R.N., Moens, M. & Jones, J.T. (eds.). Cyst Nematodes. CABI Publishing, Wallingford, Chapter 4, 74-88.
- Reid, A.J.; Jones, J.T. (2014) Bioinformatic analysis of expression data to identify effector candidates., In: Birch, P., Jones, J.T. & Bos, J.I.B. (eds.). Plant-Pathogen Interactions: Methods and Protocols. Methods in Molecular Biology, Volume 1127. Humana Press, New York, 2nd ed. Chapter 2, 17-27.
- Elling, A.A.; Jones, J.T. (2014) Functional characterization of nematode effectors in plants., In: Birch, P., Jones, J.T. & Bos, J.I.B. (eds.). Plant-Pathogen Interactions: Methods and Protocols. Methods in Molecular Biology, Volume 1127. Humana Press, New York, 2nd ed. Chapter 9, 113-124..
- Birch, P.; Jones, J.; Bos, J.I. (eds). (2014) Plant-pathogen interactions: methods and protocols., Methods in Molecular Biology, Volume 1127. 2nd edition, Humana Press, New York, 306pp.
- Smant, G.; Jones, J.T. (2011) Suppression of plant defences by nematodes., In: Jones, J.T., Gheysen, G. & Fenoll, C. (eds.). Genomics and Molecular Genetics of Plant-Nematode Interactions. Springer, Dordrecht, The Netherlands, Chapter 13, 273-286.
- Jones, J.T.; Gheysen, G.; Fenoll, C. (eds.) (2011) Genomics and molecular genetics of plant-nematode interactions., Springer, Dordrecht, The Netherlands, 557pp. ISBN: 978-94-007-0433-6
- Curtis, R.H.C.; Jones, J.T.; Davies, K.G.; Sharon, E.; Spiegel, Y. (2011) Plant nematode surfaces., In: Davies, K.G. & Spiegel, Y. (eds.). Biological Control of Plant Parasitic Nematodes: Building Coherence Between Microbial Ecology and Molecular Mechanisms. Springer Academic Publishers, 115-144.
- Gheysen, G.; Jones, J.T. (2006) Molecular aspects of plant-nematode interactions., In: Perry, R.N. & Moens, M. (eds.). Plant Nematology. CABI Publishing, Wallingford, Oxon, pp234-254.
- Jones, J.T. (2002) Nematode sense organs., In: Lees, D.L. (ed.). The Biology of Nematodes. Taylor and Francis, London, pp353-368.
- Jones, J.T. (2001) Parasites of crops: Potato cyst nematode (PCN) Globodera pallida (Nematoda)., In: Halton, D.W., Behnke, J.M. & Marshall, I. (eds.). Practical Exercises in Parasitology. Cambridge University Press, Chapter 1.7, pp63-72.
- Avrova, A.O.; Birch, P.R.J.; Hein, I.; Jones, J.T.; Pritchard, L. (2010) Functional analysis of pathogen effectors: how to go from genomics to durable resistance., Annual Report of the Scottish Crop Research Institute for 2009, 39-41.
- Wale, S.; Inglis, M.; Bain, R.; Davey, T.; Evans, A.; Bradshaw, J.E.; Phillips, M.; Jones, J.T.; Fenton, B.; Cooke, D.E.L.; Ramsay, G. (2008) Welcome to the Potatoes in Partnership open meetings 2008 which form part of knowledge transfer activities for RERAD funded research., SAC Information Note 105
- Jones, J.T.; Phillips, M.S.; Blok, V.C. (2008) Potato cyst nematode genomics., Annual Report of the Scottish Crop Research Institute for 2007, pp26-27.
- Whisson, S.C.; Avrova, A.O.; Birch, P.R.J.; Adam, M.; Blok, V.C.; Jones, J.T. (2004) Functional genomic tools for the major eukaryotic pathogens of potato., Annual Report of the Scottish Crop Research Institute for 2003/2004, pp127-128.
- Whisson, S.C.; Avrova, A.O.; Armstrong, M.R.; Jones, J.T.; Venter, E.; Birch, P.R.J. (2004) Targeting late blight with gene discovery., Annual Report of the Scottish Crop Research Institute for 2002/2003, pp102-103.
- Blok, V.C.; Armstrong, M.R.; Banks, B.; Birch, P.R.J.; Bryan, G.J.; Castelli, L.; Jones, J.T.; Kumar, A.; Phillips, M.S.; Purvis, A.; Ramsay, G.; Waugh, R.; Wishart, J. (2002) Investigating gene expression in nematode-infected roots., Annual Report of the Scottish Crop Research Institute for 2001/2002, pp122-124.
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