Studholme DJ

References (10)

Title : Intraspecific diversification of the crop wild relative Brassica cretica Lam. using demographic model selection - Kioukis_2020_BMC.Genomics_21_48
Author(s) : Kioukis A , Michalopoulou VA , Briers L , Pirintsos S , Studholme DJ , Pavlidis P , Sarris PF
Ref : BMC Genomics , 21 :48 , 2020
Abstract : BACKGROUND: Crop wild relatives (CWRs) contain genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops to adapt to changing conditions that they experience due to climate change. An impressive global effort for the conservation of various CWR will facilitate their use in crop breeding for food security. The genus Brassica is listed in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture. Brassica oleracea (or wild cabbage), a species native to southern and western Europe, has become established as an important human food crop plant because of its large reserves stored over the winter in its leaves. Brassica cretica Lam. (Bc) is a CWR in the brassica group and B. cretica subsp. nivea (Bcn) has been suggested as a separate subspecies. The species Bc has been proposed as a potential gene donor to brassica crops, including broccoli, cabbage, cauliflower, oilseed rape, etc. RESULTS: We sequenced genomes of four Bc individuals, including two Bcn and two Bc. Demographic analysis based on our whole-genome sequence data suggests that populations of Bc are not isolated. Classification of the Bc into distinct subspecies is not supported by the data. Using only the non-coding part of the data (thus, the parts of the genome that has evolved nearly neutrally), we find the gene flow between different Bc population is recent and its genomic diversity is high. CONCLUSIONS: Despite predictions on the disruptive effect of gene flow in adaptation, when selection is not strong enough to prevent the loss of locally adapted alleles, studies show that gene flow can promote adaptation, that local adaptations can be maintained despite high gene flow, and that genetic architecture plays a fundamental role in the origin and maintenance of local adaptation with gene flow. Thus, in the genomic era it is important to link the selected demographic models with the underlying processes of genomic variation because, if this variation is largely selectively neutral, we cannot assume that a diverse population of crop wild relatives will necessarily exhibit the wide-ranging adaptive diversity required for further crop improvement.
ESTHER : Kioukis_2020_BMC.Genomics_21_48
PubMedSearch : Kioukis_2020_BMC.Genomics_21_48
PubMedID: 31937246
Gene_locus related to this paper: bracr-a0a3n6rng7 , bracr-a0a3n6rj72

Title : Genome sequence data from 17 accessions of Ensete ventricosum, a staple food crop for millions in Ethiopia - Yemataw_2018_Data.Brief_18_285
Author(s) : Yemataw Z , Muzemil S , Ambachew D , Tripathi L , Tesfaye K , Chala A , Farbos A , O'Neill P , Moore K , Grant M , Studholme DJ
Ref : Data Brief , 18 :285 , 2018
Abstract : We present raw sequence reads and genome assemblies derived from 17 accessions of the Ethiopian orphan crop plant enset (Ensete ventricosum (Welw.) Cheesman) using the Illumina HiSeq and MiSeq platforms. Also presented is a catalogue of single-nucleotide polymorphisms inferred from the sequence data at an average density of approximately one per kilobase of genomic DNA.
ESTHER : Yemataw_2018_Data.Brief_18_285
PubMedSearch : Yemataw_2018_Data.Brief_18_285
PubMedID: 29896517
Gene_locus related to this paper: ensve-a0a444fr62

Title : Genome characterization of a novel Burkholderia cepacia complex genomovar isolated from dieback affected mango orchards - Khan_2013_World.J.Microbiol.Biotechnol_29_2033
Author(s) : Khan A , Asif H , Studholme DJ , Khan IA , Azim MK
Ref : World J Microbiol Biotechnol , 29 :2033 , 2013
Abstract : We characterized the genome of the antibiotic resistant, caseinolytic and non-hemolytic Burkholderia sp. strain TJI49, isolated from mango trees (Mangifera indica L.) with dieback disease. This isolate produced severe disease symptoms on the indicator plants. Next generation DNA sequencing and short-read assembly generated the 60X deep 7,631,934 nucleotide draft genome of Burkholderia sp. TJI49 which comprised three chromosomes and at least one mega plasmid. Genome annotation studies revealed a total 8,992 genes, out of which 8,940 were protein coding genes. Comparative genomics and phylogenetics identified Burkholderia sp. TJI49 as a distinct species of Burkholderia cepacia complex (BCC), closely related to B. multivorans ATCC17616. Genome-wide sequence alignment of this isolate with replicons of BCC members showed conservation of core function genes but considerable variations in accessory genes. Subsystem-based gene annotation identified the active presence of wide spread colonization island and type VI secretion system in Burkholderia sp. TJI49. Sequence comparisons revealed (a) 28 novel ORFs that have no database matches and (b) 23 ORFs with orthologues in species other than Burkholderia, indicating horizontal gene transfer events. Fold recognition of novel ORFs identified genes encoding pertactin autotransporter-like proteins (a constituent of type V secretion system) and Hap adhesion-like proteins (involved in cell-cell adhesion) in the genome of Burkholderia sp. TJI49. The genomic characterization of this isolate provided additional information related to the 'pan-genome' of Burkholderia species.
ESTHER : Khan_2013_World.J.Microbiol.Biotechnol_29_2033
PubMedSearch : Khan_2013_World.J.Microbiol.Biotechnol_29_2033
PubMedID: 23653265
Gene_locus related to this paper: 9burk-a0u8m3 , 9burk-f0g8l1

Title : Genome-wide sequencing reveals two major sub-lineages in the genetically monomorphic pathogen xanthomonas campestris pathovar musacearum - Wasukira_2012_Genes.(Basel)_3_361
Author(s) : Wasukira A , Tayebwa J , Thwaites R , Paszkiewicz K , Aritua V , Kubiriba J , Smith J , Grant M , Studholme DJ
Ref : Genes (Basel) , 3 :361 , 2012
Abstract : The bacterium Xanthomonas campestris pathovar musacearum (Xcm) is the causal agent of banana Xanthomonas wilt (BXW). This disease has devastated economies based on banana and plantain crops (Musa species) in East Africa. Here we use genome-wide sequencing to discover a set of single-nucleotide polymorphisms (SNPs) among East African isolates of Xcm. These SNPs have potential as molecular markers for phylogeographic studies of the epidemiology and spread of the pathogen. Our analysis reveals two major sub-lineages of the pathogen, suggesting that the current outbreaks of BXW on Musa species in the region may have more than one introductory event, perhaps from Ethiopia. Also, based on comparisons of genome-wide sequence data from multiple isolates of Xcm and multiple strains of X. vasicola pathovar vasculorum, we identify genes specific to Xcm that could be used to specifically detect Xcm by PCR-based methods.
ESTHER : Wasukira_2012_Genes.(Basel)_3_361
PubMedSearch : Wasukira_2012_Genes.(Basel)_3_361
PubMedID: 24704974
Gene_locus related to this paper: xanax-estA1 , xanor-q5h5n1 , xanca-a0a084kxz5 , xanva-a0a0a3gsg4 , xanca-a0a0e2yn33 , xanva-a0a0n2s8c2

Title : Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana - Kemen_2011_PLoS.Biol_9_e1001094
Author(s) : Kemen E , Gardiner A , Schultz-Larsen T , Kemen AC , Balmuth AL , Robert-Seilaniantz A , Bailey K , Holub E , Studholme DJ , Maclean D , Jones JD
Ref : PLoS Biol , 9 :e1001094 , 2011
Abstract : Biotrophic eukaryotic plant pathogens require a living host for their growth and form an intimate haustorial interface with parasitized cells. Evolution to biotrophy occurred independently in fungal rusts and powdery mildews, and in oomycete white rusts and downy mildews. Biotroph evolution and molecular mechanisms of biotrophy are poorly understood. It has been proposed, but not shown, that obligate biotrophy results from (i) reduced selection for maintenance of biosynthetic pathways and (ii) gain of mechanisms to evade host recognition or suppress host defence. Here we use Illumina sequencing to define the genome, transcriptome, and gene models for the obligate biotroph oomycete and Arabidopsis parasite, Albugo laibachii. A. laibachii is a member of the Chromalveolata, which incorporates Heterokonts (containing the oomycetes), Apicomplexa (which includes human parasites like Plasmodium falciparum and Toxoplasma gondii), and four other taxa. From comparisons with other oomycete plant pathogens and other chromalveolates, we reveal independent loss of molybdenum-cofactor-requiring enzymes in downy mildews, white rusts, and the malaria parasite P. falciparum. Biotrophy also requires "effectors" to suppress host defence; we reveal RXLR and Crinkler effectors shared with other oomycetes, and also discover and verify a novel class of effectors, the "CHXCs", by showing effector delivery and effector functionality. Our findings suggest that evolution to progressively more intimate association between host and parasite results in reduced selection for retention of certain biosynthetic pathways, and particularly reduced selection for retention of molybdopterin-requiring biosynthetic pathways. These mechanisms are not only relevant to plant pathogenic oomycetes but also to human pathogens within the Chromalveolata.
ESTHER : Kemen_2011_PLoS.Biol_9_e1001094
PubMedSearch : Kemen_2011_PLoS.Biol_9_e1001094
PubMedID: 21750662
Gene_locus related to this paper: 9stra-f0vzr0 , 9stra-f0w3s0 , 9stra-f0whp7 , 9stra-f0wif4 , 9stra-f0wjy6 , 9stra-f0wpr6 , 9stra-f0wq48 , 9stra-f0wq49 , 9stra-f0wr05 , 9stra-f0wve8 , 9stra-f0wx44 , 9stra-f0wzn9 , 9stra-f0we19 , 9stra-f0wqy5 , 9stra-f0w333

Title : A draft genome sequence of Pseudomonas syringae pv. tomato T1 reveals a type III effector repertoire significantly divergent from that of Pseudomonas syringae pv. tomato DC3000 - Almeida_2009_Mol.Plant.Microbe.Interact_22_52
Author(s) : Almeida NF , Yan S , Lindeberg M , Studholme DJ , Schneider DJ , Condon B , Liu H , Viana CJ , Warren A , Evans C , Kemen E , Maclean D , Angot A , Martin GB , Jones JD , Collmer A , Setubal JC , Vinatzer BA
Ref : Mol Plant Microbe Interact , 22 :52 , 2009
Abstract : Diverse gene products including phytotoxins, pathogen-associated molecular patterns, and type III secreted effectors influence interactions between Pseudomonas syringae strains and plants, with additional yet uncharacterized factors likely contributing as well. Of particular interest are those interactions governing pathogen-host specificity. Comparative genomics of closely related pathogens with different host specificity represents an excellent approach for identification of genes contributing to host-range determination. A draft genome sequence of Pseudomonas syringae pv. tomato T1, which is pathogenic on tomato but nonpathogenic on Arabidopsis thaliana, was obtained for this purpose and compared with the genome of the closely related A. thaliana and tomato model pathogen P. syringae pv. tomato DC3000. Although the overall genetic content of each of the two genomes appears to be highly similar, the repertoire of effectors was found to diverge significantly. Several P. syringae pv. tomato T1 effectors absent from strain DC3000 were confirmed to be translocated into plants, with the well-studied effector AvrRpt2 representing a likely candidate for host-range determination. However, the presence of avrRpt2 was not found sufficient to explain A. thaliana resistance to P. syringae pv. tomato T1, suggesting that other effectors and possibly type III secretion system-independent factors also play a role in this interaction.
ESTHER : Almeida_2009_Mol.Plant.Microbe.Interact_22_52
PubMedSearch : Almeida_2009_Mol.Plant.Microbe.Interact_22_52
PubMedID: 19061402
Gene_locus related to this paper: pse14-q48ia0 , psesm-e2mn04 , psesm-IRP1 , psesm-METX , psesm-q88a39 , psesm-q881b4 , psesy-ESTA , psesy-IRP4 , psesy-PIP , psesy-PSPTO0421 , psesy-PSPTO0508 , psesy-PSPTO1504 , psesy-PSPTO1559 , psesy-PSPTO1766 , psesy-PSPTO2005 , psesy-PSPTO2134 , psesy-PSPTO2150 , psesy-PSPTO3135 , psesy-PSPTO3138 , psesy-PSPTO3306 , psesy-PSPTO4277 , psesy-PSPTO4519 , psesy-PSPTO4540 , psesy-PSPTO4964 , psesy-PSPTO5299 , psesy-PSPTO5537 , pseub-e2mf08

Title : Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes - Setubal_2009_J.Bacteriol_191_4534
Author(s) : Setubal JC , dos Santos P , Goldman BS , Ertesvag H , Espin G , Rubio LM , Valla S , Almeida NF , Balasubramanian D , Cromes L , Curatti L , Du Z , Godsy E , Goodner B , Hellner-Burris K , Hernandez JA , Houmiel K , Imperial J , Kennedy C , Larson TJ , Latreille P , Ligon LS , Lu J , Maerk M , Miller NM , Norton S , O'Carroll IP , Paulsen I , Raulfs EC , Roemer R , Rosser J , Segura D , Slater S , Stricklin SL , Studholme DJ , Sun J , Viana CJ , Wallin E , Wang B , Wheeler C , Zhu H , Dean DR , Dixon R , Wood D
Ref : Journal of Bacteriology , 191 :4534 , 2009
Abstract : Azotobacter vinelandii is a soil bacterium related to the Pseudomonas genus that fixes nitrogen under aerobic conditions while simultaneously protecting nitrogenase from oxygen damage. In response to carbon availability, this organism undergoes a simple differentiation process to form cysts that are resistant to drought and other physical and chemical agents. Here we report the complete genome sequence of A. vinelandii DJ, which has a single circular genome of 5,365,318 bp. In order to reconcile an obligate aerobic lifestyle with exquisitely oxygen-sensitive processes, A. vinelandii is specialized in terms of its complement of respiratory proteins. It is able to produce alginate, a polymer that further protects the organism from excess exogenous oxygen, and it has multiple duplications of alginate modification genes, which may alter alginate composition in response to oxygen availability. The genome analysis identified the chromosomal locations of the genes coding for the three known oxygen-sensitive nitrogenases, as well as genes coding for other oxygen-sensitive enzymes, such as carbon monoxide dehydrogenase and formate dehydrogenase. These findings offer new prospects for the wider application of A. vinelandii as a host for the production and characterization of oxygen-sensitive proteins.
ESTHER : Setubal_2009_J.Bacteriol_191_4534
PubMedSearch : Setubal_2009_J.Bacteriol_191_4534
PubMedID: 19429624
Gene_locus related to this paper: azovd-c1dex6 , azovd-c1df21 , azovd-c1dfb5 , azovd-c1dg75 , azovd-c1dgm6 , azovd-c1dh91 , azovd-c1di03 , azovd-c1dib3 , azovd-c1dif2 , azovd-c1dIq5 , azovd-c1dir1 , azovd-c1dis2 , azovd-c1djq5 , azovd-c1djw3 , azovd-c1dk37 , azovd-c1dkb2 , azovd-c1dkj0 , azovd-c1dli6 , azovd-c1dng8 , azovd-c1dni5 , azovd-c1dpr0 , azovd-c1dqu3 , azovd-c1dri5 , azovd-c1drx0 , azovd-c1dsl7 , azovd-c1dsq7 , azovd-c1dss1 , azovd-metx , azovi-PHBC , azovd-c1dem4

Title : Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans - Haas_2009_Nature_461_393
Author(s) : Haas BJ , Kamoun S , Zody MC , Jiang RH , Handsaker RE , Cano LM , Grabherr M , Kodira CD , Raffaele S , Torto-Alalibo T , Bozkurt TO , Ah-Fong AM , Alvarado L , Anderson VL , Armstrong MR , Avrova A , Baxter L , Beynon J , Boevink PC , Bollmann SR , Bos JI , Bulone V , Cai G , Cakir C , Carrington JC , Chawner M , Conti L , Costanzo S , Ewan R , Fahlgren N , Fischbach MA , Fugelstad J , Gilroy EM , Gnerre S , Green PJ , Grenville-Briggs LJ , Griffith J , Grunwald NJ , Horn K , Horner NR , Hu CH , Huitema E , Jeong DH , Jones AM , Jones JD , Jones RW , Karlsson EK , Kunjeti SG , Lamour K , Liu Z , Ma L , Maclean D , Chibucos MC , McDonald H , McWalters J , Meijer HJ , Morgan W , Morris PF , Munro CA , O'Neill K , Ospina-Giraldo M , Pinzon A , Pritchard L , Ramsahoye B , Ren Q , Restrepo S , Roy S , Sadanandom A , Savidor A , Schornack S , Schwartz DC , Schumann UD , Schwessinger B , Seyer L , Sharpe T , Silvar C , Song J , Studholme DJ , Sykes S , Thines M , van de Vondervoort PJ , Phuntumart V , Wawra S , Weide R , Win J , Young C , Zhou S , Fry W , Meyers BC , van West P , Ristaino J , Govers F , Birch PR , Whisson SC , Judelson HS , Nusbaum C
Ref : Nature , 461 :393 , 2009
Abstract : Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement. To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population. Current annual worldwide potato crop losses due to late blight are conservatively estimated at $$6.7 billion. Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars. Here we report the sequence of the P. infestans genome, which at approximately 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for approximately 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
ESTHER : Haas_2009_Nature_461_393
PubMedSearch : Haas_2009_Nature_461_393
PubMedID: 19741609
Gene_locus related to this paper: phyin-ENDO2 , phyin-q2m440 , phyin-q58g92 , phyit-d0mqp1 , phyit-d0mqp2 , phyit-d0mt75 , phyit-d0muv1 , phyit-d0mv34 , phyit-d0mv35 , phyit-d0mwf9 , phyit-d0mxu5 , phyit-d0n935 , phyit-d0nax9 , phyit-d0nfs3 , phyit-d0nhj2 , phyit-d0nhj4 , phyit-d0nhj8 , phyit-d0ni28 , phyit-d0nj14 , phyit-d0nj53 , phyit-d0nj54 , phyit-d0njf2 , phyit-d0nkm4 , phyit-d0nr53 , phyit-d0nrb1 , phyit-d0nrk9 , phyit-d0nrl4 , phyit-d0ns26 , phyit-d0ns42 , phyit-d0ns43 , phyit-d0nsr8 , phyit-d0nu41 , phyit-d0nvt3 , phyit-d0nwb6 , phyit-d0nwm8 , phyit-d0nzc0 , phyit-d0nzc1 , phyit-d0p0z1 , phyit-d0p3z2 , phyit-kex1 , phyit-d0n6q6 , phyit-d0n4i8 , phyit-d0mqf7 , phyit-d0n5g6

Title : Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana - Jones_2009_J.Proteomics_72_439
Author(s) : Jones AM , Maclean D , Studholme DJ , Serna-Sanz A , Andreasson E , Rathjen JP , Peck SC
Ref : J Proteomics , 72 :439 , 2009
Abstract : Phosphorylation is a ubiquitous regulatory mechanism, that governs the activity, subcellular localisation and molecular interactions of proteins. To identify a broad range of nuclear phosphoproteins from Arabidopsis thaliana, we enriched for nuclei from suspension cell cultures and seedlings before extensive fractionation and identification of phosphopeptides by mass spectrometry. We identified 416 phosphopeptides from 345 proteins with high confidence. Our data show that sub-cellular fractionation is an effective strategy for identifying nuclear phosphoproteins, two thirds of our dataset are known or predicted to be nuclear localised and one half of the nuclear localised proteins have novel phosphorylation sites. We identified novel phosphorylation sites on transcription factors, chromatin remodelling proteins, RNA silencing components and the spliceosome. Intriguingly, we also identified phosphorylation sites on several proteins associated with Golgi vesicle trafficking such as the exocyst complex, and speculate that these may be involved in cell plate formation during cytokinesis.
ESTHER : Jones_2009_J.Proteomics_72_439
PubMedSearch : Jones_2009_J.Proteomics_72_439
PubMedID: 19245862
Gene_locus related to this paper: arath-q84w08 , arath-MES14

Title : Multidimensional protein identification technology (MudPIT) analysis of ubiquitinated proteins in plants - Maor_2007_Mol.Cell.Proteomics_6_601
Author(s) : Maor R , Jones A , Nuhse TS , Studholme DJ , Peck SC , Shirasu K
Ref : Mol Cell Proteomics , 6 :601 , 2007
Abstract : Protein conjugation with ubiquitin, known as ubiquitination, is a key regulatory mechanism to control protein abundance, localization, and activity in eukaryotic cells. To identify ubiquitin-dependent regulatory steps in plants, we developed a robust affinity purification/identification system for ubiquitinated proteins. Using GST-tagged ubiquitin binding domains, we performed a large scale affinity purification of ubiquitinated proteins from Arabidopsis cell suspension culture. High molecular weight ubiquitinated proteins were separated by SDS-PAGE, and the trypsin-digested samples were then analyzed by a multidimensional protein identification technology (MudPIT) system. A total of 294 proteins specifically bound by the GST-tagged ubiquitin binding domains were identified. From these we determined 85 ubiquitinated lysine residues in 56 proteins, confirming the enrichment of the target class of proteins. Our data provide the first view of the ubiquitinated proteome in plants. We also provide evidence that this technique can be broadly applied to the study of protein ubiquitination in diverse plant species.
ESTHER : Maor_2007_Mol.Cell.Proteomics_6_601
PubMedSearch : Maor_2007_Mol.Cell.Proteomics_6_601
PubMedID: 17272265
Gene_locus related to this paper: arath-PLA19