{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T00:34:38Z","timestamp":1792802078199,"version":"4.5.0"},"update-to":[{"DOI":"10.1371\/journal.pgen.1011946","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,11,20]],"date-time":"2025-11-20T00:00:00Z","timestamp":1763596800000}}],"reference-count":135,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2025,11,13]],"date-time":"2025-11-13T00:00:00Z","timestamp":1762992000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100014013","name":"UK Research and Innovation","doi-asserted-by":"publisher","award":["EP\/X024415\/1"],"award-info":[{"award-number":["EP\/X024415\/1"]}],"id":[{"id":"10.13039\/100014013","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/P012574"],"award-info":[{"award-number":["BB\/P012574"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["Grant BBS\/E\/J\/000PR9797"],"award-info":[{"award-number":["Grant BBS\/E\/J\/000PR9797"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BBS\/E\/JI\/230001B"],"award-info":[{"award-number":["BBS\/E\/JI\/230001B"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Knowledge Exchange (KEC), John Innes Centre","id":[{"id":"https:\/\/ror.org\/055zmrh94","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004034","name":"John Innes Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004034","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000324","name":"Gatsby Charitable Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000324","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"abstract":"<jats:p>Obligate host-associated bacteria with reduced genomes, such as phytoplasmas, face strong evolutionary constraints, including metabolic dependence on hosts, limited opportunities for horizontal gene transfer (HGT), and frequent population bottlenecks. Despite these limitations, phytoplasmas, which are parasitic, insect-transmitted plant pathogens, maintain a diverse arsenal of secreted effectors that manipulate both plant and insect hosts to promote infection and transmission. These effectors can suppress immunity and reprogram plant development, inducing alterations such as witch\u2019s broom and leaf-like flowers, through ubiquitin-independent degradation of key transcription factors. However, how phytoplasmas diversify and maintain these effectors in the absence of frequent genetic exchange remains unclear. To address this, we analysed the effectoromes of 239 phytoplasma genomes and identified a diverse set of secreted proteins, which we designated as putative Phytoplasma Effectors (PhAMEs). We found that PhAMEs targeting evolutionarily conserved and structurally constrained surfaces of host proteins are widespread across phytoplasmas. These effectors adopt compact, efficient folds. They often function as molecular scaffolds with dual interaction surfaces capable of linking host proteins or integrating signalling pathways. Such scaffolding PhAMEs have evolved multiple times independently, providing clear evidence of convergent evolution. Despite severe genomic constrains imposed by genome reduction and limited HGT, gene duplications, interface variations, domain fusions, and repeat expansions have helped the shaping effector fold and diversity. While the overall effector repertoire of phytoplasmas appeared largely unique, some PhAME domains share similarities with proteins from other mollicutes and pathogens. Collectively, our findings shed light on how genome-reduced bacteria innovate molecular functions and offer insights into phytoplasma biology, effector evolution, and host-pathogen dynamics. They also lay the groundwork for protein engineering approaches aimed at discovering or designing novel biomolecules with biotechnological potential.<\/jats:p>","DOI":"10.1371\/journal.pgen.1011946","type":"journal-article","created":{"date-parts":[[2025,11,13]],"date-time":"2025-11-13T18:53:57Z","timestamp":1763060037000},"page":"e1011946","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":5,"title":["Effector innovation in genome-reduced phytoplasmas and other host-dependent mollicutes"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3323-2348","authenticated-orcid":true,"given":"Federico G.","family":"Mirkin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sam T.","family":"Mugford","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vera","family":"Thole","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1591-0309","authenticated-orcid":true,"given":"Mar","family":"Marzo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1371-5606","authenticated-orcid":true,"given":"Saskia A.","family":"Hogenhout","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,11,13]]},"reference":[{"key":"pgen.1011946.ref001","doi-asserted-by":"crossref","first-page":"72","DOI":"10.3389\/fgene.2017.00072","article-title":"The Evolution of Bacterial Genome Architecture","volume":"8","author":"L-M Bobay","year":"2017","journal-title":"Front Genet"},{"issue":"7","key":"pgen.1011946.ref002","doi-asserted-by":"crossref","first-page":"2873","DOI":"10.1073\/pnas.93.7.2873","article-title":"Accelerated evolution and Muller\u2019s rachet in endosymbiotic bacteria","volume":"93","author":"NA Moran","year":"1996","journal-title":"Proc Natl Acad Sci"},{"issue":"6","key":"pgen.1011946.ref003","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1093\/femsre\/fuw028","article-title":"Winding paths to simplicity: genome evolution in facultative insect symbionts","volume":"40","author":"W-S Lo","year":"2016","journal-title":"FEMS Microbiol Rev"},{"key":"pgen.1011946.ref004","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1146\/annurev-micro-091213-112901","article-title":"The tiniest tiny genomes","volume":"68","author":"NA Moran","year":"2014","journal-title":"Annu Rev Microbiol"},{"issue":"1","key":"pgen.1011946.ref005","doi-asserted-by":"crossref","first-page":"79","DOI":"10.18699\/vjgb-25-10","article-title":"Symbiosis of intracellular bacteria Wolbachia with insects: a hundred years of study summarized","volume":"29","author":"OD Shishkina","year":"2025","journal-title":"Vavilov Journal of Genetics and Breeding"},{"key":"pgen.1011946.ref006","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1146\/annurev.genet.41.110306.130119","article-title":"Genomics and evolution of heritable bacterial symbionts","volume":"42","author":"NA Moran","year":"2008","journal-title":"Annu Rev Genet"},{"issue":"2","key":"pgen.1011946.ref007","doi-asserted-by":"crossref","DOI":"10.1111\/mpp.13437","article-title":"Phytoplasma: A plant pathogen that cannot be ignored in agricultural production-Research progress and outlook","volume":"25","author":"R Wang","year":"2024","journal-title":"Mol Plant Pathol"},{"key":"pgen.1011946.ref008","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.pbi.2018.02.002","article-title":"A multi-layered mechanistic modelling approach to understand how effector genes extend beyond phytoplasma to modulate plant hosts, insect vectors and the environment","volume":"44","author":"M Tomkins","year":"2018","journal-title":"Curr Opin Plant Biol"},{"issue":"10","key":"pgen.1011946.ref009","doi-asserted-by":"crossref","first-page":"1379","DOI":"10.1016\/j.molp.2020.08.010","article-title":"Bacterial Vector-Borne Plant Diseases: Unanswered Questions and Future Directions","volume":"13","author":"W Huang","year":"2020","journal-title":"Mol Plant"},{"key":"pgen.1011946.ref010","doi-asserted-by":"crossref","first-page":"2727","DOI":"10.1099\/ijs.0.048983-0","article-title":"Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes","volume":"63","author":"JJ Davis","year":"2013","journal-title":"Int J Syst Evol Microbiol"},{"issue":"2","key":"pgen.1011946.ref011","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1128\/mr.42.2.414-470.1978","article-title":"The mycoplasmas","volume":"42","author":"S Razin","year":"1978","journal-title":"Microbiol Rev"},{"issue":"1","key":"pgen.1011946.ref012","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1146\/annurev.micro.54.1.221","article-title":"Phytoplasma: phytopathogenic mollicutes","volume":"54","author":"IM Lee","year":"2000","journal-title":"Annu Rev Microbiol"},{"issue":"10","key":"pgen.1011946.ref013","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1016\/S0764-4469(01)01372-5","article-title":"Mycoplasmas, plants, insect vectors: a matrimonial triangle","volume":"324","author":"M Garnier","year":"2001","journal-title":"C R Acad Sci III"},{"issue":"4","key":"pgen.1011946.ref014","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.1128\/MMBR.62.4.1094-1156.1998","article-title":"Molecular biology and pathogenicity of mycoplasmas","volume":"62","author":"S Razin","year":"1998","journal-title":"Microbiol Mol Biol Rev"},{"issue":"5867","key":"pgen.1011946.ref015","doi-asserted-by":"crossref","first-page":"1215","DOI":"10.1126\/science.1151721","article-title":"Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome","volume":"319","author":"DG Gibson","year":"2008","journal-title":"Science"},{"issue":"7","key":"pgen.1011946.ref016","doi-asserted-by":"crossref","DOI":"10.1016\/j.cell.2017.10.029","article-title":"Drastic Genome Reduction in an Herbivore\u2019s Pectinolytic Symbiont","volume":"171","author":"H Salem","year":"2017","journal-title":"Cell"},{"issue":"5235","key":"pgen.1011946.ref017","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1126\/science.270.5235.397","article-title":"The minimal gene complement of Mycoplasma genitalium","volume":"270","author":"CM Fraser","year":"1995","journal-title":"Science"},{"issue":"5","key":"pgen.1011946.ref018","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.0030075","article-title":"Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome","volume":"3","author":"P Sirand-Pugnet","year":"2007","journal-title":"PLoS Genet"},{"key":"pgen.1011946.ref019","doi-asserted-by":"crossref","first-page":"773608","DOI":"10.3389\/fmicb.2022.773608","article-title":"Comparative genome analysis of \u2018Candidatus Phytoplasma luffae\u2019 reveals the influential roles of potential mobile units in phytoplasma evolution","volume":"13","author":"CT Huang","year":"2022","journal-title":"Front Microbiol"},{"issue":"8","key":"pgen.1011946.ref020","doi-asserted-by":"crossref","first-page":"836","DOI":"10.3390\/genes11080836","article-title":"Genomic Islands in Mycoplasmas","volume":"11","author":"C Citti","year":"2020","journal-title":"Genes (Basel)"},{"issue":"6","key":"pgen.1011946.ref021","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.01958-14","article-title":"Chromosomal transfers in mycoplasmas: when minimal genomes go mobile","volume":"5","author":"E Dordet-Frisoni","year":"2014","journal-title":"mBio"},{"issue":"6","key":"pgen.1011946.ref022","doi-asserted-by":"crossref","first-page":"1406","DOI":"10.1111\/j.1365-2958.2010.07296.x","article-title":"Phytoplasma PMU1 exists as linear chromosomal and circular extrachromosomal elements and has enhanced expression in insect vectors compared with plant hosts","volume":"77","author":"TY Toru\u00f1o","year":"2010","journal-title":"Mol Microbiol"},{"issue":"4","key":"pgen.1011946.ref023","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1111\/j.1364-3703.2008.00472.x","article-title":"Phytoplasmas: bacteria that manipulate plants and insects","volume":"9","author":"SA Hogenhout","year":"2008","journal-title":"Mol Plant Pathol"},{"key":"pgen.1011946.ref024","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1146\/annurev.ento.51.110104.151039","article-title":"Insect vectors of phytoplasmas","volume":"51","author":"PG Weintraub","year":"2006","journal-title":"Annu Rev Entomol"},{"issue":"1","key":"pgen.1011946.ref025","doi-asserted-by":"crossref","first-page":"4291","DOI":"10.1038\/s41598-020-61042-x","article-title":"Spatiotemporal dynamics and quantitative analysis of phytoplasmas in insect vectors","volume":"10","author":"H Koinuma","year":"2020","journal-title":"Sci Rep"},{"issue":"1","key":"pgen.1011946.ref026","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1038\/ng1277","article-title":"Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma","volume":"36","author":"K Oshima","year":"2004","journal-title":"Nat Genet"},{"issue":"10","key":"pgen.1011946.ref027","doi-asserted-by":"crossref","first-page":"3682","DOI":"10.1128\/JB.188.10.3682-3696.2006","article-title":"Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts","volume":"188","author":"X Bai","year":"2006","journal-title":"J Bacteriol"},{"key":"pgen.1011946.ref028","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1186\/1471-2164-9-306","article-title":"The linear chromosome of the plant-pathogenic mycoplasma \u201cCandidatus Phytoplasma mali\u201d","volume":"9","author":"M Kube","year":"2008","journal-title":"BMC Genomics"},{"key":"pgen.1011946.ref029","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1007\/978-1-4939-8837-2_5","article-title":"Symptoms of Phytoplasma Diseases","volume":"1875","author":"P Ermacora","year":"2019","journal-title":"Methods Mol Biol"},{"issue":"20","key":"pgen.1011946.ref030","doi-asserted-by":"crossref","DOI":"10.1016\/j.cell.2021.08.029","article-title":"Parasitic modulation of host development by ubiquitin-independent protein degradation","volume":"184","author":"W Huang","year":"2021","journal-title":"Cell"},{"issue":"9","key":"pgen.1011946.ref031","doi-asserted-by":"crossref","first-page":"2637","DOI":"10.1094\/PDIS-10-20-2112-RE","article-title":"Witches\u2019 Broom Disease of Lime Contributes to Phytoplasma Epidemics and Attracts Insect Vectors","volume":"105","author":"AM Al-Subhi","year":"2021","journal-title":"Plant Dis"},{"issue":"1","key":"pgen.1011946.ref032","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1094\/MPMI-22-1-0018","article-title":"AY-WB phytoplasma secretes a protein that targets plant cell nuclei","volume":"22","author":"X Bai","year":"2009","journal-title":"Mol Plant Microbe Interact"},{"issue":"49","key":"pgen.1011946.ref033","article-title":"Bimodular architecture of bacterial effector SAP05 that drives ubiquitin-independent targeted protein degradation","volume":"120","author":"Q Liu","year":"2023","journal-title":"Proc Natl Acad Sci"},{"issue":"3","key":"pgen.1011946.ref034","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1111\/nph.12721","article-title":"The small phytoplasma virulence effector SAP11 contains distinct domains required for nuclear targeting and CIN-TCP binding and destabilization","volume":"202","author":"A Sugio","year":"2014","journal-title":"New Phytol"},{"issue":"9","key":"pgen.1011946.ref035","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1008035","article-title":"Phytoplasma SAP11 effector destabilization of TCP transcription factors differentially impact development and defence of Arabidopsis versus maize","volume":"15","author":"P Pecher","year":"2019","journal-title":"PLoS Pathog"},{"issue":"48","key":"pgen.1011946.ref036","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.1105664108","article-title":"Phytoplasma protein effector SAP11 enhances insect vector reproduction by manipulating plant development and defense hormone biosynthesis","volume":"108","author":"A Sugio","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"14","key":"pgen.1011946.ref037","doi-asserted-by":"crossref","first-page":"4415","DOI":"10.1093\/jxb\/erw225","article-title":"Phytoplasma SAP11 alters 3-isobutyl-2-methoxypyrazine biosynthesis in Nicotiana benthamiana by suppressing NbOMT1","volume":"67","author":"CM Tan","year":"2016","journal-title":"J Exp Bot"},{"issue":"1","key":"pgen.1011946.ref038","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1186\/s12870-024-05087-4","article-title":"\u2018Candidatus Phytoplasma mali\u2019 SAP11\u2011Like protein modulates expression of genes involved in energy production, photosynthesis, and defense in Nicotiana occidentalis leaves","volume":"24","author":"C Mittelberger","year":"2024","journal-title":"BMC Plant Biology"},{"issue":"2","key":"pgen.1011946.ref039","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1104\/pp.111.181586","article-title":"Phytoplasma effector SAP54 induces indeterminate leaf-like flower development in Arabidopsis plants","volume":"157","author":"AM MacLean","year":"2011","journal-title":"Plant Physiol"},{"issue":"4","key":"pgen.1011946.ref040","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1111\/tpj.12495","article-title":"Recognition of floral homeotic MADS domain transcription factors by a phytoplasmal effector, phyllogen, induces phyllody","volume":"78","author":"K Maejima","year":"2014","journal-title":"Plant J"},{"issue":"4","key":"pgen.1011946.ref041","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.1001835","article-title":"Phytoplasma effector SAP54 hijacks plant reproduction by degrading MADS-box proteins and promotes insect colonization in a RAD23-dependent manner","volume":"12","author":"AM MacLean","year":"2014","journal-title":"PLoS Biol"},{"issue":"4","key":"pgen.1011946.ref042","doi-asserted-by":"crossref","first-page":"952","DOI":"10.1016\/j.bbrc.2019.04.060","article-title":"Crystal structure of phyllogen, a phyllody-inducing effector protein of phytoplasma","volume":"513","author":"N Iwabuchi","year":"2019","journal-title":"Biochem Biophys Res Commun"},{"issue":"5","key":"pgen.1011946.ref043","doi-asserted-by":"crossref","DOI":"10.1093\/plcell\/koac062","article-title":"A phytoplasma effector acts as a ubiquitin-like mediator between floral MADS-box proteins and proteasome shuttle proteins","volume":"34","author":"Y Kitazawa","year":"2022","journal-title":"Plant Cell"},{"key":"pgen.1011946.ref044","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.98992.3","article-title":"The phytoplasma SAP54 effector acts as a molecular matchmaker for leafhopper vectors by targeting plant MADS\u2011box factor SVP","volume":"13","author":"Z Orlovskis","year":"2025","journal-title":"eLife"},{"key":"pgen.1011946.ref045","doi-asserted-by":"crossref","first-page":"885","DOI":"10.3389\/fpls.2016.00885","article-title":"A Bacterial Parasite Effector Mediates Insect Vector Attraction in Host Plants Independently of Developmental Changes","volume":"7","author":"Z Orlovskis","year":"2016","journal-title":"Front Plant Sci"},{"key":"pgen.1011946.ref046","doi-asserted-by":"crossref","first-page":"7399","DOI":"10.1038\/srep07399","article-title":"The phytoplasmal virulence factor TENGU causes plant sterility by downregulating of the jasmonic acid and auxin pathways","volume":"4","author":"N Minato","year":"2014","journal-title":"Sci Rep"},{"issue":"6","key":"pgen.1011946.ref047","doi-asserted-by":"crossref","first-page":"1473","DOI":"10.1111\/tpj.16029","article-title":"The \u201cCandidatus Phytoplasma tritici\u201d effector SWP12 degrades the transcription factor TaWRKY74 to suppress wheat resistance","volume":"112","author":"B Bai","year":"2022","journal-title":"Plant J"},{"issue":"22","key":"pgen.1011946.ref048","article-title":"A phytoplasma effector destabilizes chloroplastic glutamine synthetase inducing chlorotic leaves that attract leafhopper vectors","volume":"121","author":"X-F Zhang","year":"2024","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"pgen.1011946.ref049","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1111\/nph.70172","article-title":"A witches\u2019 broom phytoplasma effector induces stunting by stabilizing a bHLH transcription factor in Ziziphus jujuba plants","volume":"247","author":"S Yang","year":"2025","journal-title":"New Phytol"},{"issue":"1","key":"pgen.1011946.ref050","doi-asserted-by":"crossref","DOI":"10.1093\/plphys\/kiae601","article-title":"Virulence effectors encoded in the rice yellow dwarf phytoplasma genome participate in pathogenesis","volume":"197","author":"S Zhang","year":"2024","journal-title":"Plant Physiol"},{"issue":"11","key":"pgen.1011946.ref051","doi-asserted-by":"crossref","first-page":"4252","DOI":"10.1073\/pnas.0508668103","article-title":"Interaction between the membrane protein of a pathogen and insect microfilament complex determines insect-vector specificity","volume":"103","author":"S Suzuki","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"7","key":"pgen.1011946.ref052","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0022571","article-title":"The major antigenic membrane protein of \u201cCandidatus Phytoplasma asteris\u201d selectively interacts with ATP synthase and actin of leafhopper vectors","volume":"6","author":"L Galetto","year":"2011","journal-title":"PLoS One"},{"issue":"7","key":"pgen.1011946.ref053","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1094\/MPMI-11-11-0303","article-title":"An immunodominant membrane protein (Imp) of \u201cCandidatus Phytoplasma mali\u201d binds to plant actin","volume":"25","author":"K Boonrod","year":"2012","journal-title":"Mol Plant Microbe Interact"},{"issue":"2","key":"pgen.1011946.ref054","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1111\/1574-6968.12620","article-title":"Onion yellow phytoplasma P38 protein plays a role in adhesion to the hosts","volume":"361","author":"Y Neriya","year":"2014","journal-title":"FEMS Microbiol Lett"},{"issue":"11","key":"pgen.1011946.ref055","doi-asserted-by":"crossref","first-page":"1487","DOI":"10.1094\/MPMI-04-19-0107-R","article-title":"\u201cCandidatus Phytoplasma mali\u201d Genome Encodes a Protein that Functions as an E3 Ubiquitin Ligase and Could Inhibit Plant Basal Defense","volume":"32","author":"A Strohmayer","year":"2019","journal-title":"Mol Plant Microbe Interact"},{"issue":"7873","key":"pgen.1011946.ref056","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"J Jumper","year":"2021","journal-title":"Nature"},{"issue":"7","key":"pgen.1011946.ref057","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"DH Parks","year":"2015","journal-title":"Genome Res"},{"issue":"1","key":"pgen.1011946.ref058","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.1038\/s41467-024-45521-7","article-title":"Molecular basis of SAP05-mediated ubiquitin-independent proteasomal degradation of transcription factors","volume":"15","author":"X Yan","year":"2024","journal-title":"Nat Commun"},{"issue":"2","key":"pgen.1011946.ref059","doi-asserted-by":"crossref","first-page":"108892","DOI":"10.1016\/j.isci.2024.108892","article-title":"Structure basis for recognition of plant Rpn10 by phytoplasma SAP05 in ubiquitin-independent protein degradation","volume":"27","author":"L Zhang","year":"2024","journal-title":"iScience"},{"issue":"4","key":"pgen.1011946.ref060","doi-asserted-by":"crossref","first-page":"706","DOI":"10.1111\/tpj.14463","article-title":"Structural insights into the interaction between phytoplasmal effector causing phyllody 1 and MADS transcription factors","volume":"100","author":"Y-T Liao","year":"2019","journal-title":"Plant J"},{"issue":"9","key":"pgen.1011946.ref061","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1094\/MPMI-02-20-0028-R","article-title":"Structural Requirements of the Phytoplasma Effector Protein SAP54 for Causing Homeotic Transformation of Floral Organs","volume":"33","author":"M-B Aurin","year":"2020","journal-title":"Mol Plant Microbe Interact"},{"issue":"7983","key":"pgen.1011946.ref062","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1038\/s41586-023-06510-w","article-title":"Clustering predicted structures at the scale of the known protein universe","volume":"622","author":"I Barrio-Hernandez","year":"2023","journal-title":"Nature"},{"issue":"6","key":"pgen.1011946.ref063","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1093\/bioinformatics\/btm006","article-title":"On the relationship between sequence and structure similarities in proteomics","volume":"23","author":"E Krissinel","year":"2007","journal-title":"Bioinformatics"},{"key":"pgen.1011946.ref064","doi-asserted-by":"crossref","first-page":"661524","DOI":"10.3389\/fmicb.2021.661524","article-title":"Comparison of Current Methods for Signal Peptide Prediction in Phytoplasmas","volume":"12","author":"C Garcion","year":"2021","journal-title":"Front Microbiol"},{"issue":"11","key":"pgen.1011946.ref065","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1139\/W10-079","article-title":"Hemolytic phospholipase Rv0183 of Mycobacterium tuberculosis induces inflammatory response and apoptosis in alveolar macrophage RAW264.7 cells","volume":"56","author":"G Xu","year":"2010","journal-title":"Can J Microbiol"},{"issue":"11","key":"pgen.1011946.ref066","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1038\/nbt.3988","article-title":"MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets","volume":"35","author":"M Steinegger","year":"2017","journal-title":"Nat Biotechnol"},{"key":"pgen.1011946.ref067","article-title":"Multiple protein structure alignment at scale with FoldMason","author":"CLM Gilchrist","year":"2022","journal-title":"bioRxiv"},{"issue":"1","key":"pgen.1011946.ref068","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.jmb.2004.01.015","article-title":"A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors","volume":"337","author":"K Yamasaki","year":"2004","journal-title":"J Mol Biol"},{"issue":"5","key":"pgen.1011946.ref069","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1016\/j.celrep.2012.10.012","article-title":"DNA binding by GATA transcription factor suggests mechanisms of DNA looping and long-range gene regulation","volume":"2","author":"Y Chen","year":"2012","journal-title":"Cell Rep"},{"key":"pgen.1011946.ref070","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkad1011","article-title":"AlphaFold Protein Structure Database in 2024: Providing Structure Coverage for Over 214 Million Protein Sequences","volume":"52","author":"M Varadi","year":"2024","journal-title":"Nucleic Acids Research"},{"issue":"10","key":"pgen.1011946.ref071","doi-asserted-by":"crossref","first-page":"1322","DOI":"10.1111\/mpp.12981","article-title":"Functional variation in phyllogen, a phyllody-inducing phytoplasma effector family, attributable to a single amino acid polymorphism","volume":"21","author":"N Iwabuchi","year":"2020","journal-title":"Mol Plant Pathol"},{"issue":"5","key":"pgen.1011946.ref072","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/87575","volume":"8","author":"BL Bertolaet","year":"2001","journal-title":"Nat Struct Biol"},{"issue":"4","key":"pgen.1011946.ref073","doi-asserted-by":"crossref","first-page":"1281","DOI":"10.1111\/tpj.16546","article-title":"Protein interaction mapping reveals widespread targeting of development-related host transcription factors by phytoplasma effectors","volume":"117","author":"M Correa Marrero","year":"2024","journal-title":"Plant J"},{"issue":"1","key":"pgen.1011946.ref074","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1093\/nar\/gkac1171","article-title":"DNA-TCP complex structures reveal a unique recognition mechanism for TCP transcription factor families","volume":"51","author":"Y Zhang","year":"2023","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"pgen.1011946.ref075","doi-asserted-by":"crossref","first-page":"700","DOI":"10.1093\/bioinformatics\/17.8.700","article-title":"AL2CO: calculation of positional conservation in a protein sequence alignment","volume":"17","author":"J Pei","year":"2001","journal-title":"Bioinformatics"},{"key":"pgen.1011946.ref076","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gky360","article-title":"RepeatsDB-lite: a web server for unit annotation of tandem repeat proteins","volume":"46","author":"L Hirsh","year":"2018","journal-title":"Nucleic Acids Research"},{"issue":"6","key":"pgen.1011946.ref077","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1093\/bioinformatics\/btn039","article-title":"De novo identification of highly diverged protein repeats by probabilistic consistency","volume":"24","author":"A Biegert","year":"2008","journal-title":"Bioinformatics"},{"issue":"11","key":"pgen.1011946.ref078","article-title":"Structural basis for SdgB- and SdgA-mediated glycosylation of staphylococcal adhesive proteins","volume":"77","author":"DG Kim","year":"2021","journal-title":"Acta Crystallogr Sect Struct Biol"},{"key":"pgen.1011946.ref079","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkab1061","article-title":"AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models","volume":"50","author":"M Varadi","year":"2022","journal-title":"Nucleic Acids Research"},{"issue":"2","key":"pgen.1011946.ref080","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1038\/s41587-023-01773-0","article-title":"Fast and accurate protein structure search with Foldseek","volume":"42","author":"M van Kempen","year":"2024","journal-title":"Nat Biotechnol"},{"issue":"5","key":"pgen.1011946.ref081","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"RC Edgar","year":"2004","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pgen.1011946.ref082","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1099\/00207713-34-1-11","article-title":"Acholeplasma florum, a new species isolated from plants","volume":"34","author":"RE Mccoy","year":"1984","journal-title":"Int J Syst Bacteriol"},{"key":"pgen.1011946.ref083","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1186\/1471-2180-9-139","article-title":"Intracellular Mycoplasma genitalium infection of human vaginal and cervical epithelial cells elicits distinct patterns of inflammatory cytokine secretion and provides a possible survival niche against macrophage-mediated killing","volume":"9","author":"CL McGowin","year":"2009","journal-title":"BMC Microbiol"},{"issue":"3","key":"pgen.1011946.ref084","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1012973","article-title":"Dynamics of the adhesion complex of the human pathogens Mycoplasma pneumoniae and Mycoplasma genitalium","volume":"21","author":"D Vizarraga","year":"2025","journal-title":"PLoS Pathog"},{"issue":"23","key":"pgen.1011946.ref085","doi-asserted-by":"crossref","first-page":"5293","DOI":"10.1093\/nar\/gkf667","article-title":"The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans","volume":"30","author":"Y Sasaki","year":"2002","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"pgen.1011946.ref086","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1128\/JB.06297-11","article-title":"Genome sequence of Mycoplasma iowae strain 695, an unusual pathogen causing deaths in turkeys","volume":"194","author":"S Wei","year":"2012","journal-title":"J Bacteriol"},{"issue":"1","key":"pgen.1011946.ref087","doi-asserted-by":"crossref","first-page":"96","DOI":"10.21037\/tau-20-920","article-title":"The role of Ureaplasma parvum serovar-3 or serovar-14 infection in female patients with chronic micturition urethral pain and recurrent microscopic hematuria","volume":"10","author":"MS Kim","year":"2021","journal-title":"Transl Androl Urol"},{"issue":"3","key":"pgen.1011946.ref088","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1099\/00207713-47-3-713","article-title":"Spiroplasma chrysopicola sp. nov., Spiroplasma gladiatoris sp. nov., Spiroplasma helicoides sp. nov., and Spiroplasma tabanidicola sp. nov., from Tabanid (Diptera: Tabanidae) flies","volume":"47","author":"RF Whitcomb","year":"1997","journal-title":"Int J Syst Evol Microbiol"},{"issue":"1","key":"pgen.1011946.ref089","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1186\/s12864-021-07637-8","article-title":"Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors","volume":"22","author":"R Rattner","year":"2021","journal-title":"BMC Genomics"},{"issue":"3","key":"pgen.1011946.ref090","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1099\/00207713-35-3-296","article-title":"Spiroplasma melliferum, a new species from the honeybee (Apis mellifera)","volume":"35","author":"TB Clark","year":"1985","journal-title":"Int J Syst Bacteriol"},{"issue":"9","key":"pgen.1011946.ref091","doi-asserted-by":"crossref","first-page":"2735","DOI":"10.1099\/ijsem.0.003548","article-title":"Genome analysis-based union of the genus Mesoplasma with the genus Entomoplasma","volume":"69","author":"GE Gasparich","year":"2019","journal-title":"Int J Syst Evol Microbiol"},{"issue":"2","key":"pgen.1011946.ref092","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1099\/00207713-40-2-138","article-title":"Mycoplasma lactucae sp. nov., a sterol-requiring mollicute from a plant surface","volume":"40","author":"DL Rose","year":"1990","journal-title":"Int J Syst Bacteriol"},{"issue":"3","key":"pgen.1011946.ref093","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1016\/j.rvsc.2004.09.004","article-title":"Detection of Mycoplasma mycoides subspecies mycoides SC in bovine lung and lymph node tissues by culture, sandwich ELISA and polymerase chain reaction systems","volume":"78","author":"JB Bashiruddin","year":"2005","journal-title":"Res Vet Sci"},{"issue":"2","key":"pgen.1011946.ref094","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1099\/00207713-40-2-143","article-title":"Mycoplasma melaleucae sp. nov., a sterol-requiring mollicute from flowers of several tropical plants","volume":"40","author":"JG Tully","year":"1990","journal-title":"Int J Syst Bacteriol"},{"issue":"4","key":"pgen.1011946.ref095","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1099\/00207713-44-4-685","article-title":"Taxonomic descriptions of eight new non-sterol-requiring mollicutes assigned to the genus Mesoplasma","volume":"44","author":"JG Tully","year":"1994","journal-title":"Int J Syst Bacteriol"},{"issue":"4","key":"pgen.1011946.ref096","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1099\/00207713-48-4-1197","article-title":"Entomoplasma freundtii sp. nov., a new species from a green tiger beetle (Coleoptera: Cicindelidae)","volume":"48","author":"JG Tully","year":"1998","journal-title":"Int J Syst Bacteriol"},{"issue":"2","key":"pgen.1011946.ref097","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1099\/00207713-38-2-164","article-title":"Acholeplasma entomophilum sp. nov. from gut contents of a wide range of host insects","volume":"38","author":"JG Tully","year":"1988","journal-title":"Int J Syst Bacteriol"},{"issue":"22","key":"pgen.1011946.ref098","doi-asserted-by":"crossref","first-page":"4520","DOI":"10.1016\/j.jmb.2013.08.010","article-title":"Structure of internalin InlK from the human pathogen Listeria monocytogenes","volume":"425","author":"D Neves","year":"2013","journal-title":"J Mol Biol"},{"issue":"8","key":"pgen.1011946.ref099","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1002168","article-title":"Recruitment of the major vault protein by InlK: a Listeria monocytogenes strategy to avoid autophagy","volume":"7","author":"L Dortet","year":"2011","journal-title":"PLoS Pathog"},{"issue":"1","key":"pgen.1011946.ref100","doi-asserted-by":"crossref","first-page":"2211","DOI":"10.1038\/s41598-023-29341-1","article-title":"Flavescence dor\u00e9e phytoplasma enters insect cells by a clathrin-mediated endocytosis allowing infection of its insect vector","volume":"13","author":"N Arricau-Bouvery","year":"2023","journal-title":"Sci Rep"},{"key":"pgen.1011946.ref101","doi-asserted-by":"crossref","first-page":"1289100","DOI":"10.3389\/fcimb.2023.1289100","article-title":"A knockdown gene approach identifies an insect vector membrane protein with leucin-rich repeats as one of the receptors for the VmpA adhesin of flavescence dor\u00e9e phytoplasma","volume":"13","author":"F Canuto","year":"2023","journal-title":"Front Cell Infect Microbiol"},{"key":"pgen.1011946.ref102","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1099\/mic.0.26521-0","article-title":"Secretion of immunodominant membrane protein from onion yellows phytoplasma through the Sec protein-translocation system in Escherichia coli","volume":"150","author":"S Kakizawa","year":"2004","journal-title":"Microbiology (Reading)"},{"issue":"7","key":"pgen.1011946.ref103","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1094\/PHYTO-98-7-0769","article-title":"Cloning and characterization of the antigenic membrane protein (Amp) gene and in situ detection of Amp from malformed flowers infected with Japanese hydrangea phyllody phytoplasma","volume":"98","author":"R Arashida","year":"2008","journal-title":"Phytopathology"},{"key":"pgen.1011946.ref104","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1107\/S2052252524003075","article-title":"Structural insights into the molecular mechanism of phytoplasma immunodominant membrane protein","volume":"11","author":"CY Liu","year":"2024","journal-title":"IUCrJ"},{"issue":"2","key":"pgen.1011946.ref105","doi-asserted-by":"crossref","first-page":"968","DOI":"10.3390\/ijms24020968","article-title":"Identification of the Actin-Binding Region and Binding to Host Plant Apple Actin of Immunodominant Transmembrane Protein of \u201cCandidatus Phytoplasma mali\u201d","volume":"24","author":"K Boonrod","year":"2023","journal-title":"Int J Mol Sci"},{"issue":"2","key":"pgen.1011946.ref106","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1073\/pnas.1518648113","article-title":"A ribosome-inactivating protein in a Drosophila defensive symbiont","volume":"113","author":"PT Hamilton","year":"2016","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"7443","key":"pgen.1011946.ref107","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1038\/nature12004","article-title":"Proteolytic elimination of N-myristoyl modifications by the Shigella virulence factor IpaJ","volume":"496","author":"N Burnaevskiy","year":"2013","journal-title":"Nature"},{"issue":"2","key":"pgen.1011946.ref108","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1093\/protein\/12.2.85","article-title":"Twilight zone of protein sequence alignments","volume":"12","author":"B Rost","year":"1999","journal-title":"Protein Eng"},{"issue":"5","key":"pgen.1011946.ref109","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1002\/iub.1992","article-title":"New paradigm of functional regulation by DNA mimic proteins: Recent updates","volume":"71","author":"H-C Wang","year":"2019","journal-title":"IUBMB Life"},{"issue":"8","key":"pgen.1011946.ref110","doi-asserted-by":"crossref","first-page":"1769","DOI":"10.1111\/jipb.13710","article-title":"The processed C-terminus of AvrRps4 effector suppresses plant immunity via targeting multiple WRKYs","volume":"66","author":"Q-M Nguyen","year":"2024","journal-title":"J Integr Plant Biol"},{"issue":"50","key":"pgen.1011946.ref111","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2113996118","article-title":"Perception of structurally distinct effectors by the integrated WRKY domain of a plant immune receptor","volume":"118","author":"N Mukhi","year":"2021","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pgen.1011946.ref112","doi-asserted-by":"crossref","first-page":"17115","DOI":"10.1038\/nplants.2017.115","article-title":"Mechanism of host substrate acetylation by a YopJ family effector","volume":"3","author":"Z-M Zhang","year":"2017","journal-title":"Nat Plants"},{"key":"pgen.1011946.ref113","doi-asserted-by":"crossref","first-page":"872","DOI":"10.3389\/fpls.2015.00872","article-title":"Repeat\u2011containing protein effectors of plant\u2011associated organisms","volume":"6","author":"CH Mesarich","year":"2015","journal-title":"Front Plant Sci"},{"issue":"4","key":"pgen.1011946.ref114","article-title":"Comparative analysis of the peanut witches\u2019-broom phytoplasma genome reveals horizontal transfer of potential mobile units and effectors","volume":"8","author":"W-C Chung","year":"2013","journal-title":"PLoS One"},{"issue":"2","key":"pgen.1011946.ref115","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0239956","article-title":"\u201cCandidatus Phytoplasma asteris\u201d subgroups display distinct disease progression dynamics during the carrot growing season","volume":"16","author":"J Clements","year":"2021","journal-title":"PLoS One"},{"issue":"5","key":"pgen.1011946.ref116","article-title":"Horizontal transfer of potential mobile units in phytoplasmas","volume":"3","author":"C Ku","year":"2013","journal-title":"Mob Genet Elements"},{"key":"pgen.1011946.ref117","doi-asserted-by":"crossref","first-page":"1132432","DOI":"10.3389\/fgene.2023.1132432","article-title":"Potential mobile units drive the horizontal transfer of phytoplasma effector phyllogen genes","volume":"14","author":"R Tokuda","year":"2023","journal-title":"Frontiers in Genetics"},{"key":"pgen.1011946.ref118","doi-asserted-by":"crossref","first-page":"1809","DOI":"10.1099\/mic.0.26806-0","article-title":"Sequence analysis of two plasmids from the phytoplasma beet leafhopper-transmitted virescence agent","volume":"150","author":"LW Liefting","year":"2004","journal-title":"Microbiology (Reading)"},{"issue":"9","key":"pgen.1011946.ref119","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"A Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"issue":"1","key":"pgen.1011946.ref120","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"L-T Nguyen","year":"2015","journal-title":"Mol Biol Evol"},{"issue":"4","key":"pgen.1011946.ref121","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1016\/j.jmb.2004.05.028","article-title":"Improved prediction of signal peptides: SignalP 3.0","volume":"340","author":"J Dyrl\u00f8v Bendtsen","year":"2004","journal-title":"J Mol Biol"},{"issue":"3","key":"pgen.1011946.ref122","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","article-title":"Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes","volume":"305","author":"A Krogh","year":"2001","journal-title":"J Mol Biol"},{"key":"pgen.1011946.ref123","unstructured":"Mirkin FG, Mugford ST, Thole V, Marzo M, Hogenhout SA. Alphafold structural models for putative phytoplasma effectors (phames). 2025. https:\/\/doi.org\/10.5281\/zenodo.17379298"},{"issue":"6","key":"pgen.1011946.ref124","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/s41592-022-01488-1","article-title":"ColabFold: making protein folding accessible to all","volume":"19","author":"M Mirdita","year":"2022","journal-title":"Nat Methods"},{"issue":"1","key":"pgen.1011946.ref125","doi-asserted-by":"crossref","first-page":"2542","DOI":"10.1038\/s41467-018-04964-5","article-title":"Clustering huge protein sequence sets in linear time","volume":"9","author":"M Steinegger","year":"2018","journal-title":"Nat Commun"},{"issue":"11","key":"pgen.1011946.ref126","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"P Shannon","year":"2003","journal-title":"Genome Res"},{"issue":"17","key":"pgen.1011946.ref127","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"S Altschul","year":"1997","journal-title":"Nucleic Acids Research"},{"issue":"23","key":"pgen.1011946.ref128","doi-asserted-by":"crossref","first-page":"4575","DOI":"10.1093\/bioinformatics\/btab631","article-title":"Socket2: a program for locating, visualizing and analyzing coiled-coil interfaces in protein structures","volume":"37","author":"P Kumar","year":"2021","journal-title":"Bioinformatics"},{"key":"pgen.1011946.ref129","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1186\/1471-2105-7-339","article-title":"Tools for integrated sequence-structure analysis with UCSF Chimera","volume":"7","author":"EC Meng","year":"2006","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"pgen.1011946.ref130","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1002\/pro.3943","article-title":"UCSF ChimeraX: Structure visualization for researchers, educators, and developers","volume":"30","author":"EF Pettersen","year":"2021","journal-title":"Protein Sci"},{"issue":"8","key":"pgen.1011946.ref131","doi-asserted-by":"crossref","first-page":"1194","DOI":"10.1016\/j.molp.2020.06.009","article-title":"TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data","volume":"13","author":"C Chen","year":"2020","journal-title":"Mol Plant"},{"key":"pgen.1011946.ref132","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool","volume":"52","author":"I Letunic","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"pgen.1011946.ref133","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkae1082","article-title":"InterPro: the protein sequence classification resource in 2025","volume":"53","author":"M Blum","year":"2025","journal-title":"Nucleic Acids Research"},{"key":"pgen.1011946.ref134","first-page":"107","article-title":"Yeast transformation by the LiAc\/SS Carrier DNA\/PEG method","volume":"313","author":"RD Gietz","year":"2006","journal-title":"Methods Mol Biol"},{"issue":"1","key":"pgen.1011946.ref135","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1016\/0003-2697(91)90045-U","article-title":"Development of hydrophobicity parameters to analyze proteins which bear post- or cotranslational modifications","volume":"193","author":"SD Black","year":"1991","journal-title":"Anal Biochem"}],"updated-by":[{"DOI":"10.1371\/journal.pgen.1011946","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,11,20]],"date-time":"2025-11-20T00:00:00Z","timestamp":1763596800000}}],"container-title":["PLOS Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1011946","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,20]],"date-time":"2025-11-20T18:47:40Z","timestamp":1763664460000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1011946"}},"subtitle":[],"editor":[{"given":"Frank O.","family":"Aylward","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,11,13]]},"references-count":135,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2025,11,13]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1011946","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.07.14.664665","asserted-by":"object"}]},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,13]]}}}