{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T13:18:01Z","timestamp":1776172681431,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2020,11,13]],"date-time":"2020-11-13T00:00:00Z","timestamp":1605225600000},"content-version":"vor","delay-in-days":317,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["307986\/2012-8"],"award-info":[{"award-number":["307986\/2012-8"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002322","name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","doi-asserted-by":"publisher","award":["3371\/2013"],"award-info":[{"award-number":["3371\/2013"]}],"id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002322","name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","doi-asserted-by":"publisher","award":["001"],"award-info":[{"award-number":["001"]}],"id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","doi-asserted-by":"publisher","award":["2011\/05477-4"],"award-info":[{"award-number":["2011\/05477-4"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"name":"scientific initiation scholarship","award":["PIBIC\/CNPq\/UNESP"],"award-info":[{"award-number":["PIBIC\/CNPq\/UNESP"]}]},{"DOI":"10.13039\/501100004612","name":"Funda\u00e7\u00e3o Arauc\u00e1ria","doi-asserted-by":"publisher","award":["CP09\/2016"],"award-info":[{"award-number":["CP09\/2016"]}],"id":[{"id":"10.13039\/501100004612","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Citrus canker type A is a serious disease caused by Xanthomonas citri subsp. citri (X. citri), which is responsible for severe losses to growers and to the citrus industry worldwide. To date, no canker-resistant citrus genotypes are available, and there is limited information regarding the molecular and genetic mechanisms involved in the early stages of the citrus canker development. Here, we present the CitrusKB knowledge base. This is the first in vivo interactome database for different citrus cultivars, and it was produced to provide a valuable resource of information on citrus and their interaction with the citrus canker bacterium X. citri. CitrusKB provides tools for a user-friendly web interface to let users search and analyse a large amount of information regarding eight citrus cultivars with distinct levels of susceptibility to the disease, with controls and infected plants at different stages of infection by the citrus canker bacterium X. citri. Currently, CitrusKB comprises a reference citrus genome and its transcriptome, expressed transcripts, pseudogenes and predicted genomic variations (SNPs and SSRs). The updating process will continue over time by the incorporation of novel annotations and analysis tools. We expect that CitrusKB may substantially contribute to the field of citrus genomics. CitrusKB is accessible at http:\/\/bioinfo.deinfo.uepg.br\/citrus. Users can download all the generated raw sequences and generated datasets by this study from the CitrusKB website.<\/jats:p>","DOI":"10.1093\/database\/baaa081","type":"journal-article","created":{"date-parts":[[2020,9,1]],"date-time":"2020-09-01T07:09:51Z","timestamp":1598944191000},"source":"Crossref","is-referenced-by-count":7,"title":["CitrusKB: a comprehensive knowledge base for transcriptome and interactome of\n                    <i>Citrus<\/i>\n                    spp. infected by\n                    <i>Xanthomonas citri<\/i>\n                    subsp.\n                    <i>citri<\/i>\n                    at different infection stages"],"prefix":"10.1093","volume":"2020","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6653-1849","authenticated-orcid":false,"given":"Adriano","family":"Ferrasa","sequence":"first","affiliation":[{"name":"Departamento de Inform\u00e1tica, Universidade Estadual de Ponta Grossa (UEPG), Av. Carlos Cavalcanti, 4748, 84030-900, Ponta Grossa, PR, Brazil"},{"name":"Graduate Program in Health Sciences, School of Medicine, Pontif\u00edcia Universidade Cat\u00f3lica do Paran\u00e1 (PUCPR), R. Imaculada Concei\u00e7\u00e3o, 1155, 80215-901, Curitiba, PR, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mayara M","family":"Murata","sequence":"additional","affiliation":[{"name":"Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s\/n, 14884-900, Jaboticabal, SP, Brazil"},{"name":"Diretoria de P\u00d3s-Gradua\u00e7\u00e3o Stricto Sensu, Universidade Norte do Paran\u00e1 (UNOPAR), Av. Paris, 675, 86041-100, Londrina, PR, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Teresa D C G","family":"Cofre","sequence":"additional","affiliation":[{"name":"Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s\/n, 14884-900, Jaboticabal, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juliana S","family":"Cavallini","sequence":"additional","affiliation":[{"name":"Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s\/n, 14884-900, Jaboticabal, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gustavo","family":"Peron","sequence":"additional","affiliation":[{"name":"Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s\/n, 14884-900, Jaboticabal, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria H M","family":"Juli\u00e3o","sequence":"additional","affiliation":[{"name":"Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s\/n, 14884-900, Jaboticabal, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jos\u00e9","family":"Belasque","sequence":"additional","affiliation":[{"name":"Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura \u2018Luiz de Queiroz\u2019, Universidade de S\u00e3o Paulo (USP), Av. P\u00e1dua Dias, 11, 13418-900, Piracicaba, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Henrique","family":"Ferreira","sequence":"additional","affiliation":[{"name":"Departamento de Biologia Geral e Aplicada, Instituto de Bioci\u00eancias, Universidade Estadual Paulista (UNESP), Av. 24-A, 1515, 13506-900, Rio Claro, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria In\u00eas T","family":"Ferro","sequence":"additional","affiliation":[{"name":"Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s\/n, 14884-900, Jaboticabal, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"suffix":"Jr","given":"Rui P","family":"Leite","sequence":"additional","affiliation":[{"name":"Instituto Agron\u00f4mico do Paran\u00e1 (IAPAR), Londrina, Rod. Celso Garcia Cid, km 375, 86047-902, Londrina, PR, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Helen A","family":"Penha","sequence":"additional","affiliation":[{"name":"Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s\/n, 14884-900, Jaboticabal, SP, Brazil"},{"name":"Inprenha Biotecnologia e Desenvolvimento Avan\u00e7ado LTDA, Fazenda Lagoinha, Estrada Velha de Taquaritinga, Km 04, 14870-970, Jaboticabal, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fl\u00e1via M S","family":"Carvalho","sequence":"additional","affiliation":[{"name":"Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s\/n, 14884-900, Jaboticabal, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessandro M","family":"Varani","sequence":"additional","affiliation":[{"name":"Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s\/n, 14884-900, Jaboticabal, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9885-2735","authenticated-orcid":false,"given":"Roberto H","family":"Herai","sequence":"additional","affiliation":[{"name":"Graduate Program in Health Sciences, School of Medicine, Pontif\u00edcia Universidade Cat\u00f3lica do Paran\u00e1 (PUCPR), R. Imaculada Concei\u00e7\u00e3o, 1155, 80215-901, Curitiba, PR, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jesus A","family":"Ferro","sequence":"additional","affiliation":[{"name":"Departamento de Tecnologia, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane s\/n, 14884-900, Jaboticabal, SP, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,11,11]]},"reference":[{"key":"2020111216461542300_R1","doi-asserted-by":"crossref","first-page":"18427","DOI":"10.1073\/pnas.0705590104","article-title":"Genetic diversity of citrus bacterial canker pathogens preserved in herbarium specimens","volume":"104","author":"Li","year":"2007","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2020111216461542300_R2","doi-asserted-by":"crossref","DOI":"10.1155\/2008\/528361","article-title":"Citrus genomics","volume":"2008","author":"Talon","year":"2008","journal-title":"Int. J. Plant Genomics"},{"key":"2020111216461542300_R3","first-page":"127","article-title":"Bacterial canker disease of citrus","volume":"37","author":"Civerolo","year":"1984","journal-title":"J. Rio Gd. Val. Hortic. Soc."},{"key":"2020111216461542300_R4","volume-title":"Manual Ilustrado de Doen\u00e7as dos Citros","author":"Rossetti","year":"2001"},{"key":"2020111216461542300_R5","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.1111\/j.1365-3059.2010.02344.x","article-title":"Annual and polyetic progression of citrus canker on trees protected with copper sprays","volume":"59","author":"Behlau","year":"2010","journal-title":"Plant Pathol."},{"key":"2020111216461542300_R6","first-page":"30","article-title":"Incid\u00eancia e distribui\u00e7\u00e3o de cancro c\u00edtrico em pomares comerciais Estado de S\u00e3o Paulo e sul do Tri\u00e2ngulo Mineiro","volume":"27","author":"Barbosa","year":"2001","journal-title":"Summa Phytopathol."},{"key":"2020111216461542300_R7","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1094\/PDIS-04-14-0384-RE","article-title":"Comparison of resistance to Asiatic citrus canker among different genotypes of Citrus in a long-term canker-resistance field screening experiment in Brazil","volume":"99","author":"de Carvalho","year":"2015","journal-title":"Plant Dis."},{"key":"2020111216461542300_R8","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1016\/j.pmpp.2008.03.001","article-title":"New insights into the resistance of Nagami kumquat to canker disease","volume":"71","author":"Khalaf","year":"2007","journal-title":"Physiol. Mol. Plant Pathol."},{"key":"2020111216461542300_R9","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1111\/j.1364-3703.2008.00486.x","article-title":"Transcriptional analysis of the sweet orange interaction with the citrus canker pathogens Xanthomonas axonopodis pv. citri and Xanthomonas axonopodis pv. aurantifolii","volume":"9","author":"Cernadas","year":"2008","journal-title":"Mol. Plant Pathol."},{"issue":"7","key":"2020111216461542300_R10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0041790","article-title":"Different transcriptional response to Xanthomonas citri subsp. citri between kumquat and sweet orange with contrasting canker tolerance","volume":"7","author":"Fu","year":"2012","journal-title":"PLoS One"},{"key":"2020111216461542300_R11","doi-asserted-by":"crossref","first-page":"938","DOI":"10.1111\/pbi.12447","article-title":"An RNA-Seq-based reference transcriptome for citrus","volume":"14","author":"Terol","year":"2016","journal-title":"Plant Biotechnol. J."},{"issue":"1","key":"2020111216461542300_R12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0087723","article-title":"Citrus sinensis Annotation Project (CAP): a comprehensive database for sweet orange genome","volume":"9","author":"Wang","year":"2014","journal-title":"PLoS One"},{"key":"2020111216461542300_R13","article-title":"Novel plastid-nuclear genome combinations enhance resistance to citrus canker in cybrid grapefruit","volume":"9","author":"Murata","year":"2018","journal-title":"Front. Plant Sci."},{"key":"2020111216461542300_R14","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1038\/417459a","article-title":"Comparison of the genomes of two Xanthomonas pathogens with differing host specificities","volume":"417","author":"da Silva","year":"2002","journal-title":"Nature"},{"issue":"2","key":"2020111216461542300_R15","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0030619","article-title":"NGS QC toolkit: a toolkit for quality control of next generation sequencing data","volume":"7","author":"Patel","year":"2012","journal-title":"PLoS ONE"},{"key":"2020111216461542300_R16","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1038\/nbt.2906","article-title":"Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication","volume":"32","author":"Wu","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"2020111216461542300_R17","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2013-14-4-r36","article-title":"TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions","volume":"14","author":"Kim","year":"2013","journal-title":"Genome Biol."},{"key":"2020111216461542300_R18","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/nbt.1621","article-title":"Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation","volume":"28","author":"Trapnell","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"2020111216461542300_R19","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1007\/978-1-4939-9173-0_14","article-title":"BUSCO: assessing genome assembly and annotation completeness","volume":"1962","author":"Seppey","year":"2019","journal-title":"Methods Mol. 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