{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T10:18:10Z","timestamp":1769595490480,"version":"3.49.0"},"reference-count":58,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2019,11,4]],"date-time":"2019-11-04T00:00:00Z","timestamp":1572825600000},"content-version":"vor","delay-in-days":307,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Hatch Act and State of Iowa Funds"},{"DOI":"10.13039\/501100008982","name":"National Science Foundation","doi-asserted-by":"publisher","award":["ACI-1445606"],"award-info":[{"award-number":["ACI-1445606"]}],"id":[{"id":"10.13039\/501100008982","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008982","name":"National Science Foundation","doi-asserted-by":"publisher","award":["ACI-1548562"],"award-info":[{"award-number":["ACI-1548562"]}],"id":[{"id":"10.13039\/501100008982","id-type":"DOI","asserted-by":"publisher"}]},{"name":"North Central Soybean Research Program"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Soybean is an important worldwide crop, and farmers continue to experience significant yield loss due to the soybean cyst nematode (SCN), Heterodera glycines. This soil-borne roundworm parasite is rated the most important pathogen problem in soybean production. The infective nematodes enter into complex interactions with their host plant by inducing the development of specialized plant feeding cells that provide the parasites with nourishment. Addressing the SCN problem will require the development of genomic resources and a global collaboration of scientists to analyze and use these resources. SCNBase.org was designed as a collaborative hub for the SCN genome. All data and analyses are downloadable and can be analyzed with three integrated genomic tools: JBrowse, Feature Search and BLAST. At the time of this writing, a number of genomic and transcriptomic data sets are already available, with 43 JBrowse tracks and 21 category pages describing SCN genomic analyses on gene predictions, transcriptome and read alignments, effector-like genes, expansion and contraction of genomic repeats, orthology and synteny with related nematode species, Single Nucleotide Polymorphism (SNPs) from 15 SCN populations and novel splice sites. Standard functional gene annotations were supplemented with orthologous gene annotations using a comparison to nine related plant-parasitic nematodes, thereby enabling functional annotations for 85% of genes. These annotations led to a greater grasp on the SCN effectorome, which include over 3324 putative effector genes. By designing SCNBase as a hub, future research findings and genomic resources can easily be uploaded and made available for use by others with minimal needs for further curation. By providing these resources to nematode research community, scientists will be empowered to develop novel, more effective SCN management tools.<\/jats:p>","DOI":"10.1093\/database\/baz111","type":"journal-article","created":{"date-parts":[[2019,8,17]],"date-time":"2019-08-17T19:12:11Z","timestamp":1566069131000},"source":"Crossref","is-referenced-by-count":19,"title":["SCNBase: a genomics portal for the soybean cyst nematode (Heterodera glycines)"],"prefix":"10.1093","volume":"2019","author":[{"given":"Rick","family":"Masonbrink","sequence":"first","affiliation":[{"name":"Genome Informatics Facility, Iowa State University, Osborne Dr, Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tom R","family":"Maier","sequence":"additional","affiliation":[{"name":"Department of Plant Pathology and Microbiology, Iowa State University, Pammel Dr, Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arun S","family":"Seetharam","sequence":"additional","affiliation":[{"name":"Genome Informatics Facility, Iowa State University, Osborne Dr, Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Parijat S","family":"Juvale","sequence":"additional","affiliation":[{"name":"Department of Plant Pathology and Microbiology, Iowa State University, Pammel Dr, Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Levi","family":"Baber","sequence":"additional","affiliation":[{"name":"Research IT, Iowa State University, Osborne Dr, Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas J","family":"Baum","sequence":"additional","affiliation":[{"name":"Department of Plant Pathology and Microbiology, Iowa State University, Pammel Dr, Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew J","family":"Severin","sequence":"additional","affiliation":[{"name":"Genome Informatics Facility, Iowa State University, Osborne Dr, Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,11,13]]},"reference":[{"key":"2019111315213443300_ref1","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/j.pt.2004.01.005","article-title":"Getting to the roots of parasitism by nematodes","volume":"20","author":"Davis","year":"2004","journal-title":"Trends Parasitol."},{"key":"2019111315213443300_ref2","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1146\/annurev.phyto.43.040204.140218","article-title":"A model plant pathogen from the kingdom animalia: Heterodera glycines, the soybean cyst nematode","volume":"44","author":"Niblack","year":"2006","journal-title":"Annu. Rev. Phytopathol."},{"key":"2019111315213443300_ref3","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/j.pbi.2007.10.010","article-title":"Diverse and conserved roles of CLE peptides","volume":"11","author":"Mitchum","year":"2008","journal-title":"Curr. Opin. Plant Biol."},{"key":"2019111315213443300_ref4","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1146\/annurev-phyto-081211-173008","article-title":"Role of nematode peptides and other small molecules in plant parasitism","volume":"50","author":"Mitchum","year":"2012","journal-title":"Annu. Rev. Phytopathol."},{"key":"2019111315213443300_ref5","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1016\/j.pbi.2008.04.003","article-title":"Parasitism proteins in nematode\u2013plant interactions","volume":"11","author":"Davis","year":"2008","journal-title":"Curr. Opin. Plant Biol."},{"key":"2019111315213443300_ref6","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1111\/nph.12323","article-title":"Nematode effector proteins: an emerging paradigm of parasitism","volume":"199","author":"Mitchum","year":"2013","journal-title":"New Phytol."},{"key":"2019111315213443300_ref7","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1146\/annurev-phyto-080516-035434","article-title":"Genome evolution of plant-parasitic nematodes","volume":"55","author":"Kikuchi","year":"2017","journal-title":"Annu. Rev. Phytopathol."},{"key":"2019111315213443300_ref8","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1111\/j.1744-7348.1981.tb05122.x","article-title":"Host cell responses to endoparasitic nematode attack: structure and function of giant cells and syncytia","volume":"97","author":"Jones","year":"1981","journal-title":"Ann. Appl. 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Rep."},{"key":"2019111315213443300_ref31","doi-asserted-by":"crossref","DOI":"10.1186\/s12864-019-5485-8","article-title":"The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes","author":"Masonbrink","year":"2019"},{"key":"2019111315213443300_ref32","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1093\/molbev\/msx319","article-title":"BUSCO applications from quality assessments to gene prediction and phylogenomics","volume":"35","author":"Waterhouse","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"2019111315213443300_ref33","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1186\/s13059-016-0985-1","article-title":"The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence","volume":"17","author":"Eves-van den Akker","year":"2016","journal-title":"Genome Biol."},{"key":"2019111315213443300_ref34","doi-asserted-by":"crossref","first-page":"R43","DOI":"10.1186\/gb-2014-15-3-r43","article-title":"The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode","volume":"15","author":"Cotton","year":"2014","journal-title":"Genome Biol."},{"key":"2019111315213443300_ref35","doi-asserted-by":"crossref","first-page":"14802","DOI":"10.1073\/pnas.0805946105","article-title":"Sequence and genetic map of Meloidogyne hapla: a compact nematode genome for plant parasitism","volume":"105","author":"Opperman","year":"2008","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2019111315213443300_ref36","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1038\/nbt.1482","article-title":"Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita","volume":"26","author":"Abad","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"2019111315213443300_ref37","doi-asserted-by":"crossref","first-page":"2844","DOI":"10.1093\/gbe\/evx201","article-title":"Comparative genomics of apomictic root-knot nematodes: hybridization, ploidy, and dynamic genome change","volume":"9","author":"Szitenberg","year":"2017","journal-title":"Genome Biol. Evol."},{"key":"2019111315213443300_ref38","doi-asserted-by":"crossref","first-page":"20160942","DOI":"10.1098\/rspb.2016.0942","article-title":"The Ditylenchus destructor genome provides new insights into the evolution of plant parasitic nematodes","volume":"283","author":"Zheng","year":"2016","journal-title":"Proc. Biol. Sci."},{"key":"2019111315213443300_ref39","doi-asserted-by":"crossref","first-page":"e1002219","DOI":"10.1371\/journal.ppat.1002219","article-title":"Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus","volume":"7","author":"Kikuchi","year":"2011","journal-title":"PLoS Pathog."},{"key":"2019111315213443300_ref40","doi-asserted-by":"crossref","first-page":"127","DOI":"10.21307\/jofnem-2017-054","article-title":"The draft genome of Globodera ellingtonae","volume":"49","author":"Phillips","year":"2017","journal-title":"J. Nematol."},{"key":"2019111315213443300_ref41","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1101\/gr.6743907","article-title":"MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes","volume":"18","author":"Cantarel","year":"2008","journal-title":"Genome Res."},{"key":"2019111315213443300_ref42","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1186\/s13059-015-0721-2","article-title":"OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy","volume":"16","author":"Emms","year":"2015","journal-title":"Genome Biol."},{"key":"2019111315213443300_ref43","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2019111315213443300_ref44","volume-title":"FASTX-Toolkit","author":"Gordon","year":"2011"},{"key":"2019111315213443300_ref45","author":"Li","year":"2016"},{"key":"2019111315213443300_ref46","author":"Smit","year":"2014"},{"key":"2019111315213443300_ref47","doi-asserted-by":"crossref","first-page":"792","DOI":"10.1093\/bioinformatics\/btt054","article-title":"RepeatExplorer: a galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads","volume":"29","author":"Nov\u00e1k","year":"2013","journal-title":"Bioinformatics"},{"key":"2019111315213443300_ref48","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1007\/978-1-4939-3578-9_15","article-title":"GMAP and GSNAP for genomic sequence alignment: enhancements to speed, accuracy, and functionality","author":"Wu","year":"2016","journal-title":"Statistical Genomics"},{"key":"2019111315213443300_ref49","doi-asserted-by":"crossref","first-page":"3119","DOI":"10.1093\/bioinformatics\/btq599","article-title":"The GMOD Drupal bioinformatic server framework","volume":"26","author":"Papanicolaou","year":"2010","journal-title":"Bioinformatics"},{"key":"2019111315213443300_ref50","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bar044","article-title":"Tripal: a construction toolkit for online genome databases","volume":"2011","author":"Ficklin","year":"2011","journal-title":"Database (Oxford)"},{"key":"2019111315213443300_ref51","doi-asserted-by":"crossref","first-page":"i337","DOI":"10.1093\/bioinformatics\/btm189","article-title":"A Chado case study: an ontology-based modular schema for representing genome-associated biological information","volume":"23","author":"Mungall","year":"2007","journal-title":"Bioinformatics"},{"key":"2019111315213443300_ref52","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi0906s12","article-title":"Using Chado to store genome annotation data","volume":"12","author":"Zhou","year":"2005","journal-title":"Curr. Protoc. Bioinformatics"},{"key":"2019111315213443300_ref53","doi-asserted-by":"crossref","first-page":"R44","DOI":"10.1186\/gb-2005-6-5-r44","article-title":"The sequence ontology: a tool for the unification of genome annotations","volume":"6","author":"Eilbeck","year":"2005","journal-title":"Genome Biol."},{"key":"2019111315213443300_ref54","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"2019111315213443300_ref55","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1007\/s003440000022","article-title":"Plant parasitic nematodes: habitats, hormones, and horizontally-acquired genes","volume":"19","author":"Bird","year":"2000","journal-title":"J. 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