{"id":"https://openalex.org/W2147643078","doi":"https://doi.org/10.1093/bib/bbp039","title":"De novo sequencing of plant genomes using second-generation technologies","display_name":"De novo sequencing of plant genomes using second-generation technologies","publication_year":2009,"publication_date":"2009-11-01","ids":{"openalex":"https://openalex.org/W2147643078","doi":"https://doi.org/10.1093/bib/bbp039","mag":"2147643078","pmid":"https://pubmed.ncbi.nlm.nih.gov/19933209"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbp039","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbp039","pdf_url":"https://academic.oup.com/bib/article-pdf/10/6/609/722290/bbp039.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/10/6/609/722290/bbp039.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012636833","display_name":"Michael Imelfort","orcid":null},"institutions":[{"id":"https://openalex.org/I112745207","display_name":"Australian Centre for Plant Functional Genomics","ror":"https://ror.org/00xwvfm64","country_code":"AU","type":"facility","lineage":["https://openalex.org/I112745207"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"M. Imelfort","raw_affiliation_strings":["Australian Centre for Plant Functional Genomics, Institute for Molecular Biosciences and School of Land, Crop and Food Sciences, University of Queensland, Brisbane, QLD 4072, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Australian Centre for Plant Functional Genomics, Institute for Molecular Biosciences and School of Land, Crop and Food Sciences, University of Queensland, Brisbane, QLD 4072, Australia","institution_ids":["https://openalex.org/I112745207"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016277624","display_name":"David Edwards","orcid":"https://orcid.org/0000-0001-7599-6760"},"institutions":[{"id":"https://openalex.org/I4210133068","display_name":"Issues Research","ror":"https://ror.org/03j42jj36","country_code":"US","type":"other","lineage":["https://openalex.org/I4210133068"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. Edwards","raw_affiliation_strings":["David Edwards is an Associate Professor at the University of Queensland. His research focuses on understanding the structure and expression of complex genomes"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"David Edwards is an Associate Professor at the University of Queensland. His research focuses on understanding the structure and expression of complex genomes","institution_ids":["https://openalex.org/I4210133068"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":null,"fwci":17.6553,"has_fulltext":true,"cited_by_count":110,"citation_normalized_percentile":{"value":0.99291254,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"10","issue":"6","first_page":"609","last_page":"618"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12858","display_name":"Plant Disease Resistance and Genetics","score":0.9965000152587891,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9944000244140625,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.6071978807449341},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5948916673660278},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5714886784553528},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.47240084409713745},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4009685814380646},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2801959216594696},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.1776755154132843},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1436566710472107}],"concepts":[{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.6071978807449341},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5948916673660278},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5714886784553528},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.47240084409713745},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4009685814380646},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2801959216594696},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.1776755154132843},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1436566710472107}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018744","descriptor_name":"DNA, Plant","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018744","descriptor_name":"DNA, Plant","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018744","descriptor_name":"DNA, Plant","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbp039","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbp039","pdf_url":"https://academic.oup.com/bib/article-pdf/10/6/609/722290/bbp039.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19933209","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19933209","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:espace.library.uq.edu.au:UQ:189921","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402388","display_name":"Queensland's institutional digital repository (The University of Queensland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165143802","host_organization_name":"The University of Queensland","host_organization_lineage":["https://openalex.org/I165143802"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbp039","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbp039","pdf_url":"https://academic.oup.com/bib/article-pdf/10/6/609/722290/bbp039.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4399999976158142,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G8404678838","display_name":null,"funder_award_id":"DAN00117","funder_id":"https://openalex.org/F4320320420","funder_display_name":"Grains Research and Development Corporation"}],"funders":[{"id":"https://openalex.org/F4320315813","display_name":"Queensland Cyber Infrastructure Foundation","ror":"https://ror.org/03sd43014"},{"id":"https://openalex.org/F4320320420","display_name":"Grains Research and Development Corporation","ror":"https://ror.org/02xwr1996"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2147643078.pdf","grobid_xml":"https://content.openalex.org/works/W2147643078.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1488822382","https://openalex.org/W1494052290","https://openalex.org/W1494075612","https://openalex.org/W1560200430","https://openalex.org/W1966822396","https://openalex.org/W1968190141","https://openalex.org/W1970939265","https://openalex.org/W1974646727","https://openalex.org/W2000585348","https://openalex.org/W2016848076","https://openalex.org/W2022910024","https://openalex.org/W2023911006","https://openalex.org/W2041447426","https://openalex.org/W2048599620","https://openalex.org/W2063985242","https://openalex.org/W2088740898","https://openalex.org/W2112544455","https://openalex.org/W2113649367","https://openalex.org/W2114133992","https://openalex.org/W2115483901","https://openalex.org/W2115610250","https://openalex.org/W2120950924","https://openalex.org/W2127230663","https://openalex.org/W2127651281","https://openalex.org/W2128114769","https://openalex.org/W2132341951","https://openalex.org/W2134401483","https://openalex.org/W2136651963","https://openalex.org/W2137309192","https://openalex.org/W2139833654","https://openalex.org/W2142642738","https://openalex.org/W2142749416","https://openalex.org/W2151017710","https://openalex.org/W2151723398","https://openalex.org/W2156622081","https://openalex.org/W2159998739","https://openalex.org/W2160969485","https://openalex.org/W2166019318","https://openalex.org/W2166265186","https://openalex.org/W2168134702","https://openalex.org/W2168909179","https://openalex.org/W2171475724","https://openalex.org/W2987968264","https://openalex.org/W3216020230","https://openalex.org/W4235874578","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W1971568933","https://openalex.org/W2013243191"],"abstract_inverted_index":{"The":[0,36],"ability":[1],"to":[2,126],"sequence":[3,51,120],"the":[4,13,23,44,48,70,76,105,109,127,138,149,198,206,213],"DNA":[5,153],"of":[6,12,25,38,50,56,64,72,108,116,129,142,176,209],"an":[7],"organism":[8],"has":[9,42,122],"become":[10],"one":[11],"most":[14],"important":[15],"tools":[16],"in":[17,190],"modern":[18],"biological":[19],"research.":[20,218],"Until":[21],"recently,":[22],"sequencing":[24,40,80,154,163],"even":[26],"small":[27],"model":[28],"genomes":[29],"required":[30],"substantial":[31],"funds":[32],"and":[33,46,87,100,114,155,185,212],"international":[34],"collaboration.":[35],"development":[37],"'second-generation'":[39],"technology":[41,121,211],"increased":[43],"throughput":[45],"reduced":[47],"cost":[49],"generation":[52,162],"by":[53,84,89],"several":[54,91],"orders":[55],"magnitude.":[57],"These":[58],"new":[59],"methods":[60],"produce":[61],"vast":[62],"numbers":[63],"relatively":[65,110],"short":[66,166],"reads,":[67],"usually":[68],"at":[69],"expense":[71],"read":[73],"accuracy.":[74],"Since":[75],"first":[77],"commercial":[78],"second-generation":[79,202],"system":[81],"was":[82],"produced":[83],"454":[85],"Technologies":[86],"commercialised":[88],"Roche,":[90],"other":[92],"companies":[93],"including":[94],"Illumina,":[95],"Applied":[96],"Biosystems,":[97],"Helicos":[98],"Biosciences":[99,102],"Pacific":[101],"have":[103,135,182,187],"joined":[104],"competition.":[106],"Because":[107],"high":[111,170],"error":[112,171],"rate":[113],"lack":[115],"assembly":[117,141,147,181],"tools,":[118],"short-read":[119,180],"mainly":[123],"been":[124,183,188],"applied":[125],"re-sequencing":[128],"genomes.":[130],"However,":[131,173],"some":[132,186],"recent":[133],"applications":[134],"focused":[136],"on":[137],"de":[139],"novo":[140,146],"these":[143],"data.":[144],"De":[145],"remains":[148],"greatest":[150],"challenge":[151],"for":[152,160,179,201,215],"there":[156],"are":[157],"specific":[158],"problems":[159],"second":[161],"which":[164],"produces":[165],"reads":[167],"with":[168],"a":[169,174],"rate.":[172],"number":[175],"different":[177],"approaches":[178,200],"proposed":[184],"implemented":[189],"working":[191],"software.":[192],"In":[193],"this":[194,210],"review,":[195],"we":[196],"compare":[197],"current":[199],"genome":[203,217],"sequencing,":[204],"explore":[205],"future":[207],"direction":[208],"implications":[214],"plant":[216]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":20},{"year":2013,"cited_by_count":12},{"year":2012,"cited_by_count":21}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}