{"id":"https://openalex.org/W2950387271","doi":"https://doi.org/10.1101/039602","title":"DNA Methylation profiles of diverse Brachypodium distachyon aligns with underlying genetic diversity","display_name":"DNA Methylation profiles of diverse Brachypodium distachyon aligns with underlying genetic diversity","publication_year":2016,"publication_date":"2016-02-17","ids":{"openalex":"https://openalex.org/W2950387271","doi":"https://doi.org/10.1101/039602","mag":"2950387271"},"language":"en","primary_location":{"id":"doi:10.1101/039602","doi":"https://doi.org/10.1101/039602","is_oa":true,"landing_page_url":"https://doi.org/10.1101/039602","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.1101/039602","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056919501","display_name":"Steven R. Eichten","orcid":"https://orcid.org/0000-0003-2268-395X","observed_orcids":["https://orcid.org/0000-0003-2268-395X"]},"institutions":[{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]},{"id":"https://openalex.org/I4210102918","display_name":"ARC Centre of Excellence in Plant Energy Biology","ror":"https://ror.org/01a1mq059","country_code":"AU","type":"facility","lineage":["https://openalex.org/I118347636","https://openalex.org/I1337719021","https://openalex.org/I2801453606","https://openalex.org/I4210102918","https://openalex.org/I4210132349"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"SR Eichten","raw_affiliation_strings":["ARC Centre of Excellence in Plant Energy Biology. The Australian National University, Canberra, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ARC Centre of Excellence in Plant Energy Biology. The Australian National University, Canberra, Australia","institution_ids":["https://openalex.org/I118347636","https://openalex.org/I4210102918"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003957777","display_name":"Tim Stuart","orcid":"https://orcid.org/0000-0002-3044-0897","observed_orcids":["https://orcid.org/0000-0002-3044-0897"]},"institutions":[{"id":"https://openalex.org/I177877127","display_name":"The University of Western Australia","ror":"https://ror.org/047272k79","country_code":"AU","type":"education","lineage":["https://openalex.org/I177877127"]},{"id":"https://openalex.org/I4210102918","display_name":"ARC Centre of Excellence in Plant Energy Biology","ror":"https://ror.org/01a1mq059","country_code":"AU","type":"facility","lineage":["https://openalex.org/I118347636","https://openalex.org/I1337719021","https://openalex.org/I2801453606","https://openalex.org/I4210102918","https://openalex.org/I4210132349"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"T Stuart","raw_affiliation_strings":["ARC Centre of Excellence in Plant Energy Biology. University of Western Australia, Perth, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ARC Centre of Excellence in Plant Energy Biology. University of Western Australia, Perth, Australia","institution_ids":["https://openalex.org/I177877127","https://openalex.org/I4210102918"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027842783","display_name":"Akanksha Srivastava","orcid":"https://orcid.org/0000-0002-4553-9232","observed_orcids":["https://orcid.org/0000-0002-4553-9232"]},"institutions":[{"id":"https://openalex.org/I177877127","display_name":"The University of Western Australia","ror":"https://ror.org/047272k79","country_code":"AU","type":"education","lineage":["https://openalex.org/I177877127"]},{"id":"https://openalex.org/I4210102918","display_name":"ARC Centre of Excellence in Plant Energy Biology","ror":"https://ror.org/01a1mq059","country_code":"AU","type":"facility","lineage":["https://openalex.org/I118347636","https://openalex.org/I1337719021","https://openalex.org/I2801453606","https://openalex.org/I4210102918","https://openalex.org/I4210132349"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"A Srivastava","raw_affiliation_strings":["ARC Centre of Excellence in Plant Energy Biology. University of Western Australia, Perth, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ARC Centre of Excellence in Plant Energy Biology. University of Western Australia, Perth, Australia","institution_ids":["https://openalex.org/I177877127","https://openalex.org/I4210102918"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057408603","display_name":"Ryan Lister","orcid":"https://orcid.org/0000-0001-6637-7239","observed_orcids":["https://orcid.org/0000-0001-6637-7239"]},"institutions":[{"id":"https://openalex.org/I177877127","display_name":"The University of Western Australia","ror":"https://ror.org/047272k79","country_code":"AU","type":"education","lineage":["https://openalex.org/I177877127"]},{"id":"https://openalex.org/I4210102918","display_name":"ARC Centre of Excellence in Plant Energy Biology","ror":"https://ror.org/01a1mq059","country_code":"AU","type":"facility","lineage":["https://openalex.org/I118347636","https://openalex.org/I1337719021","https://openalex.org/I2801453606","https://openalex.org/I4210102918","https://openalex.org/I4210132349"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"R Lister","raw_affiliation_strings":["ARC Centre of Excellence in Plant Energy Biology. University of Western Australia, Perth, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ARC Centre of Excellence in Plant Energy Biology. University of Western Australia, Perth, Australia","institution_ids":["https://openalex.org/I177877127","https://openalex.org/I4210102918"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081111897","display_name":"Justin Borevitz","orcid":"https://orcid.org/0000-0001-8408-3699","observed_orcids":["https://orcid.org/0000-0001-8408-3699"]},"institutions":[{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]},{"id":"https://openalex.org/I4210102918","display_name":"ARC Centre of Excellence in Plant Energy Biology","ror":"https://ror.org/01a1mq059","country_code":"AU","type":"facility","lineage":["https://openalex.org/I118347636","https://openalex.org/I1337719021","https://openalex.org/I2801453606","https://openalex.org/I4210102918","https://openalex.org/I4210132349"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"JO Borevitz","raw_affiliation_strings":["ARC Centre of Excellence in Plant Energy Biology. The Australian National University, Canberra, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ARC Centre of Excellence in Plant Energy Biology. The Australian National University, Canberra, Australia","institution_ids":["https://openalex.org/I118347636","https://openalex.org/I4210102918"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5081111897"],"corresponding_institution_ids":["https://openalex.org/I118347636","https://openalex.org/I4210102918"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.7294999957084656,"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"}},"topics":[{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.7294999957084656,"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"}},{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.21299999952316284,"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/T12828","display_name":"Plant Genetic and Mutation Studies","score":0.018400000408291817,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.9900000095367432},{"id":"https://openalex.org/keywords/brachypodium-distachyon","display_name":"Brachypodium distachyon","score":0.9810000061988831},{"id":"https://openalex.org/keywords/transposable-elements","display_name":"transposable elements","score":0.8820000290870667},{"id":"https://openalex.org/keywords/differentially-methylated-regions","display_name":"differentially methylated regions","score":0.8889999985694885},{"id":"https://openalex.org/keywords/genetic-diversity","display_name":"genetic diversity","score":0.8289999961853027},{"id":"https://openalex.org/keywords/epigenetic-variation","display_name":"epigenetic variation","score":0.6890000104904175},{"id":"https://openalex.org/keywords/bisulfite-sequencing","display_name":"bisulfite sequencing","score":0.6880000233650208}],"concepts":[{"id":"https://openalex.org/C2777911459","wikidata":"https://www.wikidata.org/wiki/Q2352209","display_name":"Brachypodium distachyon","level":4,"score":0.9731369018554688},{"id":"https://openalex.org/C2777749068","wikidata":"https://www.wikidata.org/wiki/Q157770","display_name":"Brachypodium","level":4,"score":0.8274794816970825},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.6929376721382141},{"id":"https://openalex.org/C2781316041","wikidata":"https://www.wikidata.org/wiki/Q1230584","display_name":"Diversity (politics)","level":2,"score":0.6057758331298828},{"id":"https://openalex.org/C81977670","wikidata":"https://www.wikidata.org/wiki/Q585259","display_name":"Genetic diversity","level":3,"score":0.5707248449325562},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5369884967803955},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.47866091132164},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47639432549476624},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.43833574652671814},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4286598563194275},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.42043668031692505},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.28902000188827515},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.1501351296901703},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.146767258644104},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13300779461860657},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.06334578990936279},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1101/039602","doi":"https://doi.org/10.1101/039602","is_oa":true,"landing_page_url":"https://doi.org/10.1101/039602","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1101/039602","doi":"https://doi.org/10.1101/039602","is_oa":true,"landing_page_url":"https://doi.org/10.1101/039602","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":65,"referenced_works":["https://openalex.org/W1531671305","https://openalex.org/W1972171731","https://openalex.org/W1979576560","https://openalex.org/W1984891757","https://openalex.org/W1985624299","https://openalex.org/W1988214574","https://openalex.org/W1989568035","https://openalex.org/W1990813498","https://openalex.org/W1996877067","https://openalex.org/W1999078569","https://openalex.org/W1999348612","https://openalex.org/W2000967378","https://openalex.org/W2002431756","https://openalex.org/W2014704298","https://openalex.org/W2017198614","https://openalex.org/W2020173141","https://openalex.org/W2020247237","https://openalex.org/W2026343134","https://openalex.org/W2027486853","https://openalex.org/W2028839461","https://openalex.org/W2031913559","https://openalex.org/W2036634503","https://openalex.org/W2044231545","https://openalex.org/W2049466086","https://openalex.org/W2054854463","https://openalex.org/W2056573937","https://openalex.org/W2058306179","https://openalex.org/W2063593636","https://openalex.org/W2065498897","https://openalex.org/W2067151470","https://openalex.org/W2073764626","https://openalex.org/W2076498407","https://openalex.org/W2076656039","https://openalex.org/W2085185449","https://openalex.org/W2092772797","https://openalex.org/W2102619694","https://openalex.org/W2104618447","https://openalex.org/W2118140755","https://openalex.org/W2119448074","https://openalex.org/W2123430325","https://openalex.org/W2123921804","https://openalex.org/W2126310951","https://openalex.org/W2126434569","https://openalex.org/W2131374955","https://openalex.org/W2133289818","https://openalex.org/W2134485426","https://openalex.org/W2136104477","https://openalex.org/W2139368808","https://openalex.org/W2144412579","https://openalex.org/W2147069413","https://openalex.org/W2152955481","https://openalex.org/W2153975081","https://openalex.org/W2155020101","https://openalex.org/W2155496026","https://openalex.org/W2156301924","https://openalex.org/W2156622081","https://openalex.org/W2163887455","https://openalex.org/W2164837302","https://openalex.org/W2170551349","https://openalex.org/W2171619188","https://openalex.org/W2171791108","https://openalex.org/W2297969515","https://openalex.org/W2950391511","https://openalex.org/W4235874578","https://openalex.org/W4255006325"],"related_works":["https://openalex.org/W2520882678","https://openalex.org/W3082733994","https://openalex.org/W2147069413","https://openalex.org/W2058306179","https://openalex.org/W2780548146","https://openalex.org/W2590139944","https://openalex.org/W2951822269","https://openalex.org/W6920550739","https://openalex.org/W2984616346","https://openalex.org/W2972636473"],"abstract_inverted_index":{"Abstract":[0],"DNA":[1,46,54,81,115,160,171],"methylation,":[2],"a":[3,167],"common":[4],"modification":[5],"of":[6,15,53,73,88,98,106,127,155,170,177],"genomic":[7,61],"DNA,":[8],"is":[9,121,189],"known":[10],"to":[11,184],"influence":[12],"the":[13,51,74,112,124,153,193],"expression":[14],"transposable":[16,39,57,100,118],"elements":[17],"as":[18,20,26,38],"well":[19],"some":[21],"genes.":[22],"Although":[23,80],"commonly":[24],"viewed":[25],"an":[27],"epigenetic":[28],"mark,":[29],"evidence":[30,137],"has":[31],"shown":[32],"that":[33,138],"underlying":[34],"genetic":[35,128,156],"variation,":[36,56],"such":[37],"element":[40,58,101,119],"polymorphisms,":[41],"often":[42],"associate":[43],"with":[44,123,146],"differential":[45,148],"methylation":[47,55,82,116,161,172],"states.":[48],"To":[49],"investigate":[50],"role":[52],"polymorphism,":[59],"and":[60,117,165],"diversity,":[62],"whole":[63],"genome":[64],"bisulfite":[65],"sequencing":[66],"was":[67,135],"performed":[68],"on":[69],"genetically":[70],"diverse":[71,174],"lines":[72],"model":[75,179],"cereal":[76,180],"Brachypodium":[77],"distachyon":[78],".":[79],"profiles":[83],"are":[84,92,144,203],"broadly":[85],"similar,":[86],"thousands":[87],"differentially":[89],"methylated":[90],"regions":[91],"observed":[93],"between":[94,131,163],"lines.":[95],"An":[96],"analysis":[97],"novel":[99,139],"indel":[102],"variation":[103,120,129,157,162],"highlighted":[104],"hundreds":[105],"new":[107],"polymorphisms":[108],"not":[109],"seen":[110],"in":[111,192],"reference":[113],"sequence.":[114],"correlated":[122],"genome-wide":[125],"amount":[126],"present":[130],"samples.":[132],"However,":[133],"there":[134],"minimal":[136],"transposon":[140],"insertion":[141],"or":[142],"deletions":[143],"associated":[145],"nearby":[147],"methylation.":[149],"This":[150],"study":[151],"highlights":[152],"importance":[154],"when":[158],"assessing":[159],"samples":[164],"provides":[166],"valuable":[168],"map":[169],"across":[173],"re-sequenced":[175],"accessions":[176],"this":[178],"species.":[181],"Reviewer":[182],"Link":[183],"deposited":[185],"data":[186,188],"All":[187],"publicly":[190],"available":[191,204],"NCBI":[194],"short":[195],"read":[196],"archive":[197],"under":[198],"BioProject":[199],"PRJNA281014.":[200],"Data":[201],"tables":[202],"for":[205],"download":[206],"at":[207],"https://drive.google.com/file/d/0BzBxfoxlBCneNkY1TFJDU29iSUU/view?usp=sharing":[208]},"counts_by_year":[],"updated_date":"2026-10-14T16:39:01.820549","created_date":"2019-06-27T00:00:00"}
