{"id":"https://openalex.org/W7225399174","doi":"https://doi.org/10.64898/2026.11.04.764316","title":"Transcriptome reallocation during infection reshapes synonymous codon demand in Botrytis cinerea","display_name":"Transcriptome reallocation during infection reshapes synonymous codon demand in Botrytis cinerea","publication_year":2026,"publication_date":"2026-11-06","ids":{"openalex":"https://openalex.org/W7225399174","doi":"https://doi.org/10.64898/2026.11.04.764316"},"language":"en","primary_location":{"id":"doi:10.64898/2026.11.04.764316","doi":"https://doi.org/10.64898/2026.11.04.764316","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.04.764316","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/06/2026.11.04.764316.full.pdf","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","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/06/2026.11.04.764316.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5161021817","display_name":"Jordan Dowell","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I121820613","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57","country_code":"US","type":"education","lineage":["https://openalex.org/I121820613"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jordan Dowell","raw_affiliation_strings":["Louisiana State University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Louisiana State University","institution_ids":["https://openalex.org/I121820613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5161091995","display_name":"Lori Pradhan","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I121820613","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57","country_code":"US","type":"education","lineage":["https://openalex.org/I121820613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lori Pradhan","raw_affiliation_strings":["Louisiana State University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Louisiana State University","institution_ids":["https://openalex.org/I121820613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5104268645","display_name":"Melanie Madrigal","orcid":"https://orcid.org/0009-0004-4125-5533","observed_orcids":["https://orcid.org/0009-0004-4125-5533"]},"institutions":[{"id":"https://openalex.org/I121820613","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57","country_code":"US","type":"education","lineage":["https://openalex.org/I121820613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Melanie Madrigal","raw_affiliation_strings":["Louisiana State University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Louisiana State University","institution_ids":["https://openalex.org/I121820613"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5161021817"],"corresponding_institution_ids":["https://openalex.org/I121820613"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.7509999871253967,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.7509999871253967,"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/T10825","display_name":"Plant Pathogens and Fungal Diseases","score":0.0494999997317791,"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/T10497","display_name":"Fungal and yeast genetics research","score":0.04600000008940697,"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/botrytis-cinerea","display_name":"Botrytis cinerea","score":0.9980000257492065},{"id":"https://openalex.org/keywords/codon-usage","display_name":"codon usage","score":0.6600000262260437},{"id":"https://openalex.org/keywords/fungal-infection","display_name":"fungal infection","score":0.492000013589859},{"id":"https://openalex.org/keywords/host-pathogen-interaction","display_name":"host-pathogen interaction","score":0.8870000243186951},{"id":"https://openalex.org/keywords/gene-expression-dynamics","display_name":"gene expression dynamics","score":0.6740000247955322},{"id":"https://openalex.org/keywords/arabidopsis-thaliana","display_name":"Arabidopsis thaliana","score":0.9950000047683716},{"id":"https://openalex.org/keywords/physcomitrella-patens","display_name":"Physcomitrella patens","score":0.9940000176429749},{"id":"https://openalex.org/keywords/codon-preference","display_name":"codon preference","score":0.4309999942779541},{"id":"https://openalex.org/keywords/translation-biology","display_name":"translation (biology)","score":0.3330000042915344},{"id":"https://openalex.org/keywords/rna-stability","display_name":"RNA stability","score":0.703000009059906}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8417999744415283},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.7846999764442444},{"id":"https://openalex.org/C2775867217","wikidata":"https://www.wikidata.org/wiki/Q1135851","display_name":"Botrytis cinerea","level":2,"score":0.6744999885559082},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6187999844551086},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5895000100135803},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.5454999804496765},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4659000039100647},{"id":"https://openalex.org/C2775992057","wikidata":"https://www.wikidata.org/wiki/Q16956568","display_name":"Translational efficiency","level":5,"score":0.4498000144958496},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.4422999918460846},{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.4287000000476837},{"id":"https://openalex.org/C138025448","wikidata":"https://www.wikidata.org/wiki/Q7662597","display_name":"Synonymous substitution","level":5,"score":0.42160001397132874},{"id":"https://openalex.org/C2779491563","wikidata":"https://www.wikidata.org/wiki/Q157892","display_name":"Arabidopsis","level":4,"score":0.37529999017715454},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.3659999966621399},{"id":"https://openalex.org/C20580545","wikidata":"https://www.wikidata.org/wiki/Q28354","display_name":"Stop codon","level":3,"score":0.3531000018119812},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3474999964237213},{"id":"https://openalex.org/C7386963","wikidata":"https://www.wikidata.org/wiki/Q3954859","display_name":"Negative selection","level":4,"score":0.311599999666214},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.2703000009059906},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.26739999651908875},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.2651999890804291},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.26159998774528503},{"id":"https://openalex.org/C2775988993","wikidata":"https://www.wikidata.org/wiki/Q158695","display_name":"Arabidopsis thaliana","level":4,"score":0.25929999351501465},{"id":"https://openalex.org/C91779695","wikidata":"https://www.wikidata.org/wiki/Q3780824","display_name":"Coding region","level":3,"score":0.2549000084400177}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.11.04.764316","doi":"https://doi.org/10.64898/2026.11.04.764316","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.04.764316","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/06/2026.11.04.764316.full.pdf","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","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.11.04.764316","doi":"https://doi.org/10.64898/2026.11.04.764316","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.04.764316","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/06/2026.11.04.764316.full.pdf","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","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310395","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7225399174.pdf","grobid_xml":"https://content.openalex.org/works/W7225399174.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1607969426","https://openalex.org/W1897344135","https://openalex.org/W1993023683","https://openalex.org/W1996769980","https://openalex.org/W2013321787","https://openalex.org/W2018590530","https://openalex.org/W2026021379","https://openalex.org/W2079517684","https://openalex.org/W2115816285","https://openalex.org/W2124099741","https://openalex.org/W2147109452","https://openalex.org/W2161163382","https://openalex.org/W2583343680","https://openalex.org/W2592811885","https://openalex.org/W2793389063","https://openalex.org/W2953251842","https://openalex.org/W3010788784","https://openalex.org/W3036200011","https://openalex.org/W3084711464","https://openalex.org/W3094437928","https://openalex.org/W3097922760","https://openalex.org/W3114972866","https://openalex.org/W3130039809","https://openalex.org/W4214858427","https://openalex.org/W4311928790","https://openalex.org/W4385741429","https://openalex.org/W4400429983","https://openalex.org/W4401884794","https://openalex.org/W4405677424","https://openalex.org/W4406089827","https://openalex.org/W4412677860","https://openalex.org/W7131268112","https://openalex.org/W7133511846"],"related_works":["https://openalex.org/W4405677424","https://openalex.org/W4205378360","https://openalex.org/W2794062815","https://openalex.org/W7204228790","https://openalex.org/W3175656168","https://openalex.org/W3009638192","https://openalex.org/W7123345691","https://openalex.org/W3094437928","https://openalex.org/W2127064445","https://openalex.org/W7125792651"],"abstract_inverted_index":{"While":[0],"genomic":[1],"codon":[2,65],"usage":[3],"is":[4],"fixed":[5,63],"within":[6,73],"an":[7],"individual":[8],"isolate,":[9],"the":[10,112,187,191],"synonymous":[11,74,188],"codons":[12],"represented":[13],"in":[14,46,86,138,145],"its":[15],"RNA":[16,209],"pool":[17],"can":[18],"change":[19],"when":[20],"transcription":[21],"shifts":[22],"among":[23,120],"genes.":[24,108],"We":[25],"tested":[26],"whether":[27],"this":[28],"transcript-level":[29],"phenotype":[30,201],"accompanies":[31],"infection":[32],"by":[33],"reanalyzing":[34],"39":[35],"libraries":[36],"from":[37],"three":[38],"public":[39],"Botrytis":[40],"cinerea":[41],"RNA-sequencing":[42],"(RNA-seq)":[43],"time":[44,78],"series":[45],"S.":[47,139],"lycopersicum,":[48],"Arabidopsis":[49],"thaliana,":[50],"and":[51,67,104,141,150,171,177,202,211],"Physcomitrium":[52],"patens.":[53,147],"Gene":[54],"counts":[55],"were":[56,117,160],"corrected":[57],"for":[58,80,205,208],"coding":[59],"length,":[60],"combined":[61],"with":[62],"gene-specific":[64],"inventories,":[66],"analyzed":[68],"as":[69],"centered":[70],"log":[71],"ratios":[72],"amino-acid":[75],"families.":[76],"Sampling":[77],"accounted":[79],"95-98%":[81],"of":[82,106,128,190],"fungal":[83,193],"codon-demand":[84],"variation":[85],"each":[87],"series.":[88],"The":[89],"association":[90],"persisted":[91],"after":[92],"effective-length":[93],"correction,":[94],"unique-only":[95],"competitive":[96],"mapping,":[97],"host-homology":[98],"exclusion,":[99],"depth":[100],"equalization,":[101],"protein-family":[102],"weighting,":[103],"removal":[105],"translation-associated":[107],"Change":[109],"vectors":[110],"over":[111],"interpolated,":[113],"time-aligned":[114],"16-24-h":[115],"interval":[116],"positively":[118],"aligned":[119],"studies,":[121],"whereas":[122],"later":[123],"trajectories":[124,131],"diverged.":[125],"Matched":[126],"reassignments":[127],"complete":[129],"expression":[130,151],"showed":[132],"more":[133],"full-series":[134],"organization":[135],"than":[136],"expected":[137],"lycopersicum":[140],"Arabidopsis,":[142],"but":[143],"not":[144,161],"P.":[146],"Codon-preference-weighted":[148],"abundance":[149],"breadth":[152],"also":[153],"changed":[154],"through":[155],"infection,":[156],"although":[157,174],"their":[158,175],"directions":[159],"universal.":[162],"Across":[163],"systems,":[164],"large":[165],"non-translation":[166],"contributors":[167],"repeatedly":[168,185],"carried":[169],"ATP-synthase/respiratory":[170],"extracellular":[172],"annotations,":[173],"timing":[176],"companion":[178],"functions":[179],"differed.":[180],"Infection-associated":[181],"transcriptional":[182],"reallocation":[183],"therefore":[184],"restructures":[186],"composition":[189],"inferred":[192],"transcript":[194],"pool.":[195],"This":[196],"establishes":[197],"a":[198,203],"dynamic":[199],"allocation":[200],"basis":[204],"testing":[206],"consequences":[207],"stability":[210],"translation":[212],"during":[213],"host-pathogen":[214],"interactions.":[215]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-11-07T00:00:00"}
