Genome assembly, structural and functional annotation of orange rust (Puccinia kuehnii) and brown rust (Puccinia melanocephala), phytopathogens of sugarcane

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dc.contributor.advisorTrujillo Montenegro, Jhon Henry
dc.contributor.advisorRodriguez Castillo, Nohra
dc.contributor.authorQuiñones Olaya, Angie Valeria
dc.contributor.researchgroupBIOINFORMÁTICA Y BIOCOMPUTACIÓN
dc.date.accessioned2026-09-22T14:30:58Z
dc.date.available2026-09-22T14:30:58Z
dc.date.issued2026
dc.description.abstractBACKGROUND Puccinia melanocephala (brown rust) and Puccinia kuehnii (orange rust) are major biotrophic pathogens severely affecting sugarcane production worldwide. Despite their economic impact, genomic resources for these species remain limited due to challenges inherent to obligate biotrophy, contamination during field sampling, and highly repetitive, dikaryotic genomes. This study aimed to generate high-quality phased genome assemblies for Colombian isolates of both pathogens and to perform structural, functional, and repeat-content analyses to provide foundational genomic resources for comparative genomics and sugarcane breeding programs. RESULTS : PacBio HiFi sequencing combined with LongPlex library preparation and phased assembly using Hifiasm enabled the generation of high-quality haplotype-resolved assemblies for both species. GenomeScope profiles indicated complex dikaryotic architectures, while BlobToolKit analyses identified and removed environmental contaminants, resulting in curated assemblies of 322.68 Mb (P. melanocephala) and 267.89 Mb (P. kuehnii). Compleasm completeness values exceeded 86% in both genomes. Transposable elements dominated both genomes, accounting for 73.7% of P. melanocephala and 68.7% of P. kuehnii, with LTR retrotransposons (Gypsy, Copia) and TIR transposons (Mutator, CACTA) being the most abundant. BRAKER predicted 32,412 and 15,690 protein-coding genes in P. melanocephala and P. kuehnii, respectively, with BUSCO completeness above 80%. Functional annotation with EggNOGmapper identified over 9,000 unique GO terms per species, and enrichment analysis of 1,849 shared genes revealed significant overrepresentation of biological processes and cellular components related to nuclear organization, intracellular signaling, protein transport, and fungal-type cell wall organization. CONCLUSIONS : These genomic assemblies represent the first genomic resources for Colombian isolates of P. melanocephala and P. kuehnii. The strong TE-driven genome expansion, diverse gene repertoires, and enriched functional categories highlight the evolutionary dynamics underlying pathotype diversification and host adaptation. These genomic resources provide a foundation for effector discovery, comparative genomics, and molecular surveillance, and offer valuable tools for sugarcane breeding programs aimed at developing durable resistance against rust pathogens.
dc.description.degreelevelMaestríaspa
dc.description.degreenameMAGISTER EN BIOTECNOLOGÍAspa
dc.description.researchareaADN: ARGUMENTACION, DISCURSO Y NARRACION
dc.format.extent1 recurso (66 páginas)
dc.format.mimetypeapplication/pdf
dc.identifier.notificationemailangie.valeria.quinones@correounivalle.edu.co
dc.identifier.notificationnameAngie Valeria Quiñones Olaya, 1144206036
dc.identifier.urihttps://hdl.handle.net/10893/41777
dc.language.isoeng
dc.publisherUniversidad del Vallespa
dc.publisher.branchSede Cali
dc.publisher.facultyFACULTAD DE CIENCIAS NATURALES Y EXACTASspa
dc.publisher.placeColombiaspa
dc.publisher.programMAESTRÍA EN BIOTECNOLOGÍAspa
dc.rights.accessrightsinfo:eu-repo/semantics/openAccessspa
dc.rights.coarhttp://purl.org/coar/access_right/c_abf2spa
dc.rights.licenseAtribución-NoComercial-SinDerivadas 4.0 Internacional (CC BY-NC-ND 4.0)spa
dc.subject.lembRoya
dc.subject.lembCaña de azucar
dc.subject.lembFitopatógenos
dc.subject.lembBiotecnología
dc.titleGenome assembly, structural and functional annotation of orange rust (Puccinia kuehnii) and brown rust (Puccinia melanocephala), phytopathogens of sugarcaneeng
dc.typeTrabajo de grado - Maestríaspa
dc.type.coarhttp://purl.org/coar/resource_type/c_bdcc
dc.type.coarversionhttp://purl.org/coar/version/c_970fb48d4fbd8a85spa
dc.type.contentText
dc.type.driverinfo:eu-repo/semantics/masterThesis
dc.type.redcolhttp://purl.org/redcol/resource_type/TM
dc.type.versioninfo:eu-repo/semantics/publishedVersionspa
dspace.entity.typePublication
person.identifier.orcid0009-0004-2418-7663
person.identifier.orcid0000-0002-3310-6149
relation.isAuthorOfPublication2cc3a813-a28d-489b-98b5-e25a62237372
relation.isAuthorOfPublication.latestForDiscovery2cc3a813-a28d-489b-98b5-e25a62237372
relation.isDirectorOfPublication93aced9e-9829-4ae6-a5e5-065a3aac821d
relation.isDirectorOfPublication6626ecb4-405b-4d54-b651-96647e18bb92
relation.isDirectorOfPublication.latestForDiscovery93aced9e-9829-4ae6-a5e5-065a3aac821d
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