Fishing for NUMTs: exploring mitochondrial insertions in fish

NUMTs can be defined as fragments of mitochondrial DNA that have been integrated into the nuclear genome through evolutionary processes. Once NUMTs are inserted they can potentially disrupt protein-coding genes, leading to disease or integrate successfully into the genome and change the phenotype of...

Full description

Autores:
Rodríguez Otálora, Silvia Cristina
Tipo de recurso:
Trabajo de grado de pregrado
Fecha de publicación:
2025
Institución:
Universidad de los Andes
Repositorio:
Séneca: repositorio Uniandes
Idioma:
eng
OAI Identifier:
oai:repositorio.uniandes.edu.co:1992/76222
Acceso en línea:
https://hdl.handle.net/1992/76222
Palabra clave:
NUMTs
Mitochondrial DNA
Nuclear Genome
Evolutionary Biology
Fish Genomics
Biología
Rights
openAccess
License
Attribution-NoDerivatives 4.0 International
id UNIANDES2_4ee0a2b24121c06dc71575ba38d874ef
oai_identifier_str oai:repositorio.uniandes.edu.co:1992/76222
network_acronym_str UNIANDES2
network_name_str Séneca: repositorio Uniandes
repository_id_str
dc.title.eng.fl_str_mv Fishing for NUMTs: exploring mitochondrial insertions in fish
title Fishing for NUMTs: exploring mitochondrial insertions in fish
spellingShingle Fishing for NUMTs: exploring mitochondrial insertions in fish
NUMTs
Mitochondrial DNA
Nuclear Genome
Evolutionary Biology
Fish Genomics
Biología
title_short Fishing for NUMTs: exploring mitochondrial insertions in fish
title_full Fishing for NUMTs: exploring mitochondrial insertions in fish
title_fullStr Fishing for NUMTs: exploring mitochondrial insertions in fish
title_full_unstemmed Fishing for NUMTs: exploring mitochondrial insertions in fish
title_sort Fishing for NUMTs: exploring mitochondrial insertions in fish
dc.creator.fl_str_mv Rodríguez Otálora, Silvia Cristina
dc.contributor.advisor.none.fl_str_mv Reyes Muñoz, Alejandro
dc.contributor.author.none.fl_str_mv Rodríguez Otálora, Silvia Cristina
dc.subject.keyword.eng.fl_str_mv NUMTs
Mitochondrial DNA
Nuclear Genome
Evolutionary Biology
Fish Genomics
topic NUMTs
Mitochondrial DNA
Nuclear Genome
Evolutionary Biology
Fish Genomics
Biología
dc.subject.themes.spa.fl_str_mv Biología
description NUMTs can be defined as fragments of mitochondrial DNA that have been integrated into the nuclear genome through evolutionary processes. Once NUMTs are inserted they can potentially disrupt protein-coding genes, leading to disease or integrate successfully into the genome and change the phenotype of the organisms and thus its survival. NUMTs have been used to define phylogenetic outgroups and elucidate mtDNA evolution. While NUMTs have been extensively studied in vertebrates, their distribution, frequency, and evolutionary significance in fish remain largely unexplored. In this study, a novel bioinformatics pipeline using LAST is suggested as a potential method to identify NUMTs in the genomes of ten fish species. A total of 583 NUMTs were detected, with significant variation in NUMT content across species. Our findings suggest that genome size is not a strong predictor of NUMT abundance in fish. Additionally, an analysis of ancient NUMTs revealed that only Elasmobranchii (sharks and rays) retained conserved NUMT sequences, likely due to their slow genomic evolutionary rates. No ancient NUMTs were identified in Actinopterygii, possibly due to their high evolutionary divergence. These results provide new insights into the distribution and evolutionary history of NUMTs in fish and highlight the potential of NUMTs as markers for studying genome evolution. Further research on NUMTs in closely related fish taxa and improvements in the workflow could refine our understanding of their functional and evolutionary implications, particularly in species with highly conserved genomes.
publishDate 2025
dc.date.accessioned.none.fl_str_mv 2025-05-30T13:05:52Z
dc.date.available.none.fl_str_mv 2025-05-30T13:05:52Z
dc.date.issued.none.fl_str_mv 2025-05-29
dc.type.none.fl_str_mv Trabajo de grado - Pregrado
dc.type.driver.none.fl_str_mv info:eu-repo/semantics/bachelorThesis
dc.type.version.none.fl_str_mv info:eu-repo/semantics/acceptedVersion
dc.type.coar.none.fl_str_mv http://purl.org/coar/resource_type/c_7a1f
dc.type.content.none.fl_str_mv Text
dc.type.redcol.none.fl_str_mv http://purl.org/redcol/resource_type/TP
format http://purl.org/coar/resource_type/c_7a1f
status_str acceptedVersion
dc.identifier.uri.none.fl_str_mv https://hdl.handle.net/1992/76222
dc.identifier.instname.none.fl_str_mv instname:Universidad de los Andes
dc.identifier.reponame.none.fl_str_mv reponame:Repositorio Institucional Séneca
dc.identifier.repourl.none.fl_str_mv repourl:https://repositorio.uniandes.edu.co/
url https://hdl.handle.net/1992/76222
identifier_str_mv instname:Universidad de los Andes
reponame:Repositorio Institucional Séneca
repourl:https://repositorio.uniandes.edu.co/
dc.language.iso.none.fl_str_mv eng
language eng
dc.rights.en.fl_str_mv Attribution-NoDerivatives 4.0 International
dc.rights.uri.none.fl_str_mv http://creativecommons.org/licenses/by-nd/4.0/
dc.rights.accessrights.none.fl_str_mv info:eu-repo/semantics/openAccess
dc.rights.coar.none.fl_str_mv http://purl.org/coar/access_right/c_abf2
rights_invalid_str_mv Attribution-NoDerivatives 4.0 International
http://creativecommons.org/licenses/by-nd/4.0/
http://purl.org/coar/access_right/c_abf2
eu_rights_str_mv openAccess
dc.format.extent.none.fl_str_mv 21 Páginas
dc.format.mimetype.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Universidad de los Andes
dc.publisher.program.none.fl_str_mv Biología
dc.publisher.faculty.none.fl_str_mv Facultad de Ciencias
dc.publisher.department.none.fl_str_mv Departamento de Ciencias Biológicas
publisher.none.fl_str_mv Universidad de los Andes
institution Universidad de los Andes
bitstream.url.fl_str_mv https://repositorio.uniandes.edu.co/bitstreams/53a9be5f-eccf-4f91-b2b0-a272e1bd6f7c/download
https://repositorio.uniandes.edu.co/bitstreams/38b59e34-13f7-4901-b69b-399cc65877de/download
https://repositorio.uniandes.edu.co/bitstreams/3449f762-c551-4c5f-928c-40ef03c6a266/download
https://repositorio.uniandes.edu.co/bitstreams/aae8ab81-2056-450d-a3b7-0cff683f731b/download
https://repositorio.uniandes.edu.co/bitstreams/4bd8bd4e-3e38-41a8-b525-7aff2aba3b07/download
https://repositorio.uniandes.edu.co/bitstreams/1452eace-4d07-4ca7-8244-1d3d2848c5ab/download
https://repositorio.uniandes.edu.co/bitstreams/5e6cfc88-3f11-499d-b4c3-df24df113e1b/download
https://repositorio.uniandes.edu.co/bitstreams/0fc96949-c53c-4b89-b521-01c7eebcd009/download
bitstream.checksum.fl_str_mv a828fb193c04f550a6d6370b9fe3f54b
d138ec60f4995fe368980a39ce8cc52c
f7d494f61e544413a13e6ba1da2089cd
ae9e573a68e7f92501b6913cc846c39f
22a93f2a4a461b22d1701a33c020f520
4af5a5adeda85136bd9655d2e83fab89
349adf8108de08b8fe81d98471ffdfbd
ecdd2dc451533d400dcec8555ae59178
bitstream.checksumAlgorithm.fl_str_mv MD5
MD5
MD5
MD5
MD5
MD5
MD5
MD5
repository.name.fl_str_mv Repositorio institucional Séneca
repository.mail.fl_str_mv adminrepositorio@uniandes.edu.co
_version_ 1837005012605075456
spelling Reyes Muñoz, Alejandrovirtual::24122-1Rodríguez Otálora, Silvia Cristina2025-05-30T13:05:52Z2025-05-30T13:05:52Z2025-05-29https://hdl.handle.net/1992/76222instname:Universidad de los Andesreponame:Repositorio Institucional Sénecarepourl:https://repositorio.uniandes.edu.co/NUMTs can be defined as fragments of mitochondrial DNA that have been integrated into the nuclear genome through evolutionary processes. Once NUMTs are inserted they can potentially disrupt protein-coding genes, leading to disease or integrate successfully into the genome and change the phenotype of the organisms and thus its survival. NUMTs have been used to define phylogenetic outgroups and elucidate mtDNA evolution. While NUMTs have been extensively studied in vertebrates, their distribution, frequency, and evolutionary significance in fish remain largely unexplored. In this study, a novel bioinformatics pipeline using LAST is suggested as a potential method to identify NUMTs in the genomes of ten fish species. A total of 583 NUMTs were detected, with significant variation in NUMT content across species. Our findings suggest that genome size is not a strong predictor of NUMT abundance in fish. Additionally, an analysis of ancient NUMTs revealed that only Elasmobranchii (sharks and rays) retained conserved NUMT sequences, likely due to their slow genomic evolutionary rates. No ancient NUMTs were identified in Actinopterygii, possibly due to their high evolutionary divergence. These results provide new insights into the distribution and evolutionary history of NUMTs in fish and highlight the potential of NUMTs as markers for studying genome evolution. Further research on NUMTs in closely related fish taxa and improvements in the workflow could refine our understanding of their functional and evolutionary implications, particularly in species with highly conserved genomes.Pregrado21 Páginasapplication/pdfengUniversidad de los AndesBiologíaFacultad de CienciasDepartamento de Ciencias BiológicasAttribution-NoDerivatives 4.0 Internationalhttp://creativecommons.org/licenses/by-nd/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Fishing for NUMTs: exploring mitochondrial insertions in fishTrabajo de grado - Pregradoinfo:eu-repo/semantics/bachelorThesisinfo:eu-repo/semantics/acceptedVersionhttp://purl.org/coar/resource_type/c_7a1fTexthttp://purl.org/redcol/resource_type/TPNUMTsMitochondrial DNANuclear GenomeEvolutionary BiologyFish GenomicsBiología202123542Publicationhttps://scholar.google.es/citations?user=hbXF8UEAAAAJvirtual::24122-1https://scholar.google.es/citations?user=hbXF8UEAAAAJ0000-0003-2907-3265virtual::24122-10000-0003-2907-3265https://scienti.minciencias.gov.co/cvlac/visualizador/generarCurriculoCv.do?cod_rh=0000395927virtual::24122-1https://scienti.minciencias.gov.co/cvlac/visualizador/generarCurriculoCv.do?cod_rh=0000395927f71489e5-69f6-4e6b-90a6-c6b1d3fecec7virtual::24122-1f71489e5-69f6-4e6b-90a6-c6b1d3fecec7f71489e5-69f6-4e6b-90a6-c6b1d3fecec7virtual::24122-1ORIGINALFishing for NUMTs: exploring mitochondrial insertions in fish.pdfFishing for NUMTs: exploring mitochondrial insertions in fish.pdfapplication/pdf1034561https://repositorio.uniandes.edu.co/bitstreams/53a9be5f-eccf-4f91-b2b0-a272e1bd6f7c/downloada828fb193c04f550a6d6370b9fe3f54bMD52202123542_ForAutEntTesis_TraGraSisBib_202510.pdf202123542_ForAutEntTesis_TraGraSisBib_202510.pdfHIDEapplication/pdf427444https://repositorio.uniandes.edu.co/bitstreams/38b59e34-13f7-4901-b69b-399cc65877de/downloadd138ec60f4995fe368980a39ce8cc52cMD51CC-LICENSElicense_rdflicense_rdfapplication/rdf+xml; charset=utf-8799https://repositorio.uniandes.edu.co/bitstreams/3449f762-c551-4c5f-928c-40ef03c6a266/downloadf7d494f61e544413a13e6ba1da2089cdMD53LICENSElicense.txtlicense.txttext/plain; charset=utf-82535https://repositorio.uniandes.edu.co/bitstreams/aae8ab81-2056-450d-a3b7-0cff683f731b/downloadae9e573a68e7f92501b6913cc846c39fMD54TEXTFishing for NUMTs: exploring mitochondrial insertions in fish.pdf.txtFishing for NUMTs: exploring mitochondrial insertions in fish.pdf.txtExtracted texttext/plain35137https://repositorio.uniandes.edu.co/bitstreams/4bd8bd4e-3e38-41a8-b525-7aff2aba3b07/download22a93f2a4a461b22d1701a33c020f520MD55202123542_ForAutEntTesis_TraGraSisBib_202510.pdf.txt202123542_ForAutEntTesis_TraGraSisBib_202510.pdf.txtExtracted texttext/plain2019https://repositorio.uniandes.edu.co/bitstreams/1452eace-4d07-4ca7-8244-1d3d2848c5ab/download4af5a5adeda85136bd9655d2e83fab89MD57THUMBNAILFishing for NUMTs: exploring mitochondrial insertions in fish.pdf.jpgFishing for NUMTs: exploring mitochondrial insertions in fish.pdf.jpgIM Thumbnailimage/jpeg8479https://repositorio.uniandes.edu.co/bitstreams/5e6cfc88-3f11-499d-b4c3-df24df113e1b/download349adf8108de08b8fe81d98471ffdfbdMD56202123542_ForAutEntTesis_TraGraSisBib_202510.pdf.jpg202123542_ForAutEntTesis_TraGraSisBib_202510.pdf.jpgIM Thumbnailimage/jpeg15073https://repositorio.uniandes.edu.co/bitstreams/0fc96949-c53c-4b89-b521-01c7eebcd009/downloadecdd2dc451533d400dcec8555ae59178MD581992/76222oai:repositorio.uniandes.edu.co:1992/762222025-05-31 04:01:20.331http://creativecommons.org/licenses/by-nd/4.0/Attribution-NoDerivatives 4.0 Internationalopen.accesshttps://repositorio.uniandes.edu.coRepositorio institucional Sénecaadminrepositorio@uniandes.edu.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