{"id":{"repo_id":"cambridge","oai_identifier":"oai:www.repository.cam.ac.uk:1810/332883"},"canonical_url":"https://search.dev.ndltd.org/etd/cambridge/oai:www.repository.cam.ac.uk:1810/332883","repository":{"repo_id":"cambridge","name":"Cambridge University","base_url":"https://api.repository.cam.ac.uk/server/oai/request"},"display":{"title":"Duplication is a prominent mechanism of recent gene birth in Caenorhabditis elegans","abstract":"The high number of available reference genomes for different species and their comparison has enabled the elucidation of gene birth mechanisms that act over a long evolutionary timescale. However, the lack of several reference-quality genomes for different individuals of the same species has hampered the study of the mechanisms of more evolutionarily young gene births. Despite the high throughput brought about by second-generation sequencing technologies, their short read length has limited the study of genetic diversity to single nucleotide polymorphisms (SNPs) and short indels. However, in order to study gene-level events, we need to characterise the genetic diversity of a species comprehensively, including structural variants (SVs) (> 50 bp). I present the most comprehensive set of genomes and SVs for Caenorhabditis elegans. I have assembled a high-quality genome for each of 20 wild isolates of the nematode using long and short read sequencing. I show that 1,587 transcripts are deleted among the wild isolates and thus sketch the first definition of the core genome of C. elegans. I present the case of a highly proliferative transposon harbouring a transcription factor binding site (TFBS) and use it to address the question of transposon co-option in this model organism. Finally, using this dataset, I show that tandem gene duplication is a prominent gene birth mechanism, whereas horizontal gene transfer (HGT) played little or no role in the birth of recent C. elegans genes. Additionally, I show that G protein-coupled receptors (GPCRs) have high levels of presence/absence variation (PAV) and discuss the significance of this finding in light of the ecology of this little worm.","abstract_html":"The high number of available reference genomes for different species and their comparison has enabled the elucidation of gene birth mechanisms that act over a long evolutionary timescale. However, the lack of several reference-quality genomes for different individuals of the same species has hampered the study of the mechanisms of more evolutionarily young gene births. Despite the high throughput brought about by second-generation sequencing technologies, their short read length has limited the study of genetic diversity to single nucleotide polymorphisms (SNPs) and short indels. However, in order to study gene-level events, we need to characterise the genetic diversity of a species comprehensively, including structural variants (SVs) (> 50 bp). I present the most comprehensive set of genomes and SVs for Caenorhabditis elegans. I have assembled a high-quality genome for each of 20 wild isolates of the nematode using long and short read sequencing. I show that 1,587 transcripts are deleted among the wild isolates and thus sketch the first definition of the core genome of C. elegans. I present the case of a highly proliferative transposon harbouring a transcription factor binding site (TFBS) and use it to address the question of transposon co-option in this model organism. Finally, using this dataset, I show that tandem gene duplication is a prominent gene birth mechanism, whereas horizontal gene transfer (HGT) played little or no role in the birth of recent C. elegans genes. Additionally, I show that G protein-coupled receptors (GPCRs) have high levels of presence/absence variation (PAV) and discuss the significance of this finding in light of the ecology of this little worm.","abstract_has_math":false,"creators":["Riccio, Cristian"],"institution":"University of Cambridge","degree_name":"Doctor of Philosophy (PhD)","degree_level":"Doctoral","degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Hemberg, Martin","Miska, Eric Alexander"],"committee_chairs":[],"committee_members":[],"year":2022,"date_issued":"2022-05-21","date_published":"2022-05-21","updated_at":"2026-07-22T22:24:31Z","subjects":["genomics","biology","sequencing","DNA","evolution","gene birth","PacBio","Pacific Biosciences","long reads","genomes","genome assembly","bioinformatics"],"languages":["eng"],"rights":[],"rights_urls":["https://www.rioxx.net/licenses/all-rights-reserved/"],"identifier_entries":[{"key":"dc:creator.authoridentifier","label":"Author Identifier","values":["000000019561060X"],"render_values":[{"text":"0000-0001-9561-060X","href":"https://orcid.org/0000-0001-9561-060X","code":true}]}]},"links":{"outbound_url":"https://doi.org/10.17863/CAM.80314","outbound_label":"DOI","outbound_source":"dc:identifier.doi"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Hemberg, Martin","Miska, Eric Alexander"]},{"key":"dc:contributor.sponsor","label":"Sponsor","values":["Wellcome"]},{"key":"dc:creator","label":"Author","values":["Riccio, Cristian"]},{"key":"dc:creator.authoridentifier","label":"Author Identifier","values":["000000019561060X"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.issued","label":"Date","values":["2022-05-21"]},{"key":"dc:publisher.institution","label":"Dc Publisher Institution","values":["University of Cambridge"]},{"key":"dc:relation.isreferencedby.uri","label":"Dc Relation Isreferencedby URI","values":["https://www.repository.cam.ac.uk/handle/1810/332883"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"dc:type.qualificationlevel","label":"Dc Type Qualificationlevel","values":["Doctoral"]},{"key":"dc:type.qualificationname","label":"Dc Type Qualificationname","values":["Doctor of Philosophy (PhD)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["genomics","biology","sequencing","DNA","evolution","gene birth","PacBio","Pacific Biosciences","long reads","genomes","genome assembly","bioinformatics"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["eng"]},{"key":"dc:rights","label":"Dc Rights","values":["https://www.rioxx.net/licenses/all-rights-reserved/"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.doi","label":"DOI","values":["10.17863/CAM.80314"]},{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/8f0606c1-c774-400e-8a32-e35380c6c6ea/download"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["The high number of available reference genomes for different species and their comparison has enabled the elucidation of gene birth mechanisms that act over a long evolutionary timescale. 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I present the case of a highly proliferative transposon harbouring a transcription factor binding site (TFBS) and use it to address the question of transposon co-option in this model organism. Finally, using this dataset, I show that tandem gene duplication is a prominent gene birth mechanism, whereas horizontal gene transfer (HGT) played little or no role in the birth of recent C. elegans genes. 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