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dc.contributor.authorRiccio, Cristian
dc.date.accessioned2022-01-24T07:03:23Z
dc.date.available2022-01-24T07:03:23Z
dc.date.issued2022-05-21
dc.date.submitted2021-06-01
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/332883
dc.description.abstractThe 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.
dc.description.sponsorshipWellcome
dc.rightsAll Rights Reserved
dc.rights.urihttps://www.rioxx.net/licenses/all-rights-reserved/
dc.subjectgenomics
dc.subjectbiology
dc.subjectsequencing
dc.subjectDNA
dc.subjectevolution
dc.subjectgene birth
dc.subjectPacBio
dc.subjectPacific Biosciences
dc.subjectlong reads
dc.subjectgenomes
dc.subjectgenome assembly
dc.subjectbioinformatics
dc.titleDuplication is a prominent mechanism of recent gene birth in Caenorhabditis elegans
dc.typeThesis
dc.type.qualificationlevelDoctoral
dc.type.qualificationnameDoctor of Philosophy (PhD)
dc.publisher.institutionUniversity of Cambridge
dc.date.updated2022-01-21T17:40:33Z
dc.identifier.doi10.17863/CAM.80314
rioxxterms.licenseref.urihttps://www.rioxx.net/licenses/all-rights-reserved/
dc.contributor.orcidRiccio, Cristian [0000-0001-9561-060X]
rioxxterms.typeThesis
dc.publisher.collegeQueens
cam.supervisorHemberg, Martin
cam.supervisorMiska, Eric
cam.supervisor.orcidMiska, Eric [0000-0002-4450-576X]
cam.depositDate2022-01-21
pubs.licence-identifierapollo-deposit-licence-2-1
pubs.licence-display-nameApollo Repository Deposit Licence Agreement
rioxxterms.freetoread.startdate2023-01-24


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