Duplication is a prominent mechanism of recent gene birth in Caenorhabditis elegans
dc.contributor.author | Riccio, Cristian | |
dc.date.accessioned | 2022-01-24T07:03:23Z | |
dc.date.available | 2022-01-24T07:03:23Z | |
dc.date.issued | 2022-05-21 | |
dc.date.submitted | 2021-06-01 | |
dc.identifier.uri | https://www.repository.cam.ac.uk/handle/1810/332883 | |
dc.description.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. | |
dc.description.sponsorship | Wellcome | |
dc.rights | All Rights Reserved | |
dc.rights.uri | https://www.rioxx.net/licenses/all-rights-reserved/ | |
dc.subject | genomics | |
dc.subject | biology | |
dc.subject | sequencing | |
dc.subject | DNA | |
dc.subject | evolution | |
dc.subject | gene birth | |
dc.subject | PacBio | |
dc.subject | Pacific Biosciences | |
dc.subject | long reads | |
dc.subject | genomes | |
dc.subject | genome assembly | |
dc.subject | bioinformatics | |
dc.title | Duplication is a prominent mechanism of recent gene birth in Caenorhabditis elegans | |
dc.type | Thesis | |
dc.type.qualificationlevel | Doctoral | |
dc.type.qualificationname | Doctor of Philosophy (PhD) | |
dc.publisher.institution | University of Cambridge | |
dc.date.updated | 2022-01-21T17:40:33Z | |
dc.identifier.doi | 10.17863/CAM.80314 | |
rioxxterms.licenseref.uri | https://www.rioxx.net/licenses/all-rights-reserved/ | |
dc.contributor.orcid | Riccio, Cristian [0000-0001-9561-060X] | |
rioxxterms.type | Thesis | |
dc.publisher.college | Queens | |
cam.supervisor | Hemberg, Martin | |
cam.supervisor | Miska, Eric | |
cam.supervisor.orcid | Miska, Eric [0000-0002-4450-576X] | |
cam.depositDate | 2022-01-21 | |
pubs.licence-identifier | apollo-deposit-licence-2-1 | |
pubs.licence-display-name | Apollo Repository Deposit Licence Agreement | |
rioxxterms.freetoread.startdate | 2023-01-24 |