Duplication is a prominent mechanism of recent gene birth in Caenorhabditis elegans
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| Title: | Duplication is a prominent mechanism of recent gene birth in Caenorhabditis elegans |
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| Authors: | Riccio, Cristian |
| Committee Members: | Hemberg, Martin; Miska, Eric |
| Summary: | 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. |
| URL: | https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.845650 |
| Database: | OpenDissertations |
| FullText | Text: Availability: 0 |
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| Header | DbId: ddu DbLabel: OpenDissertations An: ddu.oai.ethos.bl.uk.845650 AccessLevel: 6 PubType: Dissertation/ Thesis PubTypeId: dissertation PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: Duplication is a prominent mechanism of recent gene birth in Caenorhabditis elegans – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Riccio%2C+Cristian%22">Riccio, Cristian</searchLink> – Name: Author Label: Committee Members Group: Au Data: <searchLink fieldCode="CO" term="%22Hemberg%2C+Martin%22">Hemberg, Martin</searchLink>; <searchLink fieldCode="CO" term="%22Miska%2C+Eric%22">Miska, Eric</searchLink> – Name: Abstract Label: Summary Group: Ab Data: 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. – Name: URL Label: URL Group: URL Data: <link linkTarget="URL" linkTerm="https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.845650" linkWindow="_blank">https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.845650</link> |
| PLink | https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=ddu&AN=ddu.oai.ethos.bl.uk.845650 |
| RecordInfo | BibRecord: BibEntity: Languages: – Code: eng Text: English Subjects: – SubjectFull: genomics ; biology ; sequencing ; DNA ; evolution ; gene birth ; PacBio ; Pacific Biosciences ; long reads ; genomes ; genome assembly ; bioinformatics Type: general Titles: – TitleFull: Duplication is a prominent mechanism of recent gene birth in Caenorhabditis elegans Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Riccio, Cristian IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 01 Type: published Y: 2022 |
| ResultId | 1 |
