De novo genome assemblies of endagered species and challenging chromosomes
Modern biology relies on genomic references to perform analyses in most studies. High-quality de novo genome assemblies are key to having references containing all the genomic content of a species. Here I use avant-garde technologies to generate assemblies of endangered species, challenging chromoso...
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| Tipo de recurso: | tesis doctoral |
| Estado: | Versión publicada |
| Fecha de publicación: | 2023 |
| País: | España |
| Institución: | CBUC, CESCA |
| Repositorio: | TDR. Tesis Doctorales en Red |
| OAI Identifier: | oai:www.tdx.cat:10803/689583 |
| Acceso en línea: | http://hdl.handle.net/10803/689583 |
| Access Level: | acceso abierto |
| Palabra clave: | GENOME ASSEMBLY LONG-READS CONSERVATION REPETITIVE CHROMOSOMES GENÒMICA ENSEMBLATGES CONSERVACIÓ CROMOSOMES REPETITIUS SEQÜENCIACIÓ 575 |
| Sumario: | Modern biology relies on genomic references to perform analyses in most studies. High-quality de novo genome assemblies are key to having references containing all the genomic content of a species. Here I use avant-garde technologies to generate assemblies of endangered species, challenging chromosomes, and extraordinarily giant genomes. In this work I start by presenting a high-quality long-read genome assembly of the endangered ring-tailed lemur(Lemur catta), comparing it to a previous reference and comparing its repeatome landscape to other primate genomes. Continuing by presenting long-read assemblies of seven major human Y chromosome haplogroups obtained using selective sequencing techniques and using the assemblies and reads to have a look into their structural variation landscape. And finalize generating a reference for the large genome of the Montseny brook newt (Calotriton arnoldi), and I use it to assess heterozygosity levels, genetic diversity and runs of homozygosity of wild populations. Overall, these results provide new insights into the genomic and repetitive content of the species, enhancing the possibility of future studies on threatened non-model species and neglected repetitive chromosomes. |
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