New approaches to the mapping and assembly of genomic data

TY - BOOK

T1 - New approaches to the mapping and assembly of genomic data

AU - Samaniego Castruita, Jose Alfredo

PY - 2016

Y1 - 2016

N2 - DNA sequencing has been a key technology for applying to questions that investigate the genetic basis of different species and their relationships to each other. Our knowledge about many of fields across the biological sciences has been expanded critically using these approaches, including, Evolutionary Biology, Population Genetics, Molecular Biology, among many others. Ancient genetics has also been one of these branches in biology that has grown in the last decade. This discipline went from drawing small insights based on datasets containing only a few genes, to answering complex questions that require data on the ancient genomic scale. For this reason, researchers have in recent years begun to put effort into the improvement of methods relating to the assembly of genomes while taking into account the limitations of working with ancient DNA.This thesis focuses on tackling some of these limitations by exploring new mapping and assembly methods. In the first part of the thesis, a new method to assemble organelle genomes is presented, that takes into consideration paralogue sequences, a problem that ancient DNA is more susceptible to have than modern DNA. In the second part, I investigate the effect that different reference genomes can have when mapping DNA sequences, in a context of population genetics. In the final part, I explore the use of ancestral gene reconstruction as an alternative for reference genomes when mapping ancient samples. In conclusion, I hope this thesis will help to develop future bioinformatics analyses in ancient DNA studies by addressing some of ancient DNA limitations.

AB - DNA sequencing has been a key technology for applying to questions that investigate the genetic basis of different species and their relationships to each other. Our knowledge about many of fields across the biological sciences has been expanded critically using these approaches, including, Evolutionary Biology, Population Genetics, Molecular Biology, among many others. Ancient genetics has also been one of these branches in biology that has grown in the last decade. This discipline went from drawing small insights based on datasets containing only a few genes, to answering complex questions that require data on the ancient genomic scale. For this reason, researchers have in recent years begun to put effort into the improvement of methods relating to the assembly of genomes while taking into account the limitations of working with ancient DNA.This thesis focuses on tackling some of these limitations by exploring new mapping and assembly methods. In the first part of the thesis, a new method to assemble organelle genomes is presented, that takes into consideration paralogue sequences, a problem that ancient DNA is more susceptible to have than modern DNA. In the second part, I investigate the effect that different reference genomes can have when mapping DNA sequences, in a context of population genetics. In the final part, I explore the use of ancestral gene reconstruction as an alternative for reference genomes when mapping ancient samples. In conclusion, I hope this thesis will help to develop future bioinformatics analyses in ancient DNA studies by addressing some of ancient DNA limitations.

UR - https://rex.kb.dk/primo-explore/fulldisplay?docid=KGL01010310094&context=L&vid=NUI&search_scope=KGL&tab=default_tab&lang=da_DK

M3 - Ph.D. thesis

BT - New approaches to the mapping and assembly of genomic data

PB - Natural History Museum of Denmark, Faculty of Science, University of Copenhagen

ER -