Application of genome assembly methods to human and non-human primate genomics

Application of genome assembly methods to human and non-human primate genomics

Universitat Pompey Fabra. Departamento de Ciencia Experimentales y de la Vida.

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Bibliographic Details
Main Author: Kuderna, Lukas F. K.
Other Authors: Marqués-Bonet, Tomàs
Format: tesis doctoral biblioteca
Published: CSIC-UPF - Instituto de Biología Evolutiva (IBE) 2020-01-24
Subjects:Primate genomics, Genome assembly, Long read sequencing, Y chromosome, Chimpanzees,
Online Access:http://hdl.handle.net/10261/223293
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spelling dig-ibe-es-10261-2232932021-06-15T02:31:10Z Application of genome assembly methods to human and non-human primate genomics Kuderna, Lukas F. K. Marqués-Bonet, Tomàs Primate genomics Genome assembly Long read sequencing Y chromosome Chimpanzees Universitat Pompey Fabra. Departamento de Ciencia Experimentales y de la Vida. Genomic analyses are at the center of contemporary biology. These studies heavily rely on reference genome assemblies, yet those are typically highly fragmented. Having accurate representations of complex genomes, or parts thereof, is crucial to study human and primate evolution and disease. Here, we develop and apply new sequencing strategies and technologies to improve reference assemblies. We first explore the combinatorial potential of different datasets to generate a highly improved reference for the chimpanzee, a crucial species for the study of human origins. We are able to close 77% of the over 159.000 remaining gaps in the previous iteration of this species’ assembly and increase continuity by more than 750%. We then go on to develop a workflow to assemble the first human Y chromosome of African ancestry, using native flow-sorted chromosomes sequenced on a Nanopore device. We are able to assemble the Y chromosome to a reference grade quality and achieve unprecedented sequence resolution across structurally complex regions. These results open new avenues for comparative studies including the chimpanzee genome or human Y chromosomes. 2020-11-20T12:50:05Z 2020-11-20T12:50:05Z 2020-01-24 2020-11-20T12:50:06Z tesis doctoral http://purl.org/coar/resource_type/c_db06 http://hdl.handle.net/10261/223293 Sí open CSIC-UPF - Instituto de Biología Evolutiva (IBE) Universitat Pompeu Fabra
institution IBE ES
collection DSpace
country España
countrycode ES
component Bibliográfico
access En linea
databasecode dig-ibe-es
tag biblioteca
region Europa del Sur
libraryname Biblioteca del IBE España
topic Primate genomics
Genome assembly
Long read sequencing
Y chromosome
Chimpanzees
Primate genomics
Genome assembly
Long read sequencing
Y chromosome
Chimpanzees
spellingShingle Primate genomics
Genome assembly
Long read sequencing
Y chromosome
Chimpanzees
Primate genomics
Genome assembly
Long read sequencing
Y chromosome
Chimpanzees
Kuderna, Lukas F. K.
Application of genome assembly methods to human and non-human primate genomics
description Universitat Pompey Fabra. Departamento de Ciencia Experimentales y de la Vida.
author2 Marqués-Bonet, Tomàs
author_facet Marqués-Bonet, Tomàs
Kuderna, Lukas F. K.
format tesis doctoral
topic_facet Primate genomics
Genome assembly
Long read sequencing
Y chromosome
Chimpanzees
author Kuderna, Lukas F. K.
author_sort Kuderna, Lukas F. K.
title Application of genome assembly methods to human and non-human primate genomics
title_short Application of genome assembly methods to human and non-human primate genomics
title_full Application of genome assembly methods to human and non-human primate genomics
title_fullStr Application of genome assembly methods to human and non-human primate genomics
title_full_unstemmed Application of genome assembly methods to human and non-human primate genomics
title_sort application of genome assembly methods to human and non-human primate genomics
publisher CSIC-UPF - Instituto de Biología Evolutiva (IBE)
publishDate 2020-01-24
url http://hdl.handle.net/10261/223293
work_keys_str_mv AT kudernalukasfk applicationofgenomeassemblymethodstohumanandnonhumanprimategenomics
_version_ 1777668773591908352

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