Whole‐genome sequencing and genome regions ...
Document type :
Compte-rendu et recension critique d'ouvrage
DOI :
Title :
Whole‐genome sequencing and genome regions of special interest: Lessons from major histocompatibility complex, sex determination, and plant self‐incompatibility
Author(s) :
Vekemans, Xavier [Auteur]
Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 [Evo-Eco-Paléo (EEP)]
Castric, Vincent [Auteur]
Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 [Evo-Eco-Paléo (EEP)]
Hipperson, Helen [Auteur]
Department of Animal and Plant Sciences [Sheffield]
Müller, Niels [Auteur]
Thunen Institute of Forest Ecosystems
Westerdahl, Helena [Auteur]
Skane University Hospital [Lund]
Cronk, Quentin [Auteur]
Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 [Evo-Eco-Paléo (EEP)]
Castric, Vincent [Auteur]
Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 [Evo-Eco-Paléo (EEP)]
Hipperson, Helen [Auteur]
Department of Animal and Plant Sciences [Sheffield]
Müller, Niels [Auteur]
Thunen Institute of Forest Ecosystems
Westerdahl, Helena [Auteur]
Skane University Hospital [Lund]
Cronk, Quentin [Auteur]
Journal title :
Molecular Ecology
Publisher :
Wiley
Publication date :
2021
ISSN :
0962-1083
English keyword(s) :
whole-genome sequencing
major histocompatibility complex
sex-determining region
long-read sequencing
self-incompatibility locus
major histocompatibility complex
sex-determining region
long-read sequencing
self-incompatibility locus
HAL domain(s) :
Sciences du Vivant [q-bio]/Génétique/Génétique des plantes
Sciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
Sciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
English abstract : [en]
Whole-genome sequencing of non-model organisms is now widely accessible and has allowed a range of questions in the field of molecular ecology to be investigated with greater power. However, some genomic regions that are ...
Show more >Whole-genome sequencing of non-model organisms is now widely accessible and has allowed a range of questions in the field of molecular ecology to be investigated with greater power. However, some genomic regions that are of high biological interest remain problematic for assembly and data-handling. Three such regions are the major histocompatibility complex (MHC), sex-determining regions (SDRs) and the plant self-incompatibility locus (S-locus). Using these as examples, we illustrate the challenges of both assembling and resequencing these highly polymorphic regions and how bioinformatic and technological developments are enabling new approaches to their study. Mapping short-read sequences against multiple alternative references improves genotyping comprehensiveness at the S-locus thereby contributing to more accurate assessments of allelic frequencies. Long-read sequencing, producing reads of several tens to hundreds of kilobase pairs in length, facilitates the assembly of such regions as single sequences can span the multiple duplicated gene copies of the MHC region, and sequence through repetitive stretches and translocations in SDRs and S-locus haplotypes. These advances are adding value to short-read genome resequencing approaches by allowing, for example, more accurate haplotype phasing across longer regions. Finally, we assessed further technical improvements, such as nanopore adaptive sequencing and bioinformatic tools using pangenomes, which have the potential to further expand our knowledge of a number of genomic regions that remain challenging to study with classical resequencing approaches.Show less >
Show more >Whole-genome sequencing of non-model organisms is now widely accessible and has allowed a range of questions in the field of molecular ecology to be investigated with greater power. However, some genomic regions that are of high biological interest remain problematic for assembly and data-handling. Three such regions are the major histocompatibility complex (MHC), sex-determining regions (SDRs) and the plant self-incompatibility locus (S-locus). Using these as examples, we illustrate the challenges of both assembling and resequencing these highly polymorphic regions and how bioinformatic and technological developments are enabling new approaches to their study. Mapping short-read sequences against multiple alternative references improves genotyping comprehensiveness at the S-locus thereby contributing to more accurate assessments of allelic frequencies. Long-read sequencing, producing reads of several tens to hundreds of kilobase pairs in length, facilitates the assembly of such regions as single sequences can span the multiple duplicated gene copies of the MHC region, and sequence through repetitive stretches and translocations in SDRs and S-locus haplotypes. These advances are adding value to short-read genome resequencing approaches by allowing, for example, more accurate haplotype phasing across longer regions. Finally, we assessed further technical improvements, such as nanopore adaptive sequencing and bioinformatic tools using pangenomes, which have the potential to further expand our knowledge of a number of genomic regions that remain challenging to study with classical resequencing approaches.Show less >
Language :
Anglais
Popular science :
Non
Source :
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