Best Practices in Microbial Experimental Evolution: Using Reporters and Long-Read Sequencing to Identify Copy Number Variation in Experimental Evolution.
Copy-number variant
Fluorescent CNV reporter
Genome dynamics
Long term experimental evolution
Long-read sequencing
Journal
Journal of molecular evolution
ISSN: 1432-1432
Titre abrégé: J Mol Evol
Pays: Germany
ID NLM: 0360051
Informations de publication
Date de publication:
Jun 2023
Jun 2023
Historique:
received:
28
09
2022
accepted:
21
02
2023
medline:
19
6
2023
pubmed:
4
4
2023
entrez:
3
4
2023
Statut:
ppublish
Résumé
Copy number variants (CNVs), comprising gene amplifications and deletions, are a pervasive class of heritable variation. CNVs play a key role in rapid adaptation in both natural, and experimental, evolution. However, despite the advent of new DNA sequencing technologies, detection and quantification of CNVs in heterogeneous populations has remained challenging. Here, we summarize recent advances in the use of CNV reporters that provide a facile means of quantifying de novo CNVs at a specific locus in the genome, and nanopore sequencing, for resolving the often complex structures of CNVs. We provide guidance for the engineering and analysis of CNV reporters and practical guidelines for single-cell analysis of CNVs using flow cytometry. We summarize recent advances in nanopore sequencing, discuss the utility of this technology, and provide guidance for the bioinformatic analysis of these data to define the molecular structure of CNVs. The combination of reporter systems for tracking and isolating CNV lineages and long-read DNA sequencing for characterizing CNV structures enables unprecedented resolution of the mechanisms by which CNVs are generated and their evolutionary dynamics.
Identifiants
pubmed: 37012421
doi: 10.1007/s00239-023-10102-7
pii: 10.1007/s00239-023-10102-7
pmc: PMC10275804
doi:
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
356-368Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM107466
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM134066
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM132037
Pays : United States
Informations de copyright
© 2023. The Author(s).
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