气候变化领域集成服务门户(CCPortal): Perfect match genomic landscape strategy: Refinement and customization of reference genomes

CCPortal

DOI	10.1073/PNAS.2025192118
	Perfect match genomic landscape strategy: Refinement and customization of reference genomes
	Palacios-Flores K.; Garcia-Sotelo J.; Castillo A.; Uribe C.; Morales L.; Boege M.; Davila G.; Flores M.; Palacios R.
发表日期	2021
ISSN	00278424
卷号	118 期号:14
英文摘要	When addressing a genomic question, having a reliable and adequate reference genome is of utmost importance. This drives the necessity to refine and customize reference genomes (RGs). Our laboratory has recently developed a strategy, the Perfect Match Genomic Landscape (PMGL), to detect variation between genomes [K. Palacios-Flores et al.. Genetics 208, 1631-1641 (2018)]. The PMGL is precise and sensitive and, in contrast to most currently used algorithms, is nonstatistical in nature. Here we demonstrate the power of PMGL to refine and customize RGs. As a proof-of-concept, we refined different versions of the Saccharomyces cerevisiae RG. We applied the automatic PMGL pipeline to refine the genomes of microorganisms belonging to the three domains of life: The archaea Methanococcus maripaludis and Pyrococcus furiosus; the bacteria Escherichia coli, Staphylococcus aureus, and Bacillus subtilis; and the eukarya Schizosaccharomyces pombe, Aspergillus oryzae, and several strains of Saccharomyces paradoxus. We analyzed the reference genome of the virus SARS-CoV-2 and previously published viral genomes from patients' samples with COVID-19. We performed a mutation-accumulation experiment in E. coli and show that the PMGL strategy can detect specific mutations generated at any desired step of the whole procedure. We propose that PMGL can be used as a final step for the refinement and customization of any haploid genome, independently of the strategies and algorithms used in its assembly. © 2021 National Academy of Sciences. All rights reserved.
英文关键词	Experimental evolution; Genome variation; Microbial genomes; Mutation-accumulation experiments; SARS-CoV-2
语种	英语
scopus关键词	algorithm; genetic variation; genetics; genomics; microbial genome; mutation accumulation; procedures; proof of concept; Saccharomyces cerevisiae; Algorithms; Genetic Variation; Genome, Microbial; Genomics; Mutation Accumulation; Proof of Concept Study; Saccharomyces cerevisiae; SARS-CoV-2
来源期刊	Proceedings of the National Academy of Sciences of the United States of America
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/180202
作者单位	Laboratorio Internacional de Investigación Sobre El Genoma Humano, Universidad Nacional Autónoma de México, Querétaro, 76230, Mexico; Escuela Nacional de Estudios Superiores Juriquilla, Universidad Nacional Autónoma de México, Querétaro, 76230, Mexico
推荐引用方式 GB/T 7714	Palacios-Flores K.,Garcia-Sotelo J.,Castillo A.,et al. Perfect match genomic landscape strategy: Refinement and customization of reference genomes[J],2021,118(14).
APA	Palacios-Flores K..,Garcia-Sotelo J..,Castillo A..,Uribe C..,Morales L..,...&Palacios R..(2021).Perfect match genomic landscape strategy: Refinement and customization of reference genomes.Proceedings of the National Academy of Sciences of the United States of America,118(14).
MLA	Palacios-Flores K.,et al."Perfect match genomic landscape strategy: Refinement and customization of reference genomes".Proceedings of the National Academy of Sciences of the United States of America 118.14(2021).