An Important Role for Purifying Selection in Archaeal Genome Evolution

ABSTRACT As the null hypothesis of genome evolution, population genetic theory suggests that selection strength controls genome size. Through the process of genetic drift, this theory predicts that compact genomes are maintained by strong purifying selection while complex genomes are enabled by weak...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Zhe Lyu, Zhi-Gang Li, Fei He, Ziding Zhang
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	Archaea evolution genome analysis Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/f9213d98d28146c3994908739cfeda4b
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:f9213d98d28146c3994908739cfeda4b
record_format	dspace
spelling	oai:doaj.org-article:f9213d98d28146c3994908739cfeda4b2021-12-02T19:47:33ZAn Important Role for Purifying Selection in Archaeal Genome Evolution10.1128/mSystems.00112-172379-5077https://doaj.org/article/f9213d98d28146c3994908739cfeda4b2017-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00112-17https://doaj.org/toc/2379-5077ABSTRACT As the null hypothesis of genome evolution, population genetic theory suggests that selection strength controls genome size. Through the process of genetic drift, this theory predicts that compact genomes are maintained by strong purifying selection while complex genomes are enabled by weak purifying selection. It offers a unifying framework that explains why prokaryotic genomes are much smaller than their eukaryotic counterparts. However, recent findings suggest that bigger prokaryotic genomes appear to experience stronger purifying selection, indicating that purifying selection may not dominate prokaryotic genome evolution. Since archaeal genomes were underrepresented in those studies, generalization of the conclusions to both archaeal and bacterial genomes may not be warranted. In this study, we revisited this matter by focusing on archaeal and bacterial genomes separately. We found that bigger bacterial genomes indeed experienced stronger purifying selection, but the opposite was observed in archaeal genomes. This new finding would predict an enrichment of noncoding sequences in large archaeal genomes, which was confirmed by an analysis of coding density. In contrast, coding density remained stable regardless of bacterial genome size. In conclusion, this study suggests that purifying selection may play a more important role in archaeal genome evolution than previously hypothesized, indicating that there could be a major difference between the evolutionary regimes of Archaea and Bacteria. IMPORTANCE The evolution of genome complexity is a fundamental question in biology. A hallmark of eukaryotic genome complexity is that larger genomes tend to have more noncoding sequences, which are believed to be minimal in archaeal and bacterial genomes. However, we found that archaeal genomes also possessed this eukaryotic feature while bacterial genomes did not. This could be predicted from our analysis on genetic drift, which showed a relaxation of purifying selection in larger archaeal genomes, also a eukaryotic feature. In contrast, the opposite was evident in bacterial genomes.Zhe LyuZhi-Gang LiFei HeZiding ZhangAmerican Society for MicrobiologyarticleArchaeaevolutiongenome analysisMicrobiologyQR1-502ENmSystems, Vol 2, Iss 5 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Archaea evolution genome analysis Microbiology QR1-502
spellingShingle	Archaea evolution genome analysis Microbiology QR1-502 Zhe Lyu Zhi-Gang Li Fei He Ziding Zhang An Important Role for Purifying Selection in Archaeal Genome Evolution
description	ABSTRACT As the null hypothesis of genome evolution, population genetic theory suggests that selection strength controls genome size. Through the process of genetic drift, this theory predicts that compact genomes are maintained by strong purifying selection while complex genomes are enabled by weak purifying selection. It offers a unifying framework that explains why prokaryotic genomes are much smaller than their eukaryotic counterparts. However, recent findings suggest that bigger prokaryotic genomes appear to experience stronger purifying selection, indicating that purifying selection may not dominate prokaryotic genome evolution. Since archaeal genomes were underrepresented in those studies, generalization of the conclusions to both archaeal and bacterial genomes may not be warranted. In this study, we revisited this matter by focusing on archaeal and bacterial genomes separately. We found that bigger bacterial genomes indeed experienced stronger purifying selection, but the opposite was observed in archaeal genomes. This new finding would predict an enrichment of noncoding sequences in large archaeal genomes, which was confirmed by an analysis of coding density. In contrast, coding density remained stable regardless of bacterial genome size. In conclusion, this study suggests that purifying selection may play a more important role in archaeal genome evolution than previously hypothesized, indicating that there could be a major difference between the evolutionary regimes of Archaea and Bacteria. IMPORTANCE The evolution of genome complexity is a fundamental question in biology. A hallmark of eukaryotic genome complexity is that larger genomes tend to have more noncoding sequences, which are believed to be minimal in archaeal and bacterial genomes. However, we found that archaeal genomes also possessed this eukaryotic feature while bacterial genomes did not. This could be predicted from our analysis on genetic drift, which showed a relaxation of purifying selection in larger archaeal genomes, also a eukaryotic feature. In contrast, the opposite was evident in bacterial genomes.
format	article
author	Zhe Lyu Zhi-Gang Li Fei He Ziding Zhang
author_facet	Zhe Lyu Zhi-Gang Li Fei He Ziding Zhang
author_sort	Zhe Lyu
title	An Important Role for Purifying Selection in Archaeal Genome Evolution
title_short	An Important Role for Purifying Selection in Archaeal Genome Evolution
title_full	An Important Role for Purifying Selection in Archaeal Genome Evolution
title_fullStr	An Important Role for Purifying Selection in Archaeal Genome Evolution
title_full_unstemmed	An Important Role for Purifying Selection in Archaeal Genome Evolution
title_sort	important role for purifying selection in archaeal genome evolution
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/f9213d98d28146c3994908739cfeda4b
work_keys_str_mv	AT zhelyu animportantroleforpurifyingselectioninarchaealgenomeevolution AT zhigangli animportantroleforpurifyingselectioninarchaealgenomeevolution AT feihe animportantroleforpurifyingselectioninarchaealgenomeevolution AT zidingzhang animportantroleforpurifyingselectioninarchaealgenomeevolution AT zhelyu importantroleforpurifyingselectioninarchaealgenomeevolution AT zhigangli importantroleforpurifyingselectioninarchaealgenomeevolution AT feihe importantroleforpurifyingselectioninarchaealgenomeevolution AT zidingzhang importantroleforpurifyingselectioninarchaealgenomeevolution
_version_	1718376001318158336

An Important Role for Purifying Selection in Archaeal Genome Evolution

Ejemplares similares