Tracing the <italic toggle="yes">De Novo</italic> Origin of Protein-Coding Genes in Yeast

ABSTRACT De novo genes are very important for evolutionary innovation. However, how these genes originate and spread remains largely unknown. To better understand this, we rigorously searched for de novo genes in Saccharomyces cerevisiae S288C and examined their spread and fixation in the population...

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Autores principales:	Baojun Wu, Alicia Knudson
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	DNA shuffling de novo gene GC content parallel origins purifying selection yeast Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/30c4d7b26a3a45cfba13fa4fb166ff32
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spelling	oai:doaj.org-article:30c4d7b26a3a45cfba13fa4fb166ff322021-11-15T16:00:14ZTracing the <italic toggle="yes">De Novo</italic> Origin of Protein-Coding Genes in Yeast10.1128/mBio.01024-182150-7511https://doaj.org/article/30c4d7b26a3a45cfba13fa4fb166ff322018-09-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01024-18https://doaj.org/toc/2150-7511ABSTRACT De novo genes are very important for evolutionary innovation. However, how these genes originate and spread remains largely unknown. To better understand this, we rigorously searched for de novo genes in Saccharomyces cerevisiae S288C and examined their spread and fixation in the population. Here, we identified 84 de novo genes in S. cerevisiae S288C since the divergence with their sister groups. Transcriptome and ribosome profiling data revealed at least 8 (10%) and 28 (33%) de novo genes being expressed and translated only under specific conditions, respectively. DNA microarray data, based on 2-fold change, showed that 87% of the de novo genes are regulated during various biological processes, such as nutrient utilization and sporulation. Our comparative and evolutionary analyses further revealed that some factors, including single nucleotide polymorphism (SNP)/indel mutation, high GC content, and DNA shuffling, contribute to the birth of de novo genes, while domestication and natural selection drive the spread and fixation of these genes. Finally, we also provide evidence suggesting the possible parallel origin of a de novo gene between S. cerevisiae and Saccharomyces paradoxus. Together, our study provides several new insights into the origin and spread of de novo genes. IMPORTANCE Emergence of de novo genes has occurred in many lineages during evolution, but the birth, spread, and function of these genes remain unresolved. Here we have searched for de novo genes from Saccharomyces cerevisiae S288C using rigorous methods, which reduced the effects of bad annotation and genomic gaps on the identification of de novo genes. Through this analysis, we have found 84 new genes originating de novo from previously noncoding regions, 87% of which are very likely involved in various biological processes. We noticed that 10% and 33% of de novo genes were only expressed and translated under specific conditions, therefore, verification of de novo genes through transcriptome and ribosome profiling, especially from limited expression data, may underestimate the number of bona fide new genes. We further show that SNP/indel mutation, high GC content, and DNA shuffling could be involved in the birth of de novo genes, while domestication and natural selection drive the spread and fixation of these genes. Finally, we provide evidence suggesting the possible parallel origin of a new gene.Baojun WuAlicia KnudsonAmerican Society for MicrobiologyarticleDNA shufflingde novo geneGC contentparallel originspurifying selectionyeastMicrobiologyQR1-502ENmBio, Vol 9, Iss 4 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	DNA shuffling de novo gene GC content parallel origins purifying selection yeast Microbiology QR1-502
spellingShingle	DNA shuffling de novo gene GC content parallel origins purifying selection yeast Microbiology QR1-502 Baojun Wu Alicia Knudson Tracing the <italic toggle="yes">De Novo</italic> Origin of Protein-Coding Genes in Yeast
description	ABSTRACT De novo genes are very important for evolutionary innovation. However, how these genes originate and spread remains largely unknown. To better understand this, we rigorously searched for de novo genes in Saccharomyces cerevisiae S288C and examined their spread and fixation in the population. Here, we identified 84 de novo genes in S. cerevisiae S288C since the divergence with their sister groups. Transcriptome and ribosome profiling data revealed at least 8 (10%) and 28 (33%) de novo genes being expressed and translated only under specific conditions, respectively. DNA microarray data, based on 2-fold change, showed that 87% of the de novo genes are regulated during various biological processes, such as nutrient utilization and sporulation. Our comparative and evolutionary analyses further revealed that some factors, including single nucleotide polymorphism (SNP)/indel mutation, high GC content, and DNA shuffling, contribute to the birth of de novo genes, while domestication and natural selection drive the spread and fixation of these genes. Finally, we also provide evidence suggesting the possible parallel origin of a de novo gene between S. cerevisiae and Saccharomyces paradoxus. Together, our study provides several new insights into the origin and spread of de novo genes. IMPORTANCE Emergence of de novo genes has occurred in many lineages during evolution, but the birth, spread, and function of these genes remain unresolved. Here we have searched for de novo genes from Saccharomyces cerevisiae S288C using rigorous methods, which reduced the effects of bad annotation and genomic gaps on the identification of de novo genes. Through this analysis, we have found 84 new genes originating de novo from previously noncoding regions, 87% of which are very likely involved in various biological processes. We noticed that 10% and 33% of de novo genes were only expressed and translated under specific conditions, therefore, verification of de novo genes through transcriptome and ribosome profiling, especially from limited expression data, may underestimate the number of bona fide new genes. We further show that SNP/indel mutation, high GC content, and DNA shuffling could be involved in the birth of de novo genes, while domestication and natural selection drive the spread and fixation of these genes. Finally, we provide evidence suggesting the possible parallel origin of a new gene.
format	article
author	Baojun Wu Alicia Knudson
author_facet	Baojun Wu Alicia Knudson
author_sort	Baojun Wu
title	Tracing the <italic toggle="yes">De Novo</italic> Origin of Protein-Coding Genes in Yeast
title_short	Tracing the <italic toggle="yes">De Novo</italic> Origin of Protein-Coding Genes in Yeast
title_full	Tracing the <italic toggle="yes">De Novo</italic> Origin of Protein-Coding Genes in Yeast
title_fullStr	Tracing the <italic toggle="yes">De Novo</italic> Origin of Protein-Coding Genes in Yeast
title_full_unstemmed	Tracing the <italic toggle="yes">De Novo</italic> Origin of Protein-Coding Genes in Yeast
title_sort	tracing the <italic toggle="yes">de novo</italic> origin of protein-coding genes in yeast
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/30c4d7b26a3a45cfba13fa4fb166ff32
work_keys_str_mv	AT baojunwu tracingtheitalictoggleyesdenovoitalicoriginofproteincodinggenesinyeast AT aliciaknudson tracingtheitalictoggleyesdenovoitalicoriginofproteincodinggenesinyeast
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Tracing the <italic toggle="yes">De Novo</italic> Origin of Protein-Coding Genes in Yeast

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