Tracing the De Novo Origin of Protein-Coding Genes in Yeast.

Baojun Wu,Alicia Knudson,John W Taylor

doi:10.1128/mbio.01024-18

Abstract

ABSTRACTDe 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.

Highlights

De novo genes are very important for evolutionary innovation
The mechanisms giving rise to new genes can be placed into four categories [1]: (i) gene duplication and rapid divergence, in which a new gene is derived from already existing genes in the same genome; (ii) horizontal gene transfer, in which a new gene is derived from already existing genes but from different genomes; (iii) an overprinting process, where mutations in a protein-coding gene allow the expression of a second protein-coding gene [2]; and (iv) de novo origin, in which the noncoding region evolves to an open reading frame (ORF) through single nucleotide polymorphism (SNP) and indel mutations [3, 4]
The S. cerevisiae S288C proteins that did not have significant sequence similarity (E value of 1 ϫ 10Ϫ4) from the 20 species were regarded as initial de novo genes

Summary

Introduction

De novo genes are very important for evolutionary innovation. how these genes originate and spread remains largely unknown. Together with an expression cutoff FPKM (fragments per kilobase of transcript per million mapped reads) of Ն1.0, 84 de novo genes from S. cerevisiae S288C were identified (see Table S1 at http://baojunedisonwu.weebly.com/download.html), which have no protein hit in 20 species but have noncoding orthologous sequences in sister species Saccharomyces paradoxus CBS 432 and Saccharomyces mikatae IFO1815.

Results

Conclusion