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On the possibility of death of new genes - evidence from the deletion of de novo microRNAs.

ABSTRACT: BACKGROUND:New genes are constantly formed, sometimes from non-genic sequences, creating what is referred to as de novo genes. Since the total number of genes remains relatively steady, gene deaths likely balance out new births. In metazoan genomes, microRNAs (miRs) genes, small and non-coding, account for the bulk of functional de novo genes and are particularly suited to the investigation of gene death. RESULTS:In this study, we discover a Drosophila-specific de novo miRNA (mir-977) that may be facing impending death. Strikingly, after this testis-specific gene is deleted from D. melanogaster, most components of male fitness increase, rather than decrease as had been expected. These components include male viability, fertility and males' ability to repress female re-mating. Given that mir-977 has a negative fitness effect in D. melanogaster, this de novo gene with an adaptive history for over 60 Myrs may be facing elimination. In some other species where mir-977 is not found, gene death may have already happened. CONCLUSION:The surprising result suggests that de novo genes, constantly rising and falling during evolution, may often be transiently adaptive and then purged from the genome.

SUBMITTER: Lu GA

PROVIDER: S-EPMC5966946 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

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On the possibility of death of new genes - evidence from the deletion of de novo microRNAs.

Lu Guang-An GA Zhao Yixin Y Liufu Zhongqi Z Wu Chung-I CI

BMC genomics 20180523 1

<h4>Background</h4>New genes are constantly formed, sometimes from non-genic sequences, creating what is referred to as de novo genes. Since the total number of genes remains relatively steady, gene deaths likely balance out new births. In metazoan genomes, microRNAs (miRs) genes, small and non-coding, account for the bulk of functional de novo genes and are particularly suited to the investigation of gene death.<h4>Results</h4>In this study, we discover a Drosophila-specific de novo miRNA (mir- ...[more]

PMID: 29792159

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Project description:Proteogenomics, the combination of proteomics, genomics and transcriptomics, has considerably improved genome annotation in under-studied phylogenetic groups, where homology information is missing. Yet, it can also be advantageous when re-investigating well-annotated genomes. Here, we apply an advanced proteogenomics approach, combining standard proteogenomics with peptide de novo sequencing, to refine annotation of the well-studied model fungus Sordaria macrospora. We investigated samples from different developmental and physiological conditions, resulting in detection of 104 hidden proteins and annotation changes in 575 genes, including 389 splice site refinements. Significantly, our approach provides peptide-level evidence for 113 single amino acid variations and 15 C-terminal protein elongations originating from A-to-I RNA editing, a phenomenon recently detected in fungi. Co-expression and phylostratigraphic analysis of the refined proteome suggests new functions in evolutionary young genes correlated with distinct developmental stages. In conclusion, our advanced proteogenomics approach is highly supportive to promote functional studies of model systems. Proteogenomics, the combination of proteomics, genomics and transcriptomics, has considerably improved genome annotation in under-studied phylogenetic groups, where homology information is missing. Yet, it can also be advantageous when re-investigating well-annotated genomes. Here, we apply an advanced proteogenomics approach, combining standard proteogenomics with peptide de novo sequencing, to refine annotation of the well-studied model fungus Sordaria macrospora. We investigated samples from different developmental and physiological conditions, resulting in detection of 104 hidden proteins and annotation changes in 575 genes, including 389 splice site refinements. Significantly, our approach provides peptide-level evidence for 113 single amino acid variations and 15 C-terminal protein elongations originating from A-to-I RNA editing, a phenomenon recently detected in fungi. Co-expression and phylostratigraphic analysis of the refined proteome suggests new functions in evolutionary young genes correlated with distinct developmental stages. In conclusion, our advanced proteogenomics approach is highly supportive to promote functional studies of model systems.

Dataset Information

On the possibility of death of new genes - evidence from the deletion of de novo microRNAs.

Publications

On the possibility of death of new genes - evidence from the deletion of de novo microRNAs.

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