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Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes.

ABSTRACT: The origin of 'orphan' genes, species-specific sequences that lack detectable homologues, has remained mysterious since the dawn of the genomic era. There are two dominant explanations for orphan genes: complete sequence divergence from ancestral genes, such that homologues are not readily detectable; and de novo emergence from ancestral non-genic sequences, such that homologues genuinely do not exist. The relative contribution of the two processes remains unknown. Here, we harness the special circumstance of conserved synteny to estimate the contribution of complete divergence to the pool of orphan genes. By separately comparing yeast, fly and human genes to related taxa using conservative criteria, we find that complete divergence accounts, on average, for at most a third of eukaryotic orphan and taxonomically restricted genes. We observe that complete divergence occurs at a stable rate within a phylum but at different rates between phyla, and is frequently associated with gene shortening akin to pseudogenization.

SUBMITTER: Vakirlis N

PROVIDER: S-EPMC7028367 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes.

Vakirlis Nikolaos N Carvunis Anne-Ruxandra AR McLysaght Aoife A

eLife 20200218

The origin of 'orphan' genes, species-specific sequences that lack detectable homologues, has remained mysterious since the dawn of the genomic era. There are two dominant explanations for orphan genes: complete sequence divergence from ancestral genes, such that homologues are not readily detectable; and de novo emergence from ancestral non-genic sequences, such that homologues genuinely do not exist. The relative contribution of the two processes remains unknown. Here, we harness the special c ...[more]

PMID: 32066524

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Project description:BackgroundWith every new genome that is sequenced, thousands of species-specific genes (orphans) are found, some originating from ultra-rapid mutations of existing genes, many others originating de novo from non-genic regions of the genome. If some of these genes survive across speciations, then extant organisms will contain a patchwork of genes whose ancestors first appeared at different times. Standard phylostratigraphy, the technique of partitioning genes by their age, is based solely on protein similarity algorithms. However, this approach relies on negative evidence ─ a failure to detect a homolog of a query gene. An alternative approach is to limit the search for homologs to syntenic regions. Then, genes can be positively identified as de novo orphans by tracing them to non-coding sequences in related species.ResultsWe have developed a synteny-based pipeline in the R framework. Fagin determines the genomic context of each query gene in a focal species compared to homologous sequence in target species. We tested the fagin pipeline on two focal species, Arabidopsis thaliana (plus four target species in Brassicaseae) and Saccharomyces cerevisiae (plus six target species in Saccharomyces). Using microsynteny maps, fagin classified the homology relationship of each query gene against each target genome into three main classes, and further subclasses: AAic (has a coding syntenic homolog), NTic (has a non-coding syntenic homolog), and Unknown (has no detected syntenic homolog). fagin inferred over half the "Unknown" A. thaliana query genes, and about 20% for S. cerevisiae, as lacking a syntenic homolog because of local indels or scrambled synteny.Conclusionsfagin augments standard phylostratigraphy, and extends synteny-based phylostratigraphy with an automated, customizable, and detailed contextual analysis. By comparing synteny-based phylostrata to standard phylostrata, fagin systematically identifies those orphans and lineage-specific genes that are well-supported to have originated de novo. Analyzing within-species genomes should distinguish orphan genes that may have originated through rapid divergence from de novo orphans. Fagin also delineates whether a gene has no syntenic homolog because of technical or biological reasons. These analyses indicate that some orphans may be associated with regions of high genomic perturbation.

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Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes.

Publications

Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes.

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