The evolution of novel fungal genes from non-retroviral RNA viruses
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BioMed Central
Open Access
Research article
The evolution of novel fungal genes from non-retroviral RNA viruses Derek J Taylor* and Jeremy Bruenn Address: Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY 14260, USA Email: Derek J Taylor* - [email protected]; Jeremy Bruenn - [email protected] * Corresponding author
Published: 18 December 2009 BMC Biology 2009, 7:88
doi:10.1186/1741-7007-7-88
Received: 24 October 2009 Accepted: 18 December 2009
This article is available from: http://www.biomedcentral.com/1741-7007/7/88 © 2009 Taylor and Bruenn; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract Background: Endogenous derivatives of non-retroviral RNA viruses are thought to be absent or rare in eukaryotic genomes because integration of RNA viruses in host genomes is impossible without reverse transcription. However, such derivatives have been proposed for animals, plants and fungi, often based on surrogate bioinformatic evidence. At present, there is little known of the evolution and function of integrated non-retroviral RNA virus genes. Here, we provide direct evidence of integration by sequencing across host-virus gene boundaries and carry out phylogenetic analyses of fungal hosts and totivirids (dsRNA viruses of fungi and protozoans). Further, we examine functionality by tests of neutral evolution, comparison of residues that are necessary for viral capsid functioning and assays for transcripts, dsRNA and viral particles. Results: Sequencing evidence from gene boundaries was consistent with integration. We detected previously unknown integrated Totivirus-like sequences in three fungi (Candida parapsilosis, Penicillium marneffei and Uromyces appendiculatus). The phylogenetic evidence strongly indicated that the direction of transfer was from Totivirus to fungus. However, there was evidence of transfer of Totivirus-like sequences among fungi. Tests of selection indicated that integrated genes are maintained by purifying selection. Transcripts were apparent for some gene copies, but, in most cases, the endogenous sequences lacked the residues necessary for normal viral functioning. Conclusions: Our findings reveal that horizontal gene transfer can result in novel gene formation in eukaryotes despite miniaturized genomic targets and a need for co-option of reverse transcriptase.
Background In eukaryotes, novel genes can be formed by alternative splicing, exon shuffling, horizontal gene transfer and inserted retroelements [1,2]. Indeed, many eukaryotic genomes are bloated with the raw materials (introns and retroelements) for these processes [3-5]. In most budding yeasts, however, the source of novel gene formation is obscure as there is a dearth of spliceosomal introns (< 5% of genes and < 0.5% of the genom
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