Developmental evolution facilitates rapid adaptation

Lin, Hui; Kazlauskas, Romas J.; Travisano, Michael

doi:10.1038/s41598-017-16229-0

Cited by 4 publications

(3 citation statements)

References 27 publications

(29 reference statements)

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“…Two virus genomes were identified as members of the genus Betapartitivirus : Trichoderma citrinoviride partitivirus 1 (TcPV1) (PRJNA304029; [28]) and Fusarium poae partitivirus 1-2516 (FpPV1-2516) (PRJNA319914; [15]). To our knowledge, this is the first partitivirus identified from T .…”

Section: Resultsmentioning

confidence: 99%

Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes

et al. 2019

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The distribution and diversity of RNA viruses in fungi is incompletely understood due to the often cryptic nature of mycoviral infections and the focused study of primarily pathogenic and/or economically important fungi. As most viruses that are known to infect fungi possess either single-stranded or double-stranded RNA genomes, transcriptomic data provides the opportunity to query for viruses in diverse fungal samples without any a priori knowledge of virus infection. Here we describe a systematic survey of all transcriptomic datasets from fungi belonging to the subphylum Pezizomycotina. Using a simple but effective computational pipeline that uses reads discarded during normal RNA-seq analyses, followed by identification of a viral RNA-dependent RNA polymerase (RdRP) motif in de novo assembled contigs, 59 viruses from 44 different fungi were identified. Among the viruses identified, 88% were determined to be new species and 68% are, to our knowledge, the first virus described from the fungal species. Comprehensive analyses of both nucleotide and inferred protein sequences characterize the phylogenetic relationships between these viruses and the known set of mycoviral sequences and support the classification of up to four new families and two new genera. Thus the results provide a deeper understanding of the scope of mycoviral diversity while also increasing the distribution of fungal hosts. Further, this study demonstrates the suitability of analyzing RNA-seq data to facilitate rapid discovery of new viruses.

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Section: Resultsmentioning

confidence: 99%

Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes

et al. 2019

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“…Submerged cultivation is an unusual and poorly explored system in the context of experimental evolution. One work on submerged cultivation used ascomycetous fungus Trichoderma citrinoviride that evolved hyphal fragmentation, efficient conidia production, and faster germination (Lin et al. 2017).…”

Section: Discussionmentioning

confidence: 99%

“…2000). One study performed submerged cultivation of filamentous fungus Trichoderma citrinoviride that was selected for efficient conidia formation and dispersed mycelium (Lin et al. 2017), but generally transition to submerged cultivation remains unexplored.…”

Section: Introductionmentioning

confidence: 99%

Genetics of Adaptation of the Ascomycetous Fungus Podospora anserina to Submerged Cultivation

Kudryavtseva

Safina

Vakhrusheva

et al. 2019

Genome Biology and Evolution

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Podospora anserina is a model ascomycetous fungus which shows pronounced phenotypic senescence when grown on solid medium but possesses unlimited lifespan under submerged cultivation. In order to study the genetic aspects of adaptation of P. anserina to submerged cultivation, we initiated a long-term evolution experiment. In the course of the first 4 years of the experiment, 125 single-nucleotide substitutions and 23 short indels were fixed in eight independently evolving populations. Six proteins that affect fungal growth and development evolved in more than one population; in particular, in the G-protein alpha subunit FadA, new alleles fixed in seven out of eight experimental populations, and these fixations affected just four amino acid sites, which is an unprecedented level of parallelism in experimental evolution. Parallel evolution at the level of genes and pathways, an excess of nonsense and missense substitutions, and an elevated conservation of proteins and their sites where the changes occurred suggest that many of the observed fixations were adaptive and driven by positive selection.

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Discovery of new mycoviral genomes within publicly available fungal transcriptomic datasets

Gilbert

Holcomb

Allscheid

et al. 2019

Preprint

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The distribution and diversity of RNA viruses in fungi is incompletely understood due to the often cryptic nature of mycoviral infections and the focused study of primarily pathogenic and/or economically important fungi. As most viruses that are known to infect fungi possess either single-stranded or double-stranded RNA genomes, transcriptomic data provides the opportunity to query for viruses in diverse fungal samples without any a priori knowledge of virus infection.Here we describe a systematic survey of all transcriptomic datasets from fungi belonging to the subphylum Pezizomycotina. Using a simple but effective computational pipeline that uses reads discarded during normal RNA-seq analyses, followed by identification of a viral RNA-dependent RNA polymerase (RdRP) motif in de novo assembled contigs, 59 viruses from 44 different fungi were identified. Among the viruses identified, 89% were determined to be new species and 68% are, to our knowledge, the first virus described from the fungal species. Comprehensive analyses of both nucleotide and inferred protein sequences characterize the phylogenetic relationships between these viruses and the known set of mycoviral sequences and support the classification of up to four new families and two new genera. Thus the results provide a deeper understanding of the scope of mycoviral diversity while also increasing the distribution of fungal hosts. Further, this study demonstrates the suitability of analyzing RNA-seq data to facilitate rapid discovery of new viruses.

show abstract

Developmental evolution facilitates rapid adaptation

Cited by 4 publications

References 27 publications

Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes

Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes

Genetics of Adaptation of the Ascomycetous Fungus Podospora anserina to Submerged Cultivation

Discovery of new mycoviral genomes within publicly available fungal transcriptomic datasets

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