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Genomics and metagenomics technologies to recover ribosomal DNA and single-copy genes from old fruit-body and ectomycorrhiza specimens
Univ Tartu, Nat Hist Museum, 14A Ravila, EE-51005 Tartu, Estonia.
Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-51005 Tartu, Estonia.
Univ Tartu, Estonian Genome Ctr, Riia 23b, EE-51010 Tartu, Estonia.
Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-51005 Tartu, Estonia.
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2016 (English)In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 13, 1-20 p.Article in journal (Refereed) Published
Abstract [en]

High-throughput sequencing (HTS) has become a standard technique for genomics, metagenomics and taxonomy, but these analyses typically require large amounts of high-quality DNA that is difficult to obtain from uncultivable organisms including fungi with no living culture or fruit-body representatives. By using 1 ng DNA and low coverage Illumina HiSeqHTS, we evaluated the usefulness of genomics and metagenomics tools to recover fungal barcoding genes from old and problematic specimens of fruit-bodies and ectomycorrhizal (EcM) root tips. Ribosomal DNA and single-copy genes were successfully recovered from both fruit-body and EcM specimens typically <10 years old (maximum, 17 years). Samples with maximum obtained DNA concentration <0.2 ng µl-1 were sequenced poorly. Fungal rDNA molecules assembled from complex mock community and soil revealed a large proportion of chimeras and artefactual consensus sequences of closely related taxa. Genomics and metagenomics tools enable recovery of fungal genomes from very low initial amounts of DNA from fruit-bodies and ectomycorrhizas, but these genomes include a large proportion of prokaryote and other eukaryote DNA. Nonetheless, the recovered scaffolds provide an important source for phylogenetic and phylogenomic analyses and mining of functional genes.

Place, publisher, year, edition, pages
2016. no 13, 1-20 p.
National Category
Agricultural Sciences
Identifiers
URN: urn:nbn:se:uu:diva-297242DOI: 10.3897/mycokeys.13.8140ISI: 000376791100001OAI: oai:DiVA.org:uu-297242DiVA: diva2:941417
Available from: 2016-06-22 Created: 2016-06-22 Last updated: 2016-07-07Bibliographically approved

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