A cost-effective and efficient strategy for Illumina sequencing of fungal communities: A case study of beech endophytes identified elevation as main explanatory factor for diversity and community composition

We describe an accurate and efficient workflow for highly multiplexed paired-end Illumina sequencing of fungal full-length ITS amplicons. The impact of habitat and substratum conditions on leaf-inhabiting fungal communities was analysed. Fully vital and clearly senescent leaves of European beech (Fa...

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Published inFungal ecology Vol. 20; pp. 175 - 185
Main Authors Siddique, A.B., Unterseher, M.
Format Journal Article
LanguageEnglish
Published Elsevier Ltd 01.04.2016
Subjects
autumn
Biodiversity
case studies
community structure
cost effectiveness
DNA
Ecology
Elevation
Endophytes
Environmental change
environmental factors
European beech
Fagus sylvatica
Fagus sylvatica subsp. sylvatica
fungal communities
fungi
habitats
High throughput sequencing
high-throughput nucleotide sequencing
Illumina sequencing
internal transcribed spacers
Leaf-inhabiting microfungi
leaves
Metabarcoding
physiological state
Alps region
Germany
Metabarcoding
Elevation
High throughput sequencing
Leaf-inhabiting microfungi
European beech
Endophytes
Environmental change
Ecology
Biodiversity
Illumina sequencing
Fagus sylvatica
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Abstract We describe an accurate and efficient workflow for highly multiplexed paired-end Illumina sequencing of fungal full-length ITS amplicons. The impact of habitat and substratum conditions on leaf-inhabiting fungal communities was analysed. Fully vital and clearly senescent leaves of European beech (Fagus sylvatica) were sampled along an elevation gradient of about 1000 m in the Bavarian Alps, Germany, in autumn 2013. Surface-sterilised leaves were used for genomic DNA extraction, tagging-by-amplification and high-throughput sequencing. Significant correlation of community composition with elevation was observed. The mycobiome was little affected by the physiological state of the leaves, because only a partial shift of taxonomic composition was observed from vital towards clearly senescent leaves.
AbstractList We describe an accurate and efficient workflow for highly multiplexed paired-end Illumina sequencing of fungal full-length ITS amplicons. The impact of habitat and substratum conditions on leaf-inhabiting fungal communities was analysed. Fully vital and clearly senescent leaves of European beech (Fagus sylvatica) were sampled along an elevation gradient of about 1000 m in the Bavarian Alps, Germany, in autumn 2013. Surface-sterilised leaves were used for genomic DNA extraction, tagging-by-amplification and high-throughput sequencing. Significant correlation of community composition with elevation was observed. The mycobiome was little affected by the physiological state of the leaves, because only a partial shift of taxonomic composition was observed from vital towards clearly senescent leaves.
We describe an accurate and efficient workflow for highly multiplexed paired-end Illumina sequencing of fungal full-length ITS amplicons. The impact of habitat and substratum conditions on leaf-inhabiting fungal communities was analysed. Fully vital and clearly senescent leaves of European beech (Fagus sylvatica) were sampled along an elevation gradient of about 1000 m in the Bavarian Alps, Germany, in autumn 2013. Surface-sterilised leaves were used for genomic DNA extraction, tagging-by-amplification and high-throughput sequencing. Significant correlation of community composition with elevation was observed. The mycobiome was little affected by the physiological state of the leaves, because only a partial shift of taxonomic composition was observed from vital towards clearly senescent leaves.
We describe an accurate and efficient workflow for highly multiplexed paired-end Illumina sequencing of fungal full-length ITS amplicons. The impact of habitat and substratum conditions on leaf-inhabiting fungal communities was analysed. Fully vital and clearly senescent leaves of European beech (Fagus sylvatica) were sampled along an elevation gradient of about 1000 m in the Bavarian Alps, Germany, in autumn 2013. Surface-sterilised leaves were used for genomic DNA extraction, tagging-by-amplification and high-throughput sequencing. Significant correlation of community composition with elevation was observed. The mycobiome was little affected by the physiological state of the leaves, because only a partial shift of taxonomic composition was observed from vital towards clearly senescent leaves.
Author Siddique, A.B.
Unterseher, M.
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Keywords Metabarcoding
Elevation
High throughput sequencing
Leaf-inhabiting microfungi
European beech
Endophytes
Environmental change
Ecology
Biodiversity
Illumina sequencing
Fagus sylvatica
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Snippet We describe an accurate and efficient workflow for highly multiplexed paired-end Illumina sequencing of fungal full-length ITS amplicons. The impact of habitat...
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SubjectTerms autumn
Biodiversity
case studies
community structure
cost effectiveness
DNA
Ecology
Elevation
Endophytes
Environmental change
environmental factors
European beech
Fagus sylvatica
Fagus sylvatica subsp. sylvatica
fungal communities
fungi
habitats
High throughput sequencing
high-throughput nucleotide sequencing
Illumina sequencing
internal transcribed spacers
Leaf-inhabiting microfungi
leaves
Metabarcoding
physiological state
Title A cost-effective and efficient strategy for Illumina sequencing of fungal communities: A case study of beech endophytes identified elevation as main explanatory factor for diversity and community composition
URI https://dx.doi.org/10.1016/j.funeco.2015.12.009
https://search.proquest.com/docview/1790954290
https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-191774
Volume 20
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