Software Open Access
Long- and short-read metabarcoding technologies reveal similar spatio-temporal structures in fungal communities
Furneaux, Brendan;
Bahram, Mohammad;
Rosling, Anna;
Yorou, Nourou;
Ryberg, Martin
Fungi form diverse communities and play essential roles in many terrestrial ecosystems, yet there are methodological challenges in taxonomic and phylogenetic placement of fungi from environmental sequences.
To address such challenges we investigated spatio-temporal structure of a fungal community using soil metabarcoding with four different sequencing strategies: short amplicon sequencing of the ITS2 region (300--400\ bp) with Illumina MiSeq, Ion Torrent Ion S5, and PacBio RS II, all from the same PCR library, as well as long amplicon sequencing of the full ITS and partial LSU regions (1200--1600\ bp) with PacBio RS II.
Resulting community structure and diversity depended more on statistical method than sequencing technology.
The use of long-amplicon sequencing enables construction of a phylogenetic tree from metabarcoding reads, which facilitates taxonomic identification of sequences.
However, long reads present issues for denoising algorithms in diverse communities.
We present a solution that splits the reads into shorter homologous regions prior to denoising, and then reconstructs the full denoised reads.
In the choice between short and long amplicons, we suggest a hybrid approach using short amplicons for sampling breadth and depth, and long amplicons to characterize the local species pool for improved identification and phylogenetic analyses.
The analysis pipeline can be run on Linux (or possibly OSX, but this has not been tested) using the Snakefile included in oueme-fungi-transect-1.0.0.tar.gz. Snakemake and Anaconda/Miniconda should be installed, but all other software dependencies will be installed by the pipeline via Conda.
Funding provided by: Svenska Forskningsrådet Formas
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001862
Award Number: 2014-01109
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| Name | Size | |
|---|---|---|
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FUNGuildR-0.1.0.tar.gz
md5:9942780fbe8f3b94cb74478c36229aa8 |
15.1 kB | Download |
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inferrnal-0.99.5.tar.gz
md5:99fe42117fe9c9408b1b3eb3b2def671 |
104.2 kB | Download |
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LSUx-0.99.6.tar.gz
md5:aca833d7dea62dd72b426c47971ddd87 |
565.5 kB | Download |
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oueme-fungi-transect-1.0.0.tar.gz
md5:209e5f58855c4032087fd736078c3759 |
36.8 MB | Download |
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phylotax-0.0.4.tar.gz
md5:cf927d357064a21af6e5abb109192d80 |
161.4 kB | Download |
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tzara-0.0.10.tar.gz
md5:0db74c272a949f413e70ed41dfdd1442 |
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- Publication date:
- March 22, 2021
- DOI:
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- Keyword(s):
- Metabarcoding fungi Metabarcoding community ecology DNA Barcoding environmental DNA Bioinfomatics/Phyloinfomatics
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- License (for files):
- MIT License