Coming up short: Identifying substrate and geographic biases in fungal sequence databases
Insufficient reference database coverage is a widely recognized limitation of molecular ecology approaches which are reliant on database matches for assignment of function or identity. Here, we use data from 65 amplicon high-throughput sequencing (HTS) datasets targeting the internal transcribed spa...
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ftoslouniv:oai:www.duo.uio.no:10852/67110 2023-05-15T13:49:59+02:00 Coming up short: Identifying substrate and geographic biases in fungal sequence databases Khomich, Maryia Cox, Filipa Andrew, Carrie Joy Andersen, Tom Kauserud, Håvard Davey, Marie Louise 2018-11-13T17:28:47Z http://hdl.handle.net/10852/67110 http://urn.nb.no/URN:NBN:no-70287 https://doi.org/10.1016/j.funeco.2018.08.002 EN eng NFR/196336 http://urn.nb.no/URN:NBN:no-70287 Khomich, Maryia Cox, Filipa Andrew, Carrie Joy Andersen, Tom Kauserud, Håvard Davey, Marie Louise . Coming up short: Identifying substrate and geographic biases in fungal sequence databases. Fungal ecology. 2018, 36, 75-80 http://hdl.handle.net/10852/67110 1630149 info:ofi/fmt:kev:mtx:ctx&ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Fungal ecology&rft.volume=36&rft.spage=75&rft.date=2018 Fungal ecology 36 75 80 http://dx.doi.org/10.1016/j.funeco.2018.08.002 URN:NBN:no-70287 Fulltext https://www.duo.uio.no/bitstream/handle/10852/67110/1/Khomich_et_al._FUNECO_postprint_31-07-2018-and-Suppl_postprint_31-07-2018.pdf Attribution-NonCommercial-NoDerivatives 4.0 International https://creativecommons.org/licenses/by-nc-nd/4.0/ CC-BY-NC-ND 1754-5048 Journal article Tidsskriftartikkel Peer reviewed AcceptedVersion 2018 ftoslouniv https://doi.org/10.1016/j.funeco.2018.08.002 2020-06-21T08:53:17Z Insufficient reference database coverage is a widely recognized limitation of molecular ecology approaches which are reliant on database matches for assignment of function or identity. Here, we use data from 65 amplicon high-throughput sequencing (HTS) datasets targeting the internal transcribed spacer (ITS) region of fungal rDNA to identify substrates and geographic areas whose underrepresentation in the available reference databases could have meaningful impact on our ability to draw ecological conclusions. A total of 14 different substrates were investigated. Database representation was particularly poor for the fungal communities found in aquatic (freshwater and marine) and soil ecosystems. Aquatic ecosystems are identified as priority targets for the recovery of novel fungal lineages. A subset of the data representing soil samples with global distribution were used to identify geographic locations and terrestrial biomes with poor database representation. Database coverage was especially poor in tropical, subtropical, and Antarctic latitudes, and the Amazon, Southeast Asia, Australasia, and the Indian subcontinent are identified as priority areas for improving database coverage in fungi. Article in Journal/Newspaper Antarc* Antarctic Universitet i Oslo: Digitale utgivelser ved UiO (DUO) Antarctic Indian Fungal Ecology 36 75 80 |
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Open Polar |
collection |
Universitet i Oslo: Digitale utgivelser ved UiO (DUO) |
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ftoslouniv |
language |
English |
description |
Insufficient reference database coverage is a widely recognized limitation of molecular ecology approaches which are reliant on database matches for assignment of function or identity. Here, we use data from 65 amplicon high-throughput sequencing (HTS) datasets targeting the internal transcribed spacer (ITS) region of fungal rDNA to identify substrates and geographic areas whose underrepresentation in the available reference databases could have meaningful impact on our ability to draw ecological conclusions. A total of 14 different substrates were investigated. Database representation was particularly poor for the fungal communities found in aquatic (freshwater and marine) and soil ecosystems. Aquatic ecosystems are identified as priority targets for the recovery of novel fungal lineages. A subset of the data representing soil samples with global distribution were used to identify geographic locations and terrestrial biomes with poor database representation. Database coverage was especially poor in tropical, subtropical, and Antarctic latitudes, and the Amazon, Southeast Asia, Australasia, and the Indian subcontinent are identified as priority areas for improving database coverage in fungi. |
format |
Article in Journal/Newspaper |
author |
Khomich, Maryia Cox, Filipa Andrew, Carrie Joy Andersen, Tom Kauserud, Håvard Davey, Marie Louise |
spellingShingle |
Khomich, Maryia Cox, Filipa Andrew, Carrie Joy Andersen, Tom Kauserud, Håvard Davey, Marie Louise Coming up short: Identifying substrate and geographic biases in fungal sequence databases |
author_facet |
Khomich, Maryia Cox, Filipa Andrew, Carrie Joy Andersen, Tom Kauserud, Håvard Davey, Marie Louise |
author_sort |
Khomich, Maryia |
title |
Coming up short: Identifying substrate and geographic biases in fungal sequence databases |
title_short |
Coming up short: Identifying substrate and geographic biases in fungal sequence databases |
title_full |
Coming up short: Identifying substrate and geographic biases in fungal sequence databases |
title_fullStr |
Coming up short: Identifying substrate and geographic biases in fungal sequence databases |
title_full_unstemmed |
Coming up short: Identifying substrate and geographic biases in fungal sequence databases |
title_sort |
coming up short: identifying substrate and geographic biases in fungal sequence databases |
publishDate |
2018 |
url |
http://hdl.handle.net/10852/67110 http://urn.nb.no/URN:NBN:no-70287 https://doi.org/10.1016/j.funeco.2018.08.002 |
geographic |
Antarctic Indian |
geographic_facet |
Antarctic Indian |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_source |
1754-5048 |
op_relation |
NFR/196336 http://urn.nb.no/URN:NBN:no-70287 Khomich, Maryia Cox, Filipa Andrew, Carrie Joy Andersen, Tom Kauserud, Håvard Davey, Marie Louise . Coming up short: Identifying substrate and geographic biases in fungal sequence databases. Fungal ecology. 2018, 36, 75-80 http://hdl.handle.net/10852/67110 1630149 info:ofi/fmt:kev:mtx:ctx&ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Fungal ecology&rft.volume=36&rft.spage=75&rft.date=2018 Fungal ecology 36 75 80 http://dx.doi.org/10.1016/j.funeco.2018.08.002 URN:NBN:no-70287 Fulltext https://www.duo.uio.no/bitstream/handle/10852/67110/1/Khomich_et_al._FUNECO_postprint_31-07-2018-and-Suppl_postprint_31-07-2018.pdf |
op_rights |
Attribution-NonCommercial-NoDerivatives 4.0 International https://creativecommons.org/licenses/by-nc-nd/4.0/ |
op_rightsnorm |
CC-BY-NC-ND |
op_doi |
https://doi.org/10.1016/j.funeco.2018.08.002 |
container_title |
Fungal Ecology |
container_volume |
36 |
container_start_page |
75 |
op_container_end_page |
80 |
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1766252680501526528 |