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...
Published in: | Fungal Ecology |
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2018
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Online Access: | https://research.manchester.ac.uk/en/publications/144ed523-eed9-49cc-b40a-64c3422900d7 https://doi.org/10.1016/j.funeco.2018.08.002 https://pure.manchester.ac.uk/ws/files/81470889/ComingUpShort_AAM.pdf https://linkinghub.elsevier.com/retrieve/pii/S1754504818301120 |
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ftumanchesterpub:oai:pure.atira.dk:publications/144ed523-eed9-49cc-b40a-64c3422900d7 2023-11-12T04:05:47+01:00 Coming up short: Identifying substrate and geographic biases in fungal sequence databases Khomich, Maryia Cox, Filipa Andrew, Carrie J. Andersen, Tom Kauserud, Håvard Davey, Marie L. 2018-12 application/pdf https://research.manchester.ac.uk/en/publications/144ed523-eed9-49cc-b40a-64c3422900d7 https://doi.org/10.1016/j.funeco.2018.08.002 https://pure.manchester.ac.uk/ws/files/81470889/ComingUpShort_AAM.pdf https://linkinghub.elsevier.com/retrieve/pii/S1754504818301120 eng eng info:eu-repo/semantics/openAccess Khomich , M , Cox , F , Andrew , C J , Andersen , T , Kauserud , H & Davey , M L 2018 , ' Coming up short: Identifying substrate and geographic biases in fungal sequence databases ' , Fungal Ecology , vol. 36 , pp. 75-80 . https://doi.org/10.1016/j.funeco.2018.08.002 article 2018 ftumanchesterpub https://doi.org/10.1016/j.funeco.2018.08.002 2023-10-30T09:12:56Z 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 The University of Manchester: Research Explorer Fungal Ecology 36 75 80 |
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Open Polar |
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The University of Manchester: Research Explorer |
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ftumanchesterpub |
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 J. Andersen, Tom Kauserud, Håvard Davey, Marie L. |
spellingShingle |
Khomich, Maryia Cox, Filipa Andrew, Carrie J. Andersen, Tom Kauserud, Håvard Davey, Marie L. Coming up short: Identifying substrate and geographic biases in fungal sequence databases |
author_facet |
Khomich, Maryia Cox, Filipa Andrew, Carrie J. Andersen, Tom Kauserud, Håvard Davey, Marie L. |
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 |
https://research.manchester.ac.uk/en/publications/144ed523-eed9-49cc-b40a-64c3422900d7 https://doi.org/10.1016/j.funeco.2018.08.002 https://pure.manchester.ac.uk/ws/files/81470889/ComingUpShort_AAM.pdf https://linkinghub.elsevier.com/retrieve/pii/S1754504818301120 |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_source |
Khomich , M , Cox , F , Andrew , C J , Andersen , T , Kauserud , H & Davey , M L 2018 , ' Coming up short: Identifying substrate and geographic biases in fungal sequence databases ' , Fungal Ecology , vol. 36 , pp. 75-80 . https://doi.org/10.1016/j.funeco.2018.08.002 |
op_rights |
info:eu-repo/semantics/openAccess |
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 |
_version_ |
1782342091926405120 |