# UTOPIA: an automatically UpdaTed, cOmPlete and consistent ITS reference dAtabase

Sébastien Theil, Etienne Rifa

► To cite this version:

Sébastien Theil, Etienne Rifa. UTOPIA: an automatically UpdaTed, cOmPlete and consistent ITS reference dAtabase. 5. Colloque de Génomique Environnementale, Oct 2019, La Rochelle, France. hal-02340446

HAL Id: hal-02340446

https://hal.science/hal-02340446v1

Submitted on 5 Jun 2020

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INRA
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UMRF
Fromage

# UTOPIA :
AN AUTOMATICALLY UPDATED, COMPLETE AND
CONSISTENT ITS REFERENCE DATABASE

Sebastien Theil¹, Etienne Rifa¹

¹Université Clermont Auvergne, INRA, VetAgro Sup, UMRF Unité Mixte de Recherche sur le Fromage, 20 côte de Reyne, 15000 Aurillac, France

## Context

Taxonomic assignment in metabarcoding analysis is a critical and challenging step. As more organisms being sequenced, taxonomy is evolving fast with multiple taxa rearrangement and thousand of new sequences uploaded each year. The internal transcribed spacer (ITS) is an ubiquitous sequence used as a barcode to identify fungi species in complex environmental samples.

Currently used databases like UNITE, offer a good and reliable reference, but update frequency is generally low, and new strain sequences can take several years to be integrated. UTOPIA provides a workflow that produce an updated ITS reference database directly from the NCBI genbank and taxonomy database.

## UTOPIA

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## Database statistics

### Taxon overview

Clustering threshold collapses species and few genus. Number of sequences and taxons is comparable to UNITE.

<table><thead><tr><th></th><th>utopia<br>Id90,<br>cov90</th><th>utopia<br>Id99,<br>cov99</th><th>Unite<br>Dynamic</th><th>Unite<br>Dynamic_s</th><th>unite<br>INSDC</th></tr></thead><tbody><tr><th>kindom</th><td>1</td><td>2</td><td>1</td><td>1</td><td>1</td></tr><tr><th>phylum</th><td>9</td><td>10</td><td>20</td><td>21</td><td>21</td></tr><tr><th>class</th><td>63</td><td>64</td><td>93</td><td>102</td><td>105</td></tr><tr><th>order</th><td>233</td><td>236</td><td>273</td><td>301</td><td>321</td></tr><tr><th>family</th><td>809</td><td>856</td><td>804</td><td>918</td><td>1007</td></tr><tr><th>genus</th><td>3739</td><td>4978</td><td>3578</td><td>4512</td><td>5256</td></tr><tr><th>specie</th><td>13941</td><td>42709</td><td>17278</td><td>22253</td><td>33024</td></tr><tr><th>nb_seq</th><td>28538</td><td>126317</td><td>35667</td><td>71042</td><td>887397</td></tr></tbody></table>

### Test on mock from Bakker et al. 2018

Metrics from **Edgar et al. 2018**:
- TPR: True positive rate
- MCR: Misclassification rate
- UCR: under-classification rate
- Acc: Accuracy

Utopia has best accuracy at Genus level, especially for ITS2.
Taxonomies from NCBI match better those used by Bakker et al.

<table><caption>ITS1 (26 sequences)</caption><thead><tr><th></th><th colspan="4">Family</th><th colspan="4">Genus</th></tr><tr><th></th><th>TPR</th><th>MCR</th><th>UCR</th><th>Acc</th><th>TPR</th><th>MCR</th><th>UCR</th><th>Acc</th></tr></thead><tbody><tr><th>utopia id90, cov90</th><td>0,8</td><td>0,1</td><td>0,1</td><td>0,8</td><td>0,4</td><td>0,1</td><td>0,5</td><td>0,4</td></tr><tr><th>utopia id99, cov99</th><td>0,9</td><td>0,1</td><td>0</td><td>0,8</td><td>0,7</td><td>0,2</td><td>0,1</td><td>0,7</td></tr><tr><th>Unite Dynamic</th><td>0,7</td><td>0,1</td><td>0,2</td><td>0,7</td><td>0,6</td><td>0,1</td><td>0,3</td><td>0,5</td></tr><tr><th>Unite Dynamic_s</th><td>0,6</td><td>0,1</td><td>0,3</td><td>0,6</td><td>0,5</td><td>0,1</td><td>0,5</td><td>0,5</td></tr><tr><th>Unite INSDC</th><td>0,8</td><td>0</td><td>0,2</td><td>0,7</td><td>0,5</td><td>0,1</td><td>0,3</td><td>0,5</td></tr></tbody></table>

<table><caption>ITS2 (28 sequences)</caption><thead><tr><th></th><th colspan="4">Family</th><th colspan="4">Genus</th></tr><tr><th></th><th>TPR</th><th>MCR</th><th>UCR</th><th>Acc</th><th>TPR</th><th>MCR</th><th>UCR</th><th>Acc</th></tr></thead><tbody><tr><th>utopia id90, cov90</th><td>0,7</td><td>0,2</td><td>0</td><td>0,7</td><td>0,7</td><td>0,2</td><td>0</td><td>0,7</td></tr><tr><th>utopia id99, cov99</th><td>0,7</td><td>0,1</td><td>0,2</td><td>0,7</td><td>0,6</td><td>0,1</td><td>0,2</td><td>0,6</td></tr><tr><th>Unite Dynamic</th><td>0,4</td><td>0</td><td>0,6</td><td>0,4</td><td>0,3</td><td>0</td><td>0,7</td><td>0,3</td></tr><tr><th>Unite Dynamic_s</th><td>0,5</td><td>0</td><td>0,5</td><td>0,5</td><td>0,2</td><td>0</td><td>0,8</td><td>0,2</td></tr><tr><th>Unite INSDC</th><td>0,8</td><td>0,1</td><td>0</td><td>0,8</td><td>0,6</td><td>0,1</td><td>0,3</td><td>0,6</td></tr></tbody></table>

### Test on two real datasets

ITS1 dataset from raw milk:
1348 sequences

Utopia has a better median confidence at family level, and performs the same for genus and species.
Utopia99 and UNITE provide slightly the same annotation depth.

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## Conclusions

We provide to the community a protocol and scripts to build an updated ITS database locally from the very last release of NCBI. Our database is created, filtered, and clustered fully automatically. Taxonomy is processed to obtain a 7 ranks assignment for each sequence and formatted to fit commonly used programs such as IDTAXA, or Phyloseq.

However we show here that UTOPIA is at least as good as UNITE in term of depth of annotation in real data and better in accuracy on the Bakker *et al.* mock community making our database a good alternative to assign fungus community with the latest sequences and taxonomies available.

Available on **git** repository at :
**https://forgemia.inra.fr/umrf/utopia**

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