eukaryotesV4 database

eukaryotesV4 is a curated database of V4 region of 18S rDNA. It was built to extract and taxonomically classify short metagenomic reads (mTags).

You can download it in fasta format or .txt file with additional information. A version with headers formatted to work with dada2 is also available here.

Citation

Obiol, A., Giner, C.R., Sánchez, P., Duarte, C.M., Acinas, S.G. and Massana, R. A metagenomic assessment of microbial eukaryotic diversity in the global ocean. Mol Ecol Resour. 2020; 20: 718– 731. doi: 10.1111/1755-0998.13147

Overview of the database

Here is a summary table with the taxonomic groups contained in eukaryotesV4 database.

Group	Supergroup	OTU97 sequences	Median length (bp)
Apicomplexa	Alveolata	598	369
Ciliophora	Alveolata	1975	369
Colpodellida	Alveolata	50	378
Colponemida	Alveolata	8	378
Dinoflagellata	Alveolata	1355	378
Ellobiopsidae	Alveolata	9	363
InSedAlveolata	Alveolata	81	375
MALV-I	Alveolata	599	378
MALV-II	Alveolata	2298	378
MALV-III	Alveolata	80	380
MALV-IV	Alveolata	47	381
MALV-V	Alveolata	13	376
Perkinsidae	Alveolata	203	379
Archamoebea	Amoebozoa	9	385
Cavosteliida	Amoebozoa	8	386
Dictyostelia	Amoebozoa	8	417
Discosea	Amoebozoa	151	492
Fractovitellida	Amoebozoa	3	382
Gracilipodida	Amoebozoa	17	389
InSedAmoebozoa	Amoebozoa	36	351
Myxogastria	Amoebozoa	84	436
Protosporangiida	Amoebozoa	5	421
Protosteliida	Amoebozoa	20	378
Schizoplasmodiidae	Amoebozoa	13	392
Tubulinea	Amoebozoa	88	388
Variosea	Amoebozoa	2	418
Chlorodendrophyceae	Archaeplastida	8	380
Chlorophyceae	Archaeplastida	156	378
Chloropicophyceae	Archaeplastida	17	377
Glaucophyta	Archaeplastida	5	383
InSedArchaeplastida	Archaeplastida	116	379
Mamiellophyceae	Archaeplastida	100	377
Nephroselmis	Archaeplastida	17	381
Palmophyllophyceae	Archaeplastida	19	378
Pedinophyceae	Archaeplastida	7	374
Picocystophyceae	Archaeplastida	1	381
Picozoa	Archaeplastida	30	378
Prasino-Clade-IX	Archaeplastida	8	372
Pycnococcaceae	Archaeplastida	3	381
Pyramimonadales	Archaeplastida	45	379
Rhodophyceae	Archaeplastida	387	378
Streptophyta	Archaeplastida	730	380
Trebouxiophyceae	Archaeplastida	81	380
Ulvophyceae	Archaeplastida	79	378
Mantamonas	CRuMS	2	385
Rigifilida	CRuMS	6	388
Cryptomonadales	Cryptista	100	376
Cyathomonadacea	Cryptista	4	420
Kathablepharidacea	Cryptista	21	377
Palpitomonas	Cryptista	1	375
Ancyromonadida	DeepBranching	40	380
Apusomonadida	DeepBranching	132	382
Breviatea	DeepBranching	25	380
Malawimonadidae	DeepBranching	1	386
Diplonemea	Discoba	55	538
Euglenida	Discoba	193	633
Heterolobosea	Discoba	24	486
InSedDiscoba	Discoba	1	368
Jakobida	Discoba	17	406
Kinetoplastea	Discoba	219	534
Centroplasthelida	Haptista	160	393
Pavlovales	Haptista	25	380
Prymnesiophyceae	Haptista	63	380
Fornicata	Metamonada	14	360
Parabasalia	Metamonada	159	267
Preaxostyla	Metamonada	11	390
Aphelidiomycota	Opisthokonta	34	379
Ascomycota	Opisthokonta	598	379
BasalFungi	Opisthokonta	20	382
Basidiobolomycota	Opisthokonta	3	383
Basidiomycota	Opisthokonta	410	380
Blastocladiomycota	Opisthokonta	8	404
Calcarisporiellomycota	Opisthokonta	3	378
Choanoflagellata	Opisthokonta	239	378
Chytridiomycota	Opisthokonta	183	381
Entorrhyzomycota	Opisthokonta	2	382
Filasterea	Opisthokonta	2	382
Glomeromycota	Opisthokonta	94	381
Ichthyosporea	Opisthokonta	47	378
InSedOpisthokonta	Opisthokonta	24	380
MarineOpisthokonts	Opisthokonta	26	377
Metazoa	Opisthokonta	7209	394
Microsporidia	Opisthokonta	152	213
Monoblepharomycota	Opisthokonta	7	380
Mortierellomycota	Opisthokonta	5	385
Mucoromycota	Opisthokonta	75	388
NCLC1	Opisthokonta	10	380
Neocallimastigomycota	Opisthokonta	3	381
Olpidiomycota	Opisthokonta	4	382
Rotosphaerida	Opisthokonta	67	380
Rozellomycota	Opisthokonta	119	368
Zoopagomyceta	Opisthokonta	93	420
InSedEukaryota	OtherEukaryota	386	372
Nucleomorph	OtherEukaryota	29	387
Acantharea	Rhizaria	432	368
Cercozoa	Rhizaria	1439	390
Chlorarachnea	Rhizaria	54	385
Foraminifera	Rhizaria	15	713
InSedRhizaria	Rhizaria	34	389
Polycystinea	Rhizaria	318	382
RAD-A	Rhizaria	64	386
RAD-B	Rhizaria	66	384
RAD-C	Rhizaria	28	378
Aurearenophyceae	Stramenopiles	1	396
Bicosoecida	Stramenopiles	169	374
Bolidophyceae	Stramenopiles	34	382
Cantina	Stramenopiles	1	377
Chrysomerophyceae	Stramenopiles	4	388
Chrysophyceae	Stramenopiles	262	383
Developea	Stramenopiles	6	386
Diatomea	Stramenopiles	822	381
Dictyochophyceae	Stramenopiles	93	389
Eustigmatales	Stramenopiles	20	387
Hyphochytriales	Stramenopiles	5	389
InSedStramenopiles	Stramenopiles	134	386
Labyrinthulomycetes	Stramenopiles	411	384
MAST-1	Stramenopiles	28	382
MAST-10	Stramenopiles	2	380
MAST-11	Stramenopiles	3	380
MAST-12	Stramenopiles	65	386
MAST-16	Stramenopiles	1	389
MAST-2	Stramenopiles	4	381
MAST-20	Stramenopiles	2	380
MAST-22	Stramenopiles	8	386
MAST-23	Stramenopiles	2	388
MAST-24	Stramenopiles	2	386
MAST-25	Stramenopiles	5	376
MAST-3	Stramenopiles	170	383
MAST-4	Stramenopiles	5	380
MAST-6	Stramenopiles	17	386
MAST-7	Stramenopiles	19	377
MAST-8	Stramenopiles	26	386
MAST-9	Stramenopiles	36	379
MOCH-1	Stramenopiles	21	385
MOCH-2	Stramenopiles	33	383
MOCH-3	Stramenopiles	2	388
MOCH-4	Stramenopiles	3	388
MOCH-5	Stramenopiles	7	383
Opalinata	Stramenopiles	49	379
Pelagophyceae	Stramenopiles	33	385
Peronosporomycetes	Stramenopiles	103	392
Phaeophyceae	Stramenopiles	24	394
Phaeothamniophyceae	Stramenopiles	3	388
Picophagus	Stramenopiles	3	387
Pinguiophyceae	Stramenopiles	8	389
Pirsoniales	Stramenopiles	21	388
Placidida	Stramenopiles	6	390
Raphidophyceae	Stramenopiles	10	391
Schizocladia	Stramenopiles	1	390
Synchromophyceae	Stramenopiles	4	390
Synurophyceae	Stramenopiles	30	383
Xanthophyceae	Stramenopiles	26	392
Telonemia	Telonemia	31	375

Versions

v8

Several sequences discarded, complete reclassification of Fungi and other sequences.

Detailed changes:

• Removed 77 sequences with clear errors. Discarded sequences can be found here.
• Changed taxonomy in 913 sequences, especially within BasalFungi. Table with name changes can be found here.
• 153 Fungi sequences added: 2 Basidiobolomycota and 151 Microsporidia. Added sequences can be found here.
• Added information in the tax file with closest match to pr2 database version 5.0.0.
• Removed 'SLV' prefix from all SILVA sequences to use the original accession number.
• Excavata no longer used, now separated into Discoba and Metamonada.
• Added Telonemia supergroup.
• Added DeepBranching supergroup (Ancyromonadida, Apusomonadida, Breviatea, and Malawimonadidae).

v7

Changes in tax assignation and nomenclature. Additionaly, all U's in sequences changed to T's for consistency.

Changes in Chrysophyceae

OTU	New tax
BMK7763	InSedStramenopiles
BMK5345	InSedStramenopiles
BMK5769	InSedStramenopiles
SLVKF443034	Synchromophyceae
SLVAJ130893	Synchromophyceae
SLVKF925343	Synchromophyceae
SLVJN004145	Synchromophyceae
SLVU73225	Synurophyceae
BMK10049	Synurophyceae
SLVJN991181	Synurophyceae
SLVU73226	Synurophyceae
SLVJX946340	Synurophyceae
SLVU73219	Synurophyceae
SLVU73231	Synurophyceae
SLVGU935621	Synurophyceae
SLVU73222	Synurophyceae
SLVHF549063	Synurophyceae
SLVGU935623	Synurophyceae
SLVGU935633	Synurophyceae
SLVEF165118	Synurophyceae
SLVGU935624	Synurophyceae
SLVGU935628	Synurophyceae
SLVU73221	Synurophyceae
SLVGU935622	Synurophyceae
SLVJX946336	Synurophyceae
SLVGU325513	Synurophyceae
SLVHF549067	Synurophyceae
SLVHF549064	Synurophyceae
SLVGU325515	Synurophyceae
SLVGU067831	Synurophyceae
SLVAB749074	Synurophyceae
SLVJX455151	Synurophyceae
SLVAB622324	Synurophyceae
SLVHF549070	Synurophyceae
SLVKM590553	Synurophyceae
SLVAY919713	Synurophyceae
SLVAY919803	Synurophyceae

Changes in Cryptomonadales

OTU	New tax
SLVGAIN01011745	Nucleomorph
SLVAJ420694	Nucleomorph
SLVAJ420692	Nucleomorph
SLVHF952607	Nucleomorph
SLVAM901023	Nucleomorph

Change Other-Chlorophyta to InSedArchaeplastida

OTU	New tax
MPN3330	InSedArchaeplastida

Changes in taxonomic groups nomenclature

Old	New
Diatomeae	Diatomea
Blastocystis	Opalinata

v6

Changes in tax assignation for some misclassified references:

OTU	New tax	Old tax
SLVKF651077	Colponemida_Alveolata	InSedAlveolata_Alveolata
SLVKF211436	Metazoa_Opisthokonta	Protosporangiida_Amoebozoa
SLVDQ267705	Picocystophyceae_Archaeplastida	InSedArchaeplastida_Archaeplastida
SLVAM901018	Nucleomorph_OtherEukaryota	Cryptomonadales_Cryptista
SLVJF791073	Nucleomorph_OtherEukaryota	Cryptomonadales_Cryptista
SLVAY743950	Metazoa_Opisthokonta	Jakobida_Excavata
SLVAB597203	BasalFungi_Opisthokonta	Ascomycota_Opisthokonta
SLVAB597204	BasalFungi_Opisthokonta	Ascomycota_Opisthokonta
SLVFJ816018	Rotosphaerida_Opisthokonta	BasalFungi_Opisthokonta
SLVL37733	Ascomycota_Opisthokonta	Basidiomycota_Opisthokonta
SLVJN546121	Ascomycota_Opisthokonta	Basidiomycota_Opisthokonta
BMK9285	Ancyromonadida_OtherEukaryota	Choanoflagellata_Opisthokonta
SLVAB085614	Schizocladia_Stramenopiles	Phaeophyceae_Stramenopiles

v5

Taxonomy adjusted to Adl et al (2019). Name changes in the following groups:

Old name	Updated name
Choanomonada	Choanoflagellata
Colponema	Colponemida
X-Cell	Perkinsidae
Archamoebae	Archamoebea
Fractovitelliida	Fractovitellida
Schizoplasmodiida	Schizoplasmodiidae
Charophyta	Streptophyta
Glaucocystophyceae	Glaucophyta
Nephroselmidophyceae	Nephroselmis
Rhodophyta	Rhodophyceae
Goniomonas	Cyathomonadacea
Katablepharidae	Kathablepharidacea
Kinetoplastida	Kinetoplastea
Centrohelida	Centroplasthelida
Pavlovophyceae	Pavlovales
Discicristoidea	Rotosphaerida
Acantharia	Acantharea
Chlorarachniophyta	Chlorarachnea
Bolidomonas	Bolidophyceae
Developayella	Developea
Diatomea	Diatomeae
Olisthodiscus	Raphidophyceae
Picophagea	Picophagus
Pinguiochrysidales	Pinguiophyceae
Pirsonia	Pirsoniales

Also, Picozoa supergroup was changed to Archaeplastida, according to Schön et al (2021).

v4

Sequence MPN5387 (Pyramimonadales) was misclassified as MALV-II. Corrected in this version.

v3

Updated Supergroups taxonomy:

• 'Eukaryota' is now 'OtherEukaryota' to avoid misunderstandings.
• 'Opisthokonta' is used instead of 'Obazoa'. Breviatea and Apusomonadida are then transferred to 'OtherEukaryota'.
• Mantamonas and Rigifilida supergroup is changed from 'OtherEukaryota' to 'CRuMS'.

v2

6 sequences with errors removed:

Removed sequence	Error
MPN7116_MAST-4_Stramenopiles	Missed 8 bases at position 60
BMK21470_Dinoflagellata_Alveolata	Had 4 gaps that should not be there
MPN4866_Dinoflagellata_Alveolata	Missed 5-19 bases at position 220
BMK14604_Dictyochophyceae_Stramenopiles	Seemed to be a chimera
MPN6667_Telonemia_Eukaryota	Missed 6 bp at position 280
BMK17658_Cercozoa_Rhizaria	It had 6 gaps here and there

v1

First version, used in Mol Ecol Resour paper.

How was the database built?

The database was first built using 97% clustered V4 sequences from previous environmental high-throughput sequencing (HTS) studies in European coastal systems: Blanes Bay Microbial Observatory (Giner et al., 2019) and BioMarKs project (Massana et al., 2015), and the water column of the global ocean sampled during the Malaspina cruise (Giner et al., 2020).

Then, the database was complemented with trimmed 97% clustered V4 sequences from SILVA SSU 128 (Quast et al., 2013) that were not found in environmental HTS datasets. This trimming was performed using cutadapt v1.16 (Martin, 2011) with the universal eukaryotic forward primer from Stoeck et al. (2010) and reverse primer from Balzano et al. (2015), with an error rate of 0.2.

All sequences were manually curated to discard possible chimeras and were classified at three taxonomic levels based on previous data, exhaustive inspection in multiple phylogenetic trees and iterative testing with environmental datasets to detect and correct problematic cases (i.e. distant references sequences retrieving the same mTag). These three levels were:

• OTU₉₇ level (Operational Taxonomic Units of sequences clustered at 97% similarity)
• Taxonomic group (in general a formal Class)
• Supergroup

The largest effort was the classification at the taxonomic group level, which comprised 136 groups (see following section). The final eukaryotesV4 database contains 25,849 sequences, 43% of which derive from environmental datasets.