Sanger environmental marine sequences of the V4-V5 regions

Database name: MAS_V4_DB
Version : 8952 | 15 November 2015
	Older versions: 8903 | 11 November 2015 
Contact: ramonm at icm.csic.es

DESCRIPTION

Sanger environmental marine sequences of the V4-V5 regions, retrieved until January 2010. 

Classified to class-level using phylogenetic trees

Further modifications to add missing taxa

8952 sequences, about 500 bp in size

SOURCE

Based on the sequences presented in Pernice et al. 2013. PLoS ONE 8:e57170 		(http://dx.plos.org/10.1371/journal.pone.0057170)

HISTORY OF THE DATASET

- Initially there were 8291 Sanger sequences classified in 65 taxonomic groups

- These were grouped at 99% with Usearch (~3304 sequences) and then were further verified with a few extra changes

- Metazoans and fungi were downloaded from PR2, and also grouped at 99% with Usearch. This resulted in 3593 additional sequences

- Add stramenopiles (including MAST and MOCH clades and subclades) as in Massana et al. 2014. ISME J. 8: 854-866

- Adds opisthokonta including del Campo & Ruiz-Trillo 2013. Mol. Biol. Evol. 30:802–805

ADDITIONAL COMMENTS - LIMITATIONS

- Amoebozoa not separated in classes

- Chlorophyta lacks all classes except Prasinophyceae (including Mamiellophyceae)  and Trebouxiophyceae

- Metazoa not separated in classes

- On the other hand, excavata highly separated

- Fungi checked individually
      Ascomycota - Perfect
      Basidiomicota - Perfect
      Mucoromycota - Perfect
      Chytridiomycota - Rather good
      Cryptomycota - Perfect

  There is a clade that includes all Blastocladiomycota, together with smaller clades
  with a fraction of Entomophthoromycota, Kickxellomycota, Zoopagomycota, Chytridiomycota, 
  and Mucoromycota

Changes in version 8952 (15-11-2015)

Based on MAS_V4_8903 with the following modifications

1 - Add missing taxa within previous groups (6): 3 Dinophyceae; 1 Layrinthulomycete; 2 MALV-I

2 - Add missing groups (22)
	Ellobiopsidae (3)
	Nephroselmis (3)
	Ulvophyceae (2)
	Chlorophyceae (1)
	Rhodophyta (13)

3 - Add nucleomorphs
	Retrieve all OTUs classified as nucleomorphs (98 OTUs)
	Cluster them at 97% similarity - 21 OTUs remaining
	Do a GenBank search for similar sequences
	Add 21 nucleomorphs

4 - Align all these 49 sequences together with some references from Massimo and cut to 
	keep the V4-V5 regions

5 - Separate Mamiellophytes (and Chlororendrophyceae) from Prasinophyceae

Present limitation (to imporve in the future)
	Separate Amoebozoa in classes