Table 1

Phylogenetic distribution of the eukaryotic SSD scaffolds


Number of SSD sequences


Supergroup
 Group
 18S rRNA
 28S rRNA
 EF1a
 EF2
 RPB1
 actin
 α-tubulin
 β-tubulin
 cox1
 rbcL
Total
38
 41
 11
 4
 30
 12
 13
 15
 11
 4
Rhizaria
 Cercozoa
 1
 -
 -
 -
 2
 1
 -
 -
 -
 -

Polycystinea
 3
 1
 -
 -
 -
 -
 -
 -
 -
 -
Chromalveolates
 Apicomplexa
 1
 5
 -
 1
 1
 -
 -
 -
 -
 -

Ciliophora
 1
 -
 1
 -
 1
 -
 3
 3
 -
 -

Dinophyceae
 10* (3)
 11
 1
 -
 -
 -
 3
 3
 1
 -

Stramenopiles
 1 (1)
 6 (4)
 2
 -
 -
 1
 1
 2
 2
 1
Excavates
 Euglenozoa
 1
 -
 -
 1
 -
 1
 -
 1
 -
 -

Heterolobosea
 -
 -
 -
 -
 2
 -
 -
 -
 -
 -
Plantae
 Chlorophyta
 3 (2)
 3 (3)
 2
 -
 x
 1*
 1
 1
 4
 1*

Streptophyta
 1
 1
 3
 2*
 7*
 2
 2*
 2*
 3*
 -

Rhodophyta
 -
 -
 -
 -
 4
 -
 -
 -
 -
 2
Unikonts
 Ichthyosporea
 -
 1 (1)
 -
 -
 1
 -
 -
 -
 -
 x

Arthropoda
 7
 7 (5)
 1*
 -
 -
 1
 -
 -
 -
 x

Bryozoa
 2
 1 (1)
 -
 -
 -
 -
 -
 -
 -
 x

Cnidaria
 4
 2* (1)
 -
 -
 -
 -
 -
 -
 -
 x

Fungi
 1
 1
 -
 -
 10
 3
 -
 -
 -
 x

Platyhelminthes
 1
 -
 -
 -
 2
 -
 -
 -
 -
 x

Urochordata
 -
 1 (1)
 1
 -
 -
 1
 1
 1
 1
 x
Unknown
1 (32)
 1 (25)
 -
 -
 -
 1
 -
 2
 -
 -

The number of scaffolds for which taxonomic affiliation was confirmed by phylogenetic analysis (Additional data files 1 and 2) is indicated in brackets. The taxonomic affiliation of the largest scaffold is indicated by an asterisk. The groups for which the anchor gene has no representative in the GenBank database are indicated by x.

Piganeau et al. Genome Biology 2008 9:R5   doi:10.1186/gb-2008-9-1-r5