Analyses performed on the genomic dataset of scaffolds

Analyses performed on the genomic dataset of scaffolds from the microbial
community at the ALOHA station (Pacific Ocean) where 70,000 fosmid clones
collected from seven different depths were randomly ‘end’-sequenced from both ends
of each clone (DeLong et al., 2006). Thirteen partial or full-length D1-encoding
protein sequences were detected in three photic zone depths (10 m, 70 m and 130 m),
and eight contained the R/KETTXXXSQ/H motif (three ETE, one ENE, and four EQE
triplets). The motifs identified were the same motifs dominating the GOS dataset and
were in agreement with observations from the GOS dataset; the majority (69%) of
ALOHA D1 sequences were confirmed to be of viral origin (nine out of 13 singletons
showed a viral affiliation based on neighboring sequences to the D1 or neighboring
sequences at the other fosmid-end).
The GOS and the ALOHA datasets were collected with the main emphasis
placed on the bacterial size range. The R/KETTXXXSQ/H triplet motif was then
searched for in the metagenomic dataset of 184 viral assemblages collected from the
Sargasso Sea (SAR), the Gulf of Mexico (GOM), British Columbia coastal waters
(BBC) and the Arctic Ocean (Angly et al., 2006). The viral metagenomes were
sequenced differently to the GOS metagenomes using pyrosequencing and hence the
sequences produced were very short (102 bp on average). Nevertheless, 423 D1
sequences were detected in the four viromes datasets (413 in SAR, five in BBC, five
in GOM, and zero in ARCTIC). The low occurrence of D1 sequences in the BBC,
GOM and ARCTIC stations was expected, since viral sequences related to
cyanophages were detected primarily only in the SAR station (see Fig. 3A in (Angly
et al., 2006)). Of the 423 D1 sequences, 26 contained the R/KETTXXXSQ/H motif (all
from the SAR station); eight ETE, six EDV, three ENV, three GLD, three GLV, two
ENE, one ETV, and one EAE triplets.
Angly, F., Felts, B., Breitbart, M., Salamon, P., Edwards, R., Carlson, C. et al. (2006)
The marine viromes of four oceanic regions. PLoS Biol 4: e368.
DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.-U. et al.
(2006) Community Genomics Among Stratified Microbial Assemblages in the
Ocean’s Interior. Science 311: 496-503.
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