Zostera noltii EST data
| by Massa S, Pearson GA, Serrao EA, Arnaud-Haond S |
| manuscript in preparation |
| Output type: data |
The
dwarf seagrass Zostera noltii dominates the intertidal habitats
of the Ria Formosa, either in low-water intertidal pools or in waterless
patches where temperatures can reach the lethal limits for the species (Massa
et al. 2009). The predicted increase in sea surface temperatures of
0.2ºC/decade (SST) (IPCC) is raising concerns as to the ability of this species
to survive the expected global warming, especially in this kind of habitats,
where shallow water temperature is more affected by air temperature than SST.
Here
we present the result of five EST libraries, corresponding to four moments of
the response of Zostera noltii to a sub-lethal temperature
stress (30 min, 2h, 4h and 24h) and its corresponding negative control. We aim
to identify non-neutral genes that may be implicated in the seagrass’ response
to heat shock by comparison of the heat shock libraries to the control one, as
well as determine if expressed genes change over time.
A
total of 8594 clones from all libraries were sequenced, with a total of 7799
high quality sequences. After screening for cloning relics and contamination, a
total of 113 sequences were removed, remaining a total of 7686 successful
sequences. Average percentage of successfully blasted sequences was 82%,
successfully mapped sequences 85% and successfully annotated sequences 80%. Detailed
information for each library can be found in table 1.
Fisher’s
Exact Test shows a significant difference (p<0.05) between the 30 min, 2
hours and 4 hours libraries and the control, but not between the 24 hours
library and the blank. Detailed results can be found in worksheets 2-4.
Each
library was blasted against a pooled database of all stress libraries to find
homologues. Identification of differentially expressed genes was performed
using the IDEG6 web tool, by comparing the number of reads of each TC in all 5
libraries (worksheet 5). These were then blasted against Dr. Zompo EST
databases for Zostera marina and Posidonia oceanica for
matching hits. A bar graph with the number of counts for each one of these
genes in each library can be found in worksheet 6; hits to Dr. Zompo’s
databases are also indicated.
Worksheets
7 and 8 contain pie charts for the “photosynthesis” and “response to stress”
related genes, respectively, and their evolution through time, showing the
number of counts in each library.
A total of 4734 TCs were screened for EST-SSRs. We found a total of 86 microsatellites, of which 43 are dinucleotides, 36 trinucleotides, 4 tetranucleotides and 3 hexanucleotides (worksheet 9).
References:
Massa SI, Arnaud-Haond S, Pearson GA,
Serrao EA (2009) Temperature tolerance and survival of intertidal populations
of the seagrass Zostera noltii (Hornemann) in Southern Europe (Ria Formosa,
Portugal) Hydrobiologia. 619: 195-201
