Ontology highlight
ABSTRACT:
PROVIDER: PRJNA640643 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12054993_1.fastq.gz | Fastqsanger.gz | |||
| SRR12054993_2.fastq.gz | Fastqsanger.gz |
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Project description:we used high-throughput Illumina Genome Analyzer IIx (GAIIx) technology to sequence the small RNA transcriptomes of the mangrove species, Avicennia marina. Based on sequence similarity or the secondary structure of precursors, we have identified 193 conserved miRNAs and 26 novel miRNAs in the small RNA transcriptome of Avicennia marina.
2013-01-23 | GSE43669 | GEO
Project description:we used high-throughput Illumina Genome Analyzer IIx (GAIIx) technology to sequence the small RNA transcriptomes of the mangrove species, Avicennia marina. Based on sequence similarity or the secondary structure of precursors, we have identified 193 conserved miRNAs and 26 novel miRNAs in the small RNA transcriptome of Avicennia marina. 1 sample
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Project description:Molecular responses to freshwater limitation in the mangrove tree Avicennia germinans (Acanthaceae)
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Project description:Environmental variation along the geographical space can shape populations by natural selection. In the context of global warming and changing precipitation regimes, it is crucial to understand the role of environmental heterogeneity in tropical trees adaptation, given their disproportional contribution to water and carbon biogeochemical cycles. Here, we investigated how heterogeneity in freshwater availability along tropical wetlands has influenced molecular variations of the black mangrove (Avicennia germinans). A total of 57 trees were sampled at seven sites differing markedly in precipitation regime and riverine freshwater inputs. Using 2,297 genome‐wide single nucleotide polymorphic markers, we found signatures of natural selection by the association between variations in allele frequencies and environmental variables, including the precipitation of the warmest quarter and the annual precipitation. Additionally, we found candidate loci for selection based on statistical deviations from neutral expectations of interpopulation differentiation. Most candidate loci within transcribed sequences were functionally associated with central aspects of drought tolerance or plant response to drought. Moreover, our results suggest the occurrence of the rapid evolution of a population, probably in response to sudden and persistent limitations in plant access to soil water, following a road construction in 1974. Observations supporting rapid evolution included the reduction in tree size and changes in allele frequencies and in transcript expression associated with increased drought tolerance through the accumulation of osmoprotectants and antioxidants, biosynthesis of cuticles, protection against protein degradation, stomatal closure, photorespiration and photosynthesis. We describe a major role of spatial heterogeneity in freshwater availability in the specialization of this typically tropical tree.
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Project description:Preparation of proteins from salt-gland-enriched tissues of mangrove plant is necessary for a systematic study of proteins involved in the plant’s unique desalination mechanism. Extraction of high-quality proteins from the leaves of mangrove tree species, however, is difficult due to the presence of high levels of endogenous phenolic compounds. In our study, preparation of proteins from only a part of the leaf tissues was required, rendering extraction even more challenging. By comparing several extraction methods, we developed a reliable procedure for obtaining sufficient proteins from salt gland-enriched tissues of the mangrove species Avicennia officinalis. Protein extraction was markedly improved using a phenol-based extraction method. Despite the lower protein yield obtained, one-dimensional protein gel profiles with greater resolution could be obtained, with more than twice the number of proteins detected when 1D-LC-MS/MS analyses were compared. Further analysis of proteins that were solely present in each extraction method favoured the phenol-based extraction. Phenol-based extracts contained nearly 10 times more solely-detected proteins than those were detectable in the extracts without using phenol. The protocol established could thus be applied for downstream high-throughput proteomic analyses involving LC-MS/MS or equivalent.
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Project description:LC-MS/MS M-H(methanol: water 7/3) and MET (methanol) leaves and stems extracts of Rhizophora mangle, Avicennia schaueriana and Laguncularia racemosa from Paripe river mangrove - Ceara, Brazil.
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