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Series GSE249345 Query DataSets for GSE249345
Status Public on Mar 28, 2024
Title Co-expression analysis reveals distinct alliances around two carbon fixation pathways in hydrothermal vent symbionts
Organism Candidatus Endoriftia persephone
Experiment type Expression profiling by high throughput sequencing
Summary Biological carbon fixation is foundational to the biosphere. Most autotrophs are thought to possess one carbon fixation pathway. The hydrothermal vent tubeworm Riftia pachyptila’s chemoautotrophic symbionts, however, possess two functional pathways: the Calvin Benson-Bassham (CBB) and the reductive tricarboxylic acid (rTCA) cycles. Little is known about how Riftia’s symbionts and related organisms coordinate the functioning of these two pathways. Here we investigated net carbon fixation rates, transcriptional/metabolic responses, and transcriptional co-expression patterns of Riftia pachyptila’s endosymbionts by incubating tubeworms at environmental pressures, temperature, and geochemistry. Results showed that rTCA and CBB transcriptional patterns varied in response to different geochemical regimes and that each pathway is allied to specific metabolic processes, suggesting distinctive yet complementary roles in metabolic function. Net carbon fixation rates were also exemplary, and accordingly we propose that co-activity of CBB and rTCA may be an adaptation for maintaining high carbon fixation rates, conferring a fitness advantage in dynamic vent environments.
 
Overall design In order to investigate the symbiont's response to varying conditions in our high pressure aquaria, we looked at the gene expression profiles of symbionts sampled from individual worms that were in these aquaria. These data include three samples (from three worms) from each experimental aquaria representing 10 different conditions, so 30 metatranscriptomes in total.
 
Contributor(s) Mitchell JH, Freedman A, Delaney JA, Girguis PR
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Submission date Dec 05, 2023
Last update date Mar 28, 2024
Contact name Jessica Mitchell
E-mail(s) jessicamitchell@fas.harvard.edu
Organization name Harvard University
Department Department of Organismic and Evolutionary Biology
Lab Girguis Lab
Street address 16 Divinity St, Biolabs # 3102
City Cambridge
State/province Massachusetts
ZIP/Postal code 02138
Country USA
 
Platforms (1)
GPL33985 Illumina NovaSeq 6000 (Candidatus Endoriftia persephone)
Samples (30)
GSM7937324 Riftia_trophosome_sample_H2_N_HO_biological_replicate_1
GSM7937325 Riftia_trophosome_sample_H2_N_HO_biological_replicate_2
GSM7937326 Riftia_trophosome_sample_LS_noN_HO_biological_replicate_1
Relations
BioProject PRJNA1048833

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE249345_Endoriftia_DE_limma_results.csv.gz 1.7 Mb (ftp)(http) CSV
GSE249345_Endoriftia_WGCNA_CytoscapeEdgeFile_0.05.txt.gz 980.5 Kb (ftp)(http) TXT
GSE249345_Endoriftia_WGCNA_CytoscapeNodeFile_0.05.txt.gz 22.3 Kb (ftp)(http) TXT
GSE249345_Endoriftia_WGCNA_GM_GS_sulfide_oxygen.csv.gz 460.4 Kb (ftp)(http) CSV
GSE249345_Endoriftia_rsem_gene_count.matrix.txt.gz 172.6 Kb (ftp)(http) TXT
GSE249345_README.txt 4.9 Kb (ftp)(http) TXT
Raw data are available in SRA
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