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SRX14592978: Transcriptome sequencing of Euthynema mutabile (PCSc10)
1 ILLUMINA (Illumina HiSeq 2000) run: 22.2M spots, 6.7G bases, 1.9Gb downloads

Design: Total RNA was extracted from 400 ml of well-grown cultures using TriReagent (Sigma-Aldrich) and chloroform, purified using the RNeasy mini kit (QIAGEN), and treated with DNase (QIAGEN). The sequencing library was prepared using TruSeqRNA Sample Prep Kit v2.
Submitted by: University of Ostrava
Study: An independent hydrogenosome-to-mitosome transition in the CL3 lineage of fornicates
show Abstracthide Abstract
Inferring a robust phylogeny for Fornicata, a lineage of a broader and ancient anaerobic eukaryotic clade Metamonada, is required to address numerous fundamental biological processes; such as: 1) the evolutionary trajectory of mitochondrion-related organelles (MROs), 2) life-style transitions between free-living and host-associated endobionts, and 3) derivations of alternative genetic codes. To this end, we conducted detailed microscopic and transcriptome analyses in a poorly documented strain of an anaerobic free-living marine flagellate, PCS in the so-called CL3 fornicate lineage. Fortuitously, we discovered that the original culture contained two morphologically similar and closely related CL3 representatives, which doubles the taxon representation within this lineage. We obtained a monoeukaryotic culture of one of them and formally describe it as a new member of the family Caviomonadidae, Euthynema mutabile gen. et sp. nov. In contrast to previously studied caviomonads, the endobiotic Caviomonas mobilis and Iotanema spirale, E. mutabile possesses an ultrastructurally discernible MRO. We sequenced and assembled the transcriptome of E. mutabile, and by sequence subtraction, obtained transcriptome data from the other CL3 clade representative present in the original PCS culture, denoted PCS-ghost. Transcriptome analyses showed that the reassignment of only one of the UAR stop codons to encode Gln previously reported from I. spirale does not extend to its free-living relatives and is likely due to a unique amino acid substitution in I. spirale's eRF1 protein domain responsible for termination codon recognition. The backbone fornicate phylogeny was robustly resolved in a phylogenomic analysis, with the CL3 clade amongst the earliest branching lineages. Metabolic and MRO functional reconstructions of CL3 clade members revealed that all three, including I. spirale, encode homologs of key components of the mitochondrial protein import apparatus and the ISC pathway, indicating the presence of a MRO in all of them. In silico evidence indicates that the organelles of E. mutabile and PCS-ghost host ATP and H2 production, unlike the cryptic MRO of I. spirale. These data reveal that the CL3 clade has experienced a hydrogenosome-to-mitosome transition independent from that previously documented for the lineage leading to Giardia.
Sample:
SAMN26378256 • SRS12362822 • All experiments • All runs
Library:
Name: PCSc10
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: RANDOM
Layout: PAIRED
Runs: 1 run, 22.2M spots, 6.7G bases, 1.9Gb
Run# of Spots# of BasesSizePublished
SRR1846034522,186,3106.7G1.9Gb2022-04-21

ID:
20841994

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