Antarctic salp genome and RNAseq transcriptome from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2 in the Southern Ocean from 2009-2011 (Salp_Antarctic project)
Citable URI
https://hdl.handle.net/1912/9610As published
https://lod.bco-dmo.org/id/dataset/675040Date Created
2017-01-27Location
Southern Oceanwestlimit: -74.567; southlimit: -66.183; eastlimit: 42.002; northlimit: -60.901
DOI
10.1575/1912/bco-dmo.728225Abstract
A preliminary genome sequence and complete reference transcriptome have been assembled for the Southern Ocean salp, Salpa thompsoni (Urochordata, Thaliacea). The reference transcriptome contains 216,931 sequences; 41,210 (18%) were associated with predicted, hypothetical, or known proteins; 13,058 (6%) were mapped and annotated. Whole-transcriptome (RNA-seq) analysis of 39 samples collected during austral spring and summer 2011 in the WAP, and in summer 2009 in the Indian Sector revealed clustering of samples by regions, seasons, and areas (Bray-Curtis similarity). Spring versus summer samples showed significant differential expression of 77 genes associated with environmental stress response and 51 genes associated with sexual reproduction (paired t-tests, p<0.05). Gene Ontology (GO) term enrichment analysis identified 41 GO terms responsible for spring versus summer differences, including 156 genes associated with translation (i.e., protein synthesis). The genome sequence of 318,767,936 bp covers >50% of the estimated 602 MB (±173 MB) genome size for S. thompsoni, with >50% (16,823) of sequences showing significant homology to known proteins and ~38% (12,151) of the total protein predictions associated with Gene Ontology functional information. A total of 109,958 SNP variants and 9,782 indel predictions were generated, serving as a resource for future phylogenomic and population genomic studies. Salpa thompsoni exhibits rapid rates of evolution (>1.5 times that observed for vertebrates) typical of other urochordates examined. An initial survey of small RNAs revealed the presence of known, conserved miRNAs, as well as novel miRNA genes; unique piRNAs; and mature miRNA signatures for varying developmental stages. For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/675040
Description
Dataset: Salp genome and transcriptome
Suggested Citation
Dataset: Bucklin, Ann, O'Neill, Rachel J., Payne, Diana, "Antarctic salp genome and RNAseq transcriptome from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2 in the Southern Ocean from 2009-2011 (Salp_Antarctic project)", 2018-02-23, DOI:10.1575/1912/bco-dmo.728225, https://hdl.handle.net/1912/9610The following license files are associated with this item:
Related items
Showing items related by title, author, creator and subject.
-
Salp specimen log for genomic and transcriptomic study collected from ARSV Laurence M. Gould, Umitaka-Maru, R/V Polarstern LMG1110, UM-08-09, ANT-XXVII-2 in the Southern Ocean from 2009-2011 (Salp_Antarctic project)
Bucklin, Ann; O'Neill, Rachel J.; Payne, Diana (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2018-02-23)This dataset is a sample log of the Salpa thompsoni specimens used for genomic and transcriptomic analysis. Collections were from three cruises in the Southern Ocean. Collections were made in Summer of 2009 during a cruise ... -
Genome-wide transcriptomics of aging in the rotifer Brachionus manjavacas, an emerging model system
Gribble, Kristin E.; Mark Welch, David B. (BioMed Central, 2017-03-01)Understanding gene expression changes over lifespan in diverse animal species will lead to insights to conserved processes in the biology of aging and allow development of interventions to improve health. Rotifers are small ... -
Nematostella Embryonic Transcriptome
Tulin, Sarah; Aguiar, Derek; Istrail, Sorin; Smith, Joel (2012-12-12)RNA-Seq was performed on Nematostella Embryos at 5 timepoints during early development: 0hrs, 6hrs, 12hrs, 18hrs, 24hrs after fertilization. Embryos were harvested, lysed and mRNAs were selected using Dynabeads. Directional ...