Meeting Abstract

P3.99  Monday, Jan. 6 15:30  High density, strand-specific RNA-seq analysis of the Pacific WhiteLeg Shrimp, Litopenaeus vannamei JOHNSON, JG*; KNIFFIN, CD; BURNETT, LE; BURNETT, KG; College of Charleston; College of Charleston; College of Charleston; College of Charleston jilljohnson821@gmail.com

Acclimation to hypoxia in the Pacific whiteleg shrimp involves regulation at the level of the transcriptome. Previous microarray results suggest that the hypoxia-specific transcriptomic signature is reduced or reversed with the addition of elevated carbon dioxide to the system. In the present study we use high throughput RNA sequencing (RNA-Seq) to explore the regulation of transcriptionally-based response, acclimation, and resiliency to low oxygen/high CO₂ conditions in L. vannamei, with particular focus on the two known subunits of the copper-containing respiratory pigment, hemocyanin (Hc). mRNA of juvenile L. vannamei exposed to normoxia (n = 18), hypoxia (n = 18), or hypercapnic hypoxia (n = 15) was pooled and sequenced in a strand-specific manner on the Illumina HiSeq 2500 platform. A total of 454,864,339 single end 100 bp high quality (>Q30) raw reads were generated, and 27,102 contigs with a mean length of 960 bp (262 bp minimum; 18,486 bp maximum) were assembled using the de novo assembler, Trinity (N50: 640bp). Raw reads were mapped back on to the Trinity assembly using the short-read aligner, Bowtie (81.2% RMBT). Although verification of the number of transcripts encoded in the genome is not possible in the absence of an annotated genome, the average absolute depth of read coverage across all transcripts was 1642X (Cufflinks: 17X minimum; 542,751X maximum.) Due to the extensive depth of coverage, new isoforms of the large Hc subunit have been identified. Current work is underway to assess Hc subunit usage in relation to low oxygen and high CO₂ conditions. (NSF IOS-1147008)