Depth dependent metatranscriptomes of the marine pico-/nanoplanktonic communities in the Gulf of Aqaba/Eilat during seasonal deep mixing

作者：Pfreundt Ulrike; Miller Dan; Adusumilli Lakshmi; Stambler Noga; Berman Frank Liana; Hess Wolfgang R^*

来源：Marine Genomics, 2014, 18: 93-95.

DOI：10.1016/j.margen.2014.06.005

• Gene expression
• Metatranscriptomics
• Microbial community
• RNA-Seq
• Transcriptome

Metatranscriptomics is a widely used approach to study the gene expression within a whole microbial community. Spatial or temporal differences observed between datasets point to transcriptional responses to changes or alterations in the community%26apos;s environment. No transcriptomic data has yet been published from the oligotrophic Gulf of Aqaba/Eilat, northern Red Sea. The primary objective of this study was to create a depth-specific snapshot of community gene expression ranging from the surface waters to the bottom of the mixed-layer depth during winter when thermal destratification occurs. Our secondary objective was to compare two different methods for transcriptome analysis. While random RNA sequencing (RNA-seq) is routinely used, differential RNA sequencing (dRNA-seq, enriched in primary transcripts) has never been used for metatranscriptomics. In this dataset, we used dRNA-seq for samples that were collected from three depths while applying RNA-seq for one of the samples to obtain direct comparison between the methods. We de-novo assembled the reads into contigs and show a high percentage of reads mapping back to the contigs, supporting the validity of the assembly.

• 出版日期2014-12