Premium
Creation of a pilot metatranscriptome library from eukaryotic plankton of a eutrophic bay (Tampa Bay, Florida)
Author(s) -
John David E.,
Zielinski Brian L.,
Paul John H.
Publication year - 2009
Publication title -
limnology and oceanography: methods
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.898
H-Index - 72
ISSN - 1541-5856
DOI - 10.4319/lom.2009.7.249
Subject(s) - biology , genbank , ribosomal rna , homology (biology) , gene , rna , genetics
Analysis of the suite of genes expressed by natural populations of phytoplankton can potentially elucidate valuable information about the types, cellular activity, and biogeochemical impacts of organisms present in the marine environment. Here we describe the construction of a pilot metatranscriptome library created from eukaryotic planktonic organisms in Tampa Bay, FL, USA. RNA from cells greater than 2 µm was extracted and purified, and poly(A) tailed mRNA was concentrated and amplified using linear amplification chemistry. Amplified RNA was converted to double‐stranded cDNA using reverse transcriptase and DNA polymerase I (Klenow fragment) and cloned, and 232 clones were sequenced. Sequences with significant GenBank BLAST homology revealed genes related to photosynthesis and nutrient acquisition, along with general cell functions. In total, 27% of sequenced transcript clones contained significant homology to GenBank sequences, 2% of the total were putatively derived from ribosomal RNA, and 1% were most similar to sequences originating from prokaryotes. About 70% of the identified transcripts were putatively derived from eukaryotic phytoplankton, including diatoms, chlorophytes, and dinoflagellates. Although small in scale, this study provides the basis for future efforts to characterize the metatranscriptome of marine phytoplankton populations.