Spliced leader-based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates.
Environmental transcriptomics (metatranscriptomics) for a specific lineage of eukaryotic microbes (e.g., Dinoflagellata) would be instrumental for unraveling the genetic mechanisms by which these microbes respond to the natural environment, but it has not been exploited because of technical difficulties. Using the recently discovered dinoflagellate mRNA-specific spliced leader as a selective primer, we constructed cDNA libraries (e-cDNAs) from one marine and two freshwater plankton assemblages. Small-scale sequencing of the e-cDNAs revealed functionally diverse transcriptomes proven to be of dinoflagellate origin. A set of dinoflagellate common genes and transcripts of dominant dinoflagellate species were identified. Further analyses of the dataset prompted us to delve into the existing, largely unannotated dinoflagellate EST datasets (DinoEST). Consequently, all four nucleosome core histones, two histone modification proteins, and a nucleosome assembly protein were detected, clearly indicating the presence of nucleosome-like machinery long thought not to exist in dinoflagellates. The isolation of rhodopsin from taxonomically and ecotypically diverse dinoflagellates and its structural similarity and phylogenetic affinity to xanthorhodopsin suggest a common genetic potential in dinoflagellates to use solar energy nonphotosynthetically. Furthermore, we found 55 cytoplasmic ribosomal proteins (RPs) from the e-cDNAs and 24 more from DinoEST, showing that the dinoflagellate phylum possesses all 79 eukaryotic RPs. Our results suggest that a sophisticated eukaryotic molecular machine operates in dinoflagellates that likely encodes many more unsuspected physiological capabilities and, meanwhile, demonstrate that unique spliced leaders are useful for profiling lineage-specific microbial transcriptomes in situ.
Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA. senjie.lin@uconn.edu
Senjie
S
Lin
Huan
H
Zhang
Yunyun
Y
Zhuang
Bao
B
Tran
John
J
Gill
D000595:Amino Acid Sequence; D018076:DNA, Complementary / Q000235:genetics; D004141:Dinoflagellida / Q000235:genetics*; D004777:Environment; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D014644:Genetic Variation; D018503:Genome, Protozoan / Q000235:genetics*; D006657:Histones / Q000737:chemistry / Q000378:metabolism; D008969:Molecular Sequence Data; D009707:Nucleosomes / Q000378:metabolism; D010802:Phylogeny; D010933:Plankton / Q000235:genetics; D015800:Protozoan Proteins / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D020038:RNA, Spliced Leader / Q000235:genetics*; D012243:Rhodopsin / Q000235:genetics / Q000378:metabolism; D012269:Ribosomal Proteins / Q000235:genetics / Q000378:metabolism
D018076:DNA, Complementary; D006657:Histones; D009707:Nucleosomes; D015800:Protozoan Proteins; D012333:RNA, Messenger; D020038:RNA, Spliced Leader; D012269:Ribosomal Proteins; D012243:Rhodopsin