Microbial community gene expression in ocean surface waters
- Jorge Frias-Lopez*,
- Yanmei Shi*,
- Gene W. Tyson*,
- Maureen L. Coleman*,
- Stephan C. Schuster†,
- Sallie W. Chisholm*,‡, and
- Edward F. DeLong*,§,‡
- Departments of *Civil and Environmental Engineering and
- §Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139;
- †Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802
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Edited by David M. Karl, University of Hawaii, Honolulu, HI, and approved January 22, 2008 (received for review September 19, 2007)
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Fig. 1.Community-level gene expression profile based on GOS peptide database. (A) GOS protein clusters with DNA or cDNA matches at bit scores ≥40 are shown in the Venn diagram. Numbers of reads assigned to GOS protein clusters, when >70, are plotted for both cDNA-unique protein clusters and DNA-unique protein clusters. GOS protein clusters shared by DNA and cDNA libraries (shaded in gray) were further illustrated in B. (B) GOS protein clusters shared by cDNA and DNA libraries were ranked by their cluster-based expression ratio (representation of each cluster in the cDNA library normalized by its representation in the DNA library). Furthermore, each protein cluster was categorized (and color-coded) according to its abundance in the DNA library. Representative protein clusters were highlighted from each category and discussed in the text.
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Fig. 2.Distribution of different phylogenetic groups in DNA and cDNA libraries. Percentages of the different phylogenetic groups were calculated from the MEGAN analysis results at the phylum level cutoff (SI Table 5 shows a detailed list of the distribution of number of hits and percentages for all phyla). Not assigned reads are sequences with an NR hit but a bit score <40.
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Fig. 3.Prochlorococcus gene and transcript abundance using strain MIT9301 as a reference genome. (A) Rank abundance of the 20 genes with highest frequency in the raw cDNA, reflecting transcription of the entire Prochlorococcus population. (B) Frequency of DNA hits from the natural sample along the genome of MIT9301 normalized to gene length. (C) Frequency of cDNA hits from the natural sample normalized to the DNA values in B. Gray bars indicate the location of genomic islands identified through whole-genome analysis of cultured isolates (6). Core genes, genes present in all genomes of Prochlorococcus sequenced, are shown in blue. Flexible genes, genes not present in all genomes of Prochlorococcus sequenced, are shown in pink.
Footnotes
- ‡To whom correspondence may be addressed. E-mail: delong{at}mit.edu or chisholm{at}mit.edu
- © 2008 by The National Academy of Sciences of the USA
