ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage

Kelly, L.; Huang, K. H.; Ding, H.; Chisholm, S. W.

doi:10.1093/nar/gkr1022

Title: ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage

Journal Article · Thu Nov 17 00:00:00 EST 2011 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkr1022· OSTI ID:1904689

Kelly, L. ^[1]; Huang, K. H. ^[1]; Ding, H. ^[1]; Chisholm, S. W. ^[1]

Massachusetts Institute of Technology (MIT), Cambridge, MA (United States)

ProPortal (http://proportal.mit.edu/) is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. Our goal is to provide a source of cross-referenced data across multiple scales of biological organization—from the genome to the ecosystem—embracing the full diversity of ecotypic variation within this microbial taxon, its sister group, Synechococcus and phage that infect them. The site currently contains the genomes of 13 Prochlorococcus strains, 11 Synechococcus strains and 28 cyanophage strains that infect one or both groups. Cyanobacterial and cyanophage genes are clustered into orthologous groups that can be accessed by keyword search or through a genome browser. Users can also identify orthologous gene clusters shared by cyanobacterial and cyanophage genomes. Gene expression data for Prochlorococcus ecotypes MED4 and MIT9313 allow users to identify genes that are up or downregulated in response to environmental stressors. In addition, the transcriptome in synchronized cells grown on a 24-h light–dark cycle reveals the choreography of gene expression in cells in a ‘natural’ state. Metagenomic sequences from the Global Ocean Survey from Prochlorococcus, Synechococcus and phage genomes are archived so users can examine the differences between populations from diverse habitats. Finally, an example of cyanobacterial population data from the field is included.

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Research Organization:: Harvard Univ., Cambridge, MA (United States); Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Science Foundation (NSF); Gordon and Betty Moore Foundation

Grant/Contract Number:: FG02-02ER63445; FG02-07ER64506; FG02-08ER64516; OCE-0425602; EF0424599; 495.01

OSTI ID:: 1904689

Journal Information:: Nucleic Acids Research, Vol. 40, Issue D1; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Databases for Microbiologists: TABLE 1 Zhulin, Igor B. Journal of Bacteriology, Vol. 197, Issue 15 https://doi.org/10.1128/jb.00330-15	journal	May 2015
Transcriptome and Proteome Dynamics of a Light-Dark Synchronized Bacterial Cell Cycle Waldbauer, Jacob R.; Rodrigue, Sébastien; Coleman, Maureen L. PLoS ONE, Vol. 7, Issue 8 https://doi.org/10.1371/journal.pone.0043432	journal	August 2012
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