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Functional & Integrative Genomics

, Volume 10, Issue 4, pp 523–532 | Cite as

Comparative transcriptomics for mangrove species: an expanding resource

  • Maheshi Dassanayake
  • Jeff S. Haas
  • Hans J. Bohnert
  • John M. Cheeseman
Original Paper

Abstract

We present here the Mangrove Transcriptome Database (MTDB), an integrated, web-based platform providing transcript information from all 28 mangrove species for which information is available. Sequences are annotated, and when possible, GO clustered and assigned to KEGG pathways, making MTDB a valuable resource for approaching mangrove or other extremophile biology from the transcriptomic level. As one example outlining the potential of MTDB, we highlight the analysis of mangrove microRNA (miRNA) precursor sequences, miRNA target sites, and their conservation and divergence compared with model plants. MTDB is available at http://mangrove.illinois.edu.

Keywords

Mangroves Transcriptome Database Extremophile miRNA target sequences Small RNA 

Notes

Acknowledgements

The authors are indebted to the Smithsonian Caribbean Coral Reef Ecosystem (CCRE) project, and especially to Klaus Rützler, Candy Feller, Mike Carpenter and all the Carrie Bow Cay station managers for continued support for the field work and access to Twin Cays; to the Vice Chancellor for Research at the University of Illinois at Urbana-Champaign for funding the sequencing; to Shahjahan Ali, Jyothi Thimmapuram and Deepika Vulaganthi in the Keck Center for Comparative and Functional Genomics at UIUC for sequencing and assembly; and to Robert Bocchino and Sahan Dissanayake for help with Perl scripts. This is contribution number 870 of the CCRE program, Smithsonian Institution, supported in part by the Hunterdon Oceanographic Research Endowment.

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Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Maheshi Dassanayake
    • 1
  • Jeff S. Haas
    • 2
  • Hans J. Bohnert
    • 1
  • John M. Cheeseman
    • 1
  1. 1.Department of Plant BiologyUniversity of IllinoisUrbanaUSA
  2. 2.Office of Networked Information Technologies (ONIT), School of Integrative BiologyUniversity of IllinoisUrbanaUSA

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