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Publication Type J
Authors Dassanayake, M; Haas, JS; Bohnert, HJ; Cheeseman, JM
Author Full Name Dassanayake, Maheshi; Haas, Jeff S.; Bohnert, Hans J.; Cheeseman, John M.
Title Comparative transcriptomics for mangrove species: an expanding resource
Source FUNCTIONAL & INTEGRATIVE GENOMICS
Language English
Document Type Article
Author Keywords Mangroves; Transcriptome; Database; Extremophile; miRNA target sequences; Small RNA
Keywords Plus RHIZOPHORA-MANGLE; REGULATED MICRORNAS; STRESS RESPONSES; NONCODING RNAS; PLANTS; ARABIDOPSIS; DWARF; IDENTIFICATION; CONSERVATION; BIOGENESIS
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.
Author Address [Dassanayake, Maheshi; Bohnert, Hans J.; Cheeseman, John M.] Univ Illinois, Dept Plant Biol, Urbana, IL 61801 USA; [Haas, Jeff S.] Univ Illinois, Sch Integrat Biol, ONIT, Urbana, IL 61801 USA
Reprint Address Cheeseman, JM (reprint author), Univ Illinois, Dept Plant Biol, 505 S Goodwin Ave, Urbana, IL 61801 USA.
E-mail Address j-cheese@illinois.edu
ResearcherID Number Bohnert, Hans/A-7104-2009; Dassanayake, Maheshi/B-7331-2012
ORCID Number Dassanayake, Maheshi/0000-0003-3123-3731
Funding Agency and Grant Number University of Illinois at Urbana-Champaign; Hunterdon Oceanographic Research Endowment
Funding Text The authors are indebted to the Smithsonian Caribbean Coral Reef Ecosystem (CCRE) project, and especially to Klaus Rutzler, 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 Pen l 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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Cited Reference Count 43
Times Cited 9
Total Times Cited Count (WoS, BCI, and CSCD) 9
Publisher SPRINGER HEIDELBERG
Publisher City HEIDELBERG
Publisher Address TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY
ISSN 1438-793X
29-Character Source Abbreviation FUNCT INTEGR GENOMIC
ISO Source Abbreviation Funct. Integr. Genomics
Publication Date NOV
Year Published 2010
Volume 10
Issue 4
Beginning Page 523
Ending Page 532
Digital Object Identifier (DOI) 10.1007/s10142-009-0156-5
Page Count 10
Web of Science Category Genetics & Heredity
Subject Category Genetics & Heredity
Document Delivery Number 680SN
Unique Article Identifier WOS:000284254800007
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