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 |
Plants associated with this reference |