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Version 3.22
Publication Type J
Authors Dassanayake, M; Haas, JS; Bohnert, HJ; Cheeseman, JM
Author Full Name Dassanayake, M.; Haas, J. S.; Bohnert, H. J.; Cheeseman, J. M.
Title Shedding light on an extremophile lifestyle through transcriptomics
Language English
Document Type Article
Author Keywords 454 pyrosequencing; convergent evolution; ecogenomics; extremophiles; functional genomics; mangrove; transcriptome profiling
Abstract P>The tropical intertidal ecosystem is defined by trees - mangroves - which are adapted to an extreme and extremely variable environment. The genetic basis underlying these adaptations is, however, virtually unknown. Based on advances in pyrosequencing, we present here the first transcriptome analysis for plants for which no prior genomic information was available. We selected the mangroves Rhizophora mangle (Rhizophoraceae) and Heritiera littoralis (Malvaceae) as ecologically important extremophiles employing markedly different physiological and life-history strategies for survival and dominance in this extreme environment. For maximal representation of conditional transcripts, mRNA was obtained from a variety of developmental stages, tissues types, and habitats. For each species, a normalized cDNA library of pooled mRNAs was analysed using GSFLX pyrosequencing. A total of 537 635 sequences were assembled de novo and annotated as > 13 000 distinct gene models for each species. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology annotations highlighted remarkable similarities in the mangrove transcriptome profiles, which differed substantially from the model plants Arabidopsis and Populus. Similarities in the two species suggest a unique mangrove lifestyle overarching the effects of transcriptome size, habitat, tissue type, developmental stage, and biogeographic and phylogenetic differences between them. New Phytologist (2009) 183: 764-775doi: 10.1111/j.1469-8137.2009.02913.x.
Author Address [Dassanayake, M.; Bohnert, H. J.; Cheeseman, J. M.] Univ Illinois, Dept Plant Biol, Urbana, IL 61801 USA; [Haas, J. S.] Univ Illinois, ONIT, Sch Integrat Biol, 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 Hunterdon Oceanographic Research Endowment
Funding Text This is contribution number 860 of the Caribbean Coral Reef Ecosystems Program (CCRE), Smithsonian Institution, supported in part by the Hunterdon Oceanographic Research Endowment.
Cited References Agaton C, 2002, GENE, V289, P31, DOI 10.1016/S0378-1119(02)00548-6; Altschul SF, 1997, NUCLEIC ACIDS RES, V25, P3389, DOI 10.1093/nar/25.17.3389; Banzai T, 2002, PLANT SCI, V162, P499, DOI 10.1016/S0168-9452(01)00601-X; Barbazuk WB, 2007, PLANT J, V51, P910, DOI 10.1111/j.1365-313X.2007.03193.x; Bogdanova EA, 2008, MOL BIOSYST, V4, P205, DOI 10.1039/b715110c; Brautigam A, 2008, J BIOTECHNOL, V136, P44, DOI 10.1016/j.jbiotec.2008.02.007; Bremer B, 2003, BOT J LINN SOC, V141, P399; Cheung F, 2006, BMC GENOMICS, V7, DOI 10.1186/1471-2164-7-272; Cheung F, 2008, BMC GENOMICS, V9, DOI 10.1186/1471-2164-9-542; Conant GC, 2003, NAT GENET, V34, P264, DOI 10.1038/ng1181; Crooks JA, 2002, OIKOS, V97, P153, DOI 10.1034/j.1600-0706.2002.970201.x; DOOLITTLE RF, 1994, TRENDS BIOCHEM SCI, V19, P15, DOI 10.1016/0968-0004(94)90167-8; Droege M, 2008, J BIOTECHNOL, V136, P3, DOI 10.1016/j.jbiotec.2008.03.021; Duke NC, 1998, GLOBAL ECOL BIOGEOGR, V7, P27, DOI 10.2307/2997695; EDDY J, 1996, B ECOL SOC AM, V77, P109; Ellison AM, 1999, GLOBAL ECOL BIOGEOGR, V8, P95, DOI 10.1046/j.1466-822X.1999.00126.x; Emrich SJ, 2007, GENOME RES, V17, P69, DOI 10.1101/gr.5145806; Feller IC, 2003, BIOGEOCHEMISTRY, V62, P145, DOI 10.1023/A:1021166010892; FLOWERS TJ, 1977, ANNU REV PLANT PHYS, V28, P89, DOI 10.1146/annurev.pp.28.060177.000513; Garcia-Reyero N, 2008, J FISH BIOL, V72, P2354, DOI 10.1111/j.1095-8649.2008.01904.x; Gharizadeh B, 2006, ELECTROPHORESIS, V27, P3042, DOI 10.1002/elpa.200500834; Huse SM, 2007, GENOME BIOL, V8, DOI 10.1186/gb-2007-8-7-r143; Inan G, 2004, PLANT PHYSIOL, V135, P1718, DOI 10.1104/pp.104.041723; Kandil FE, 2004, TREES-STRUCT FUNCT, V18, P518, DOI 10.1007/s00468-004-0337-8; Karrenberg S, 2008, CURR OPIN PLANT BIOL, V11, P156, DOI 10.1016/j.pbi.2008.01.004; Liang S, 2008, CHINESE SCI BULL, V53, P1708, DOI 10.1007/s11434-008-0221-9; Mavromatis K, 2007, NAT METHODS, V4, P495, DOI 10.1038/nmeth1043; Melzer S, 2008, NAT GENET, V40, P1489, DOI 10.1038/ng.253; Miyama M, 2007, PLANT SCI, V172, P948, DOI 10.1016/j.plantsci.2007.01.004; Miyama M, 2006, PLANT SCI, V171, P234, DOI 10.1016/j.plantsci.2006.03.015; Novaes E, 2008, BMC GENOMICS, V9, DOI 10.1186/1471-2164-9-312; Paliyavuth C, 2004, AQUAT BOT, V78, P349, DOI 10.1016/j.aquabot.2004.01.002; Parani M, 1998, THEOR APPL GENET, V97, P617, DOI 10.1007/s001220050937; Phillippy AM, 2008, GENOME BIOL, V9, DOI 10.1186/gb-2008-9-3-r55; Plaziat Jean-Claude, 2001, Wetlands Ecology and Management, V9, P161, DOI 10.1023/A:1011118204434; Pop M, 2008, TRENDS GENET, V24, P142, DOI 10.1016/j.tig.2007.12.006; POPP M, 1984, Z PFLANZENPHYSIOL, V113, P395; Poroyko V, 2005, PLANT PHYSIOL, V138, P1700, DOI 10.1104/pp.104.057638; Proffitt CE, 2005, WETLANDS, V25, P326, DOI 10.1672/9; Reusch TBH, 2007, MOL ECOL, V16, P3973, DOI 10.1111/j.1365-294X.2007.03454.x; Rieder MJ, 1998, NUCLEIC ACIDS RES, V26, P967, DOI 10.1093/nar/26.4.967; Saenger P, 2002, MANGROVE ECOLOGY SIL; SCHOLANDER PF, 1962, PLANT PHYSIOL, V37, P722, DOI 10.1104/pp.37.6.722; Soltis DE, 2000, BOT J LINN SOC, V133, P381, DOI 10.1006/bojl.2000.0380; Stiller JW, 2003, J PHYCOL, V39, P95, DOI 10.1046/j.1529-8817.2003.02070.x; Swaminathan K, 2007, BMC GENOMICS, V8, DOI 10.1186/1471-2164-8-132; Thompson JD, 1997, NUCLEIC ACIDS RES, V25, P4876, DOI 10.1093/nar/25.24.4876; Tomlinson P. B., 1986, BOT MANGROVES; Torres TT, 2008, GENOME RES, V18, P172, DOI 10.1101/gr.6984908; Vera JC, 2008, MOL ECOL, V17, P1636, DOI 10.1111/j.1365-294X.2008.03666.x; Weber APM, 2007, PLANT PHYSIOL, V144, P32, DOI 10.1104/pp.107.096677; Wicker T, 2006, BMC GENOMICS, V7, DOI 10.1186/1471-2164-7-275; WOOLLER MJ, 2004, J QUATERNARY SCI, V19, P1
Cited Reference Count 53
Times Cited 57
Total Times Cited Count (WoS, BCI, and CSCD) 63
Publisher City MALDEN
Publisher Address COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA
ISSN 0028-646X
29-Character Source Abbreviation NEW PHYTOL
ISO Source Abbreviation New Phytol.
Year Published 2009
Volume 183
Issue 3
Beginning Page 764
Ending Page 775
Digital Object Identifier (DOI) 10.1111/j.1469-8137.2009.02913.x
Page Count 12
Web of Science Category Plant Sciences
Subject Category Plant Sciences
Document Delivery Number 472AK
Unique Article Identifier WOS:000268100800024
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