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


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


Mangroves Transcriptome Database Extremophile miRNA target sequences Small RNA 



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.


  1. Allen E, Xie Z, Gustafson AM, Carrington JC (2005) microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121:207–221CrossRefPubMedGoogle Scholar
  2. Altschul SF, Gish W, Miller W, Meyers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410PubMedGoogle Scholar
  3. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones SAM, Marshall M, Matzke M, Ruvkun G, Tuschl T (2003) A uniform system for microRNA annotation. RNA 9:277–279. doi: 10.1261/rna.2183803 CrossRefPubMedGoogle Scholar
  4. Axtell MJ, Bartel DP (2005) Antiquity of microRNAs and their targets in land plants. Plant Cell 17:1658–1673. doi: 10.1105/tpc.105.032185 CrossRefPubMedGoogle Scholar
  5. Bari R, Datt Pant B, Stitt M, Scheible W-R (2006) PHO2, microRNA399, and PHR1 define a phosphate-signaling pathway in plants. Plant Physiol 141:988–999. doi: 10.1104/pp.106.079707 CrossRefPubMedGoogle Scholar
  6. Bohnert HJ, Sheveleva E (1998) Plant stress adaptations - making metabolism move. Curr Opin Plant Biol 1:267–274CrossRefPubMedGoogle Scholar
  7. Bonnet E, Wuyts J, Rouze P, Van de Peer Y (2004) Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20:2911–2917. doi: 10.1093/bioinformatics/bth374 CrossRefPubMedGoogle Scholar
  8. Brennecke J, Stark A, Russell RB, Cohen SM (2005) Principles of microRNA-target recognition. PloS Biol 3:e85CrossRefPubMedGoogle Scholar
  9. Brodersen P, Voinnet O (2006) The diversity of RNA silencing pathways in plants. Trends Genet 22:268–280CrossRefPubMedGoogle Scholar
  10. Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY, Sieburth L, Voinnet O (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Science 320:1185–1190. doi: 10.1126/science.1159151 CrossRefPubMedGoogle Scholar
  11. Bushati N, Cohen SM (2007) microRNA functions. Annu Rev Cell Dev Biol 23:175–205. doi: 10.1146/annurev.cellbio.23.090506.123406 CrossRefPubMedGoogle Scholar
  12. Cheeseman JM, Lovelock CE (2004) Photosynthetic characteristics of dwarf and fringe Rhizophora mangle in a Belizean mangrove. Plant Cell Environ 27:769–780CrossRefGoogle Scholar
  13. Cheeseman JM, Clough BF, Carter DR, Lovelock CE, Eong OJ, Sim RG (1991) The analysis of photosynthetic performance in leaves under field conditions: a case study using Bruguiera mangroves. Photosyn Res 29:11–22Google Scholar
  14. Cushman JC, Bohnert HJ (2000) Genomic approaches to plant stress tolerance. Curr Opin Plant Biol 3:117–124CrossRefPubMedGoogle Scholar
  15. Dassanayake M, Haas JS, Bohnert HJ, Cheeseman JM (2009) Shedding light on an extremophile lifestyle through transcriptomics. New Phytol 183:764–775CrossRefPubMedGoogle Scholar
  16. Dezulian T, Remmert M, Palatnik JF, Weigel D, Huson DH (2006) Identification of plant microRNA homologs. Bioinformatics 22:359–360. doi: 10.1093/bioinformatics/bti802 CrossRefPubMedGoogle Scholar
  17. Feller IC (1995) Effects of nutrient enrichment on growth and herbivory of dwarf red mangrove (Rhizophora mangle). Ecol Monogr 65:477–505CrossRefGoogle Scholar
  18. Filipowicz W, Bhattacharyya SN, Sonenberg N (2008) Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nature Rev Genet 9:102–114CrossRefPubMedGoogle Scholar
  19. Fujii H, Chiou T-J, Lin S-I, Aung K, Zhu J-K (2005) A miRNA involved in phosphate-starvation response in Arabidopsis. Curr Biol 15:2038–2043CrossRefPubMedGoogle Scholar
  20. Fukaki H, Okushima Y, Tasaka M, Kwang WJ (2007) Auxin-mediated lateral root formation in higher plants. Int Rev Cytol 256:111–137CrossRefPubMedGoogle Scholar
  21. Griffiths-Jones S, Saini HK, Sv D, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36:D154–D158. doi: 10.1093/nar/gkm952 CrossRefPubMedGoogle Scholar
  22. Gutschick VP, BassiriRad H (2003) Extreme events as shaping physiology, ecology, and evolution of plants: toward a unified definition and evaluation of their consequences. New Phytol 160:21–42CrossRefGoogle Scholar
  23. Hogarth P (2007) The biology of mangroves and seagrasses. Oxford University Press, New YorkCrossRefGoogle Scholar
  24. Karrenberg S, Widmer A (2008) Ecologically relevant genetic variation from a non-Arabidopsis perspective. Curr Opin Plant Biol 11:156–162. doi: 10.1016/j.pbi.2008.01.004 CrossRefPubMedGoogle Scholar
  25. Kurihara Y, Takashi Y, Watanabe Y (2006) The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis. RNA 12:206–212. doi: 10.1261/rna.2146906 CrossRefPubMedGoogle Scholar
  26. Lovelock CE, Ball MC, Choat B, Engelbrecht BMJ, Holbrook NM, Feller IC (2006) Linking physiological processes with mangrove forest structure: phosphorus deficiency limits canopy development, hydraulic conductivity and photosynthetic carbon gain in dwarf Rhizophora mangle. Plant Cell Environ 29:793–802CrossRefPubMedGoogle Scholar
  27. Morin RD, Aksay G, Dolgosheina E, Ebhardt HA, Magrini V, Mardis ER, Sahinalp SC, Unrau PJ (2008) Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Res 18:571–584. doi: 10.1101/gr.6897308 CrossRefPubMedGoogle Scholar
  28. Moxon S, Jing R, Szittya G, Schwach F, Rusholme Pilcher RL, Moulton V, Dalmay T (2008) Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res 18:1602–1609. doi: 10.1101/gr.080127.108 CrossRefPubMedGoogle Scholar
  29. Osada Y, Saito R, Tomita M (1999) Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes. Bioinformatics 15:578–581CrossRefPubMedGoogle Scholar
  30. Pillai RS, Bhattacharyya SN, Filipowicz W (2007) Repression of protein synthesis by miRNAs: how many mechanisms? Trends Cell Biol 17:118–126CrossRefPubMedGoogle Scholar
  31. Rajagopalan R, Vaucheret H, Trejo J, Bartel DP (2006) A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 20:3407–3425. doi: 10.1101/gad.1476406 CrossRefPubMedGoogle Scholar
  32. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes Dev 16:1616–1626. doi: 10.1101/gad.1004402 CrossRefPubMedGoogle Scholar
  33. Rymarquis LA, Kastenmayer JP, Hüttenhofer AG, Green PJ (2008) Diamonds in the rough: mRNA-like non-coding RNAs. Trends Plant Sci 13:329–334CrossRefPubMedGoogle Scholar
  34. Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D (2005) Specific effects of microRNAs on the plant transcriptome. Dev Cell 8:517–527CrossRefPubMedGoogle Scholar
  35. Schwarzbach AE, Ricklefs RE (2001) The use of molecular data in mangrove plant research. Wetl Ecol Manag 9:205–211CrossRefGoogle Scholar
  36. Sørensen J, Loeschcke V (2007) Studying stress responses in the post-genomic era: its ecological and evolutionary role. J Bioscience 32:447–456CrossRefGoogle Scholar
  37. Subramanian S, Fu Y, Sunkar R, Barbazuk WB, Zhu J-K, Yu O (2008) Novel and nodulation-regulated microRNAs in soybean roots. BMC Genomics 9:160CrossRefPubMedGoogle Scholar
  38. Sunkar R, Chinnusamy V, Zhu J, Zhu J-K (2007) Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci 12:301–309CrossRefPubMedGoogle Scholar
  39. Sunkar R, Zhu J-K (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16:2001–2019. doi: 10.1105/tpc.104.022830 CrossRefPubMedGoogle Scholar
  40. Young JL, Bornik ZB, Marcotte ML, Charlie KN, Wagner GN, Hinch SG, Cooke SJ (2006) Integrating physiology and life history to improve fisheries management and conservation. Fish Fish 7:262–283Google Scholar
  41. Zhang BH, Pan XP, Wang QL, Cobb GP, AT A (2005) Identification and characterization of new plant microRNAs using EST analysis. Cell Res 15:336–360CrossRefPubMedGoogle Scholar
  42. Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA (2006) Conservation and divergence of plant microRNA genes. Plant J 46:243–259CrossRefPubMedGoogle Scholar
  43. Zucker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucl Acids Res 31:3406–3415. doi: 10.1093/nar/gkg595 CrossRefGoogle Scholar

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

Personalised recommendations