What can we learn from the transcriptome of the resurrection plant Craterostigma plantagineum?
- 1.3k Downloads
The desiccation transcriptome of the resurrection plant C. plantagineum is composed of conserved protein coding transcripts, taxonomically restricted transcripts and recently evolved non-protein coding transcripts.
Research in resurrection plants has been hampered by the lack of genome sequence information, but recently introduced sequencing technologies overcome this limitation partially and provide access to the transcriptome of these plants. Transcriptome studies showed that mechanisms involved in desiccation tolerance are conserved in resurrection plants, seeds and pollen. The accumulation of protective molecules such as sugars and LEA proteins are major components in desiccation tolerance. Leaf folding, chloroplast protection and protection during rehydration must involve specific molecular mechanisms, but the basis of such mechanisms is mainly unknown. The study of regulatory regions of a desiccation-induced C. plantagineum gene suggests that cis-regulatory elements may be responsible for expression variations in desiccation tolerant and non-desiccation-tolerant plants. The analysis of the C. plantagineum transcriptome also revealed that part of it is composed of taxonomically restricted genes (TRGs) and non-protein coding RNAs (ncRNAs). TRGs are known to code for new traits required for the adaptation of organisms to particular environmental conditions. Thus the study of TRGs from resurrection plants should reveal species-specific functions related to the desiccation tolerance phenotype. Non-protein coding RNAs can regulate gene expression at epigenetic, transcriptional and post-transcriptional level and thus these RNAs may be key players in the rewiring of regulatory networks of desiccation-related genes in C. plantagineum.
KeywordsDesiccation tolerance Linderniaceae Non-protein coding RNAs Resurrection plants Taxonomically restricted genes
Craterostigma desiccation tolerant 1
Late embryogenesis abundant
Non-protein coding RNAs
Taxonomically restricted genes
- Burke MJ (1986) The glassy state and survival of anhydrous biological systems. In: Leopold AC (ed) Membranes, metabolism, and dry organisms. Cornell University Press, Ithaca, NY, pp 358–363Google Scholar
- Carrieri C, Cimatti L, Biagioli M, Beugnet A, Zucchelli S, Fedele S, Pesce E, Ferrer I, Collavin L, Santoro C, Forrest ARR, Carninci P, Biffo S, Stupka E, Gustincich S (2012) Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature 491:454–459PubMedCrossRefGoogle Scholar
- Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, Sementchenko V, Piccolboni A, Bekiranov S, Bailey DK, Ganesh M, Ghosh S, Bell I, Gerhard DS, Gingeras TR (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308:1149–1154PubMedCrossRefGoogle Scholar
- Cushman JC, Oliver MJ (2011) Understanding vegetative desiccation tolerance using integrated functional genomics approaches within a comparative evolutionary framework. In: Lüttge U, Beck E, Bartels D (eds) Plant desiccation tolerance. Ecological Studies, vol 215. Springer, Berlin Heidelberg, pp 307–338Google Scholar
- Faghihi MA, Modarresi F, Khalil AM, Wood DE, Sahagan BG, Morgan TE, Finch CE, Laurent GS, Kenny PJ, Wahlestedt C (2008) Expression of a noncoding RNA is elevated in Alzheimer’s disease and drives rapid feed-forward regulation of β-secretase. Nat Med 14:723–730PubMedCentralPubMedCrossRefGoogle Scholar
- Farrant JM, Brandt W, Lindsey GG (2007) An overview of mechanisms of desiccation tolerance in selected angiosperm resurrection plants. Plant Stress 1:72–84Google Scholar
- Fischer E (1995) Revision of the Lindernieae (Scrophulariaceae) in Madagascar. 1. The genera Lindernia Allioni and Crepidorhopalon E. Fischer. Bulletin du Muséum National d’Histoire Naturelle, section B, Adansonia: Botanique Phytochemie Ser 4, 17:227–257Google Scholar
- Gaff DF (1989) Responses of desiccation-tolerant “resurrection” plants to water stress. In: Kreeb KH, Richter H, Hinckley TM (eds) Structural and functional responses to environmental stresses: water shortages. SPB Academic, The Hague, pp 264–311Google Scholar
- Gechev TS, Benina M, Obata T, Tohge T, Sujeeth N, Minkov I, Hille J, Temanni MR, Marriott AS, Bergstrom E, Thomas-Oates J, Antonio C, Mueller-Roeber B, Schippers JH, Fernie AR, Toneva V (2013) Molecular mechanisms of desiccation tolerance in the resurrection glacial relic Haberlea rhodopensis. Cell Mol Life Sci 70:689–709PubMedCrossRefGoogle Scholar
- Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, Khalil AM, Zuk O, Amit I, Rabani M, Attardi LD, Regev A, Lander ES, Jacks T, Rinn JL (2010) A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142:409–419PubMedCentralPubMedCrossRefGoogle Scholar
- Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermuller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316:1484–1488PubMedCrossRefGoogle Scholar
- Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, Lee CS, Flockhart RJ, Groff AF, Chow J, Johnston D, Kim GE, Spitale RC, Flynn RA, Zheng GXY, Aiyer S, Raj A, Rinn JL, Chang HY, Khavari PA (2013) Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature 493:231–235PubMedCentralPubMedCrossRefGoogle Scholar
- Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, Freier SM, Bennett CF, Sharma A, Bubulya PA, Blencowe BJ, Prasanth SG, Prasanth KV (2010) The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 39:925–938PubMedCentralPubMedCrossRefGoogle Scholar