Trait-directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus
Article first published online: 18 SEP 2013
© 2013 The Authors. New Phytologist © 2013 New Phytologist Trust
Volume 201, Issue 1, pages 144–154, January 2014
How to Cite
Meharg, C., Khan, B., Norton, G., Deacon, C., Johnson, D., Reinhardt, R., Huettel, B. and Meharg, A. A. (2014), Trait-directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus. New Phytologist, 201: 144–154. doi: 10.1111/nph.12491
- Issue published online: 26 NOV 2013
- Article first published online: 18 SEP 2013
- Manuscript Accepted: 12 AUG 2013
- Manuscript Received: 1 JUL 2013
- 2012. New grass phylogeny resolves deep evolutionary relationships and discobers C4 origins. New Phytologist 193: 304–312. , , , , , , , , , et al.
- 2010. Differential expression analysis for sequence count data. Genome Biology 11: R106. , .
- 2006. Enhanced arsenate reduction by a CDC25-like tyrosine phosphatase explains increased phytochelatin accumulation in arsenate-tolerant Holcus lanatus. Plant Journal 45: 917–929. , , , , .
- 2001. Molecular diversity, structure and domestication of grasses. Genetics Research Cambridge 77: 213–218. , , .
- 2013. ALFIN-LIKE 6 is involved in root hair elongation during phosphate deficiency in Arabidopsis. New Phytologist 198: 709–720. , , , .
- 2011. Signaling network in sensing phosphate availability in plants. Annual Review of Plant Biology 62: 185–206. , .
- 2008. Blast2GO: a comprehensive suite for functional analysis in plant genomics. International Journal of Plant Genomics 2008: 619832. , .
- 1999. Enzymes and other agents that enhance cell wall extensibility. Annual Review of Plant Physiology and Plant Molecular Biology 50: 391–417. .
- 2009. Phosphate signaling in Arabidopsis and Oryza sativa. Plant Science 176: 170–180. , , , , .
- 2001. Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. Annals of Botany 89: 3–10. , .
- 2012. The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency. Nature 488: 535–541. , , , , , , , , , .
- 2012. Characterization of transcriptional activation and inserted-into-gene preference of various transposable elements in the Brassica species. Molecular Biology Reports 39: 7513–7523. , , , , , , , , , .
- 2009. Root uptake regulation: a central process for NPS homeostasis in plants. Current Opinion in Plant Biology 12: 328–338. , , .
- 2010. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology Evolution 27: 221–224. , , .
- 1998. Activation of plant retrotransposons under stress conditions. Trends in Plant Science 3: 181–187. .
- 2011. To thy proteins be true: RNA editing in plants. Plant Physiology 156: 453–454. .
- 2012. Advances in plant genome sequencing. Plant Journal 70: 177–190. , .
- 2006. Morphology and response of roots of pasture species to phosphorus and nitrogen nutrition. Plant and Soil 286: 7–19. , , , .
- 2009. Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Plant Physiology 151: 2120–2132. , , , , , , , .
- 2012. Transcriptomic changes and signaling pathways induced by arsenic stress in rice roots. Plant Molecular Biology 80: 587–608. , , , , , .
- 2011. Sequencing crop genomes: approaches and applications. New Phytologist 191: 915–925. , , , , .
- 2012. Identification of RNA editing sites in cotton (Gossypium hirsutum) chloroplasts and editing events that affect secondary and three-dimensional protein structures. Genetics Molecular Research 11: 987–1001. , , , , .
- 2013. MAFFT multiple sequence alignment software version 7:improvements in performance and usability. Molecular Biology Evolution 30: 772–780. , .
- 2009. Phenome analysis in plant species using loss-of-function and gain-of-function metants. Plant Cell Physiology 50: 1215–1231. , , , , .
- 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10: R25. , , , .
- 2009. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 324: 1210–1213. , , , , , , , , .
- 2009. Arsenite efflux is not enhanced in the arsenate-tolerant phenotype of Holcus lanatus. New Phytologist 183: 340–348. , , , , .
- 1992. The genetics of arsenate tolerance in Yorkshire Fog, Holcus lanatus L. Heredity 69: 325–335. , , .
- 2012. Transposable element small RNAs as regulators of gene expression. Trends in Genetics 28: 616–623. , .
- 1993. Pre–adaptation of Holcus lanatus L. to arsenate tolerance. Evolution 47: 313–316. , , .
- 1992a. Suppression of the phosphate uptake system: a mechanism of arsenate tolerance in Holcus lanatus L. Journal of Experimental Botany 43: 519–524. , .
- 1992b. Genetic correlation between arsenate tolerance and the rate of arsenate and phosphate uptake in Holcus lanatus L. Heredity 69: 336–341. , .
- 1992c. Polymorphism and physiology of arsenate tolerance in Holcus lanatus L. from an uncontaminated site. Plant and Soil 146: 219–225. , .
- 2011. Epigenetic contribution to stress adaptation in plants. Current Opinion in Plant Biology 14: 267–274. , .
- 2012. Non-model organisms. Nature Methods 9: 37. .
- 1996. A polymorphism for phosphate/arsenate tolerance in Holcus lanatus L.: is there a correlation with edaphic or environmental factors? Heredity 77: 509–517. , , , .
- 2001. Silencing of transposable elements in plants. Trends in Plant Science 6: 527–534. , .
- 2013. An RNA-Seq transcriptome analysis of othophosphate-deficient white lupin reveals novel insights into phosphorus acclimation in plants. Plant Physiology 161: 705–724. , , , , , , , , , et al.
- 2012. Accurate identification of human Alu and non-Alu RNA editing sites. Nature Methods 9: 579–581. , , , , , .
- 2002. The Bioperl Toolkit: perl modules for life sciences. Genome Research 12: 1611–1618. , , , , , , , , , et al.
- 2012. The cutting crew - ribonucleases are key players in the control of plastid gene expression. Journal of Experimental Botany 63: 1663–1673. , .
- 2010. Transcriptome of the dessication-tolerant resurrection plant Craterostigma plantagineum. Plant Journal 63: 212–228. , , , , , , , , .
- 2012. Multiple organellar RNA editing factor (MORF) family proteins are required for RNA editing in mitochondria and plastids of plants. Proceedings of the National Academy of Sciences, USA 109: 5104–5109. , , , , , .
- The International Brachypodium Initiative. 2010. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763–768.
- 2009. Chloroplast ribonucleoprotein CP31A is required for editing and stability of specific chloroplast mRNAs. Proceedings of the National Academy of Sciences, USA 7106: 6002–6007. , , , , , , , , , .
- 2012. Systems and trans-system level analysis identifies conserved iron deficiency responses in the plant lineage. Plant Cell 24: 3921–3948. , , , , , , , , , .
- 2013. Improvement of phosphorus efficiency in rice on the basis of understanding phosphate signaling and homeostasis. Current Opinion in Plant Biology 16: 205–212. , , , .
- 2012. Pathways of arsenic uptake and efflux. Current Topics in Membranes 69: 325–358. , , , .
- 2009. Arsenic uptake and metabolism in plants. New Phytologist 181: 777–794. , , , .