Trait‐directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus

Abstract

SummaryThe aim of this study was to characterize the transcriptome of a balanced polymorphism, under the regulation of a single gene, for phosphate fertilizer responsiveness/arsenate tolerance in wild grass Holcus lanatus genotypes screened from the same habitat.De novo transcriptome sequencing, RNAseq (RNA sequencing) and single nucleotide polymorphism (SNP) calling were conducted on RNA extracted from H. lanatus. Roche 454 sequencing data were assembled into c. 22 000 isotigs, and paired-end Illumina reads for phosphorus-starved (PÀ) and phosphorus-treated (P+) genovars of tolerant (T) and nontolerant (N) phenotypes were mapped to this reference transcriptome.Heatmaps of the gene expression data showed strong clustering of each P+/PÀ treated genovar, as well as clustering by N/T phenotype. Statistical analysis identified 87 isotigs to be significantly differentially expressed between N and T phenotypes and 258 between P+ and PÀ treated plants. SNPs and transcript expression that systematically differed between N and T phenotypes had regulatory function, namely proteases, kinases and ribonuclear RNAbinding protein and transposable elements.A single gene for arsenate tolerance led to distinct phenotype transcriptomes and SNP profiles, with large differences in upstream post-translational and post-transcriptional regulatory genes rather than in genes directly involved in P nutrition transport and metabolism per se.

Stem rust resistance in wheat is suppressed by a subunit of the mediator complex

“…We accessed publicly available leaf RNAseq data for eight grass species (Supplementary Table 13) 82,83 , performed de novo transcriptome assembly using Trinity 84 (version r20140717) using the parameters "--min_kmer_cov 2 --normalize_max_read_cov 20 -trimmomatic", and identified Med15 homologs using BLAST. PRANK (v.140603) and RAxML (v8.2.9) were used for codon-based alignment and phylogenetic tree construction, respectively [85][86][87] . Default parameters were used for PRANK and RAxML parameters include the GTRCAT model using rice Med15 as an outgroup.…”

Effects of Phosphorus on In-vitro Seed Germination and Seedling Growth of Brassica rapa L. in Arsenic Condition

“…Accumulation of As mainly occurs in the root system in plants, and in the aboveground organs to a lesser degree (Stoeva et al, 2005;Khan et al, 2013;Meharg et al, 2014). As interrupts the biochemical function of cells and severely impedes different plant metabolic processes including transpiration, respiration, photosynthesis etc., by reacting with proteins and enzymes which culminates in stunted plant growth (Meharg and Hartley-Whitaker, 2002).…”

“…On the other hand, phosphorus (P) -an essential plant nutrient that regulates cellular energy transfer, respiration, and photosynthesis (Marschner, 1995) -is a chemical analogue of As (Raghothama, 1999;Khan et al, 2013;Meharg et al, 2014). Therefore, in plant uptake of nutrients, P contests As due to their chemical similarity (Meharg and Macnair, 1992ab;Lee et al, 2003).…”

Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

“…All assembled transcripts were initially BLASTed against plant-refseq, protozoa-refseq, fungi-refseq and the Rhizophagus irregularis protein database, and annotated transcripts were merged with a previously published H . lanatus 454 transcriptome assembly [ 38 ]. Duplicated annotations were removed based on retention of the transcript with the best BLAST score for each primary accession ID.…”

“…lanatus colonizes a wide range of soils with strongly contrasting abiotic stresses including acid bogs, calcareous soils, saline soils and metal(loid)-contaminated mine spoils [ 33 ]. Such an adaptive range implies selection for different ecotypes, involving genetic changes under differential selection pressures [ 34 , 35 ], and genetic changes associated with edaphic stress adaptation and plasticity have been observed in this species [ 36 – 38 ]. H .…”