TriticeaeExpDB

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Tissue and Stage

Project ID	Title	Related Publication	Sequencing Type	Description	Notes
PRJEB35461	Secale cereale L. inbred line 'Lo7' Illumina RNA-Seq and PacBio Sequel reads	Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential	Sequel	This study contains the Illumina RNA-Seq and the PacBio Sequel reads for the submission of the Secale cereale L. inbred line 'Lo7' genome assembly paper Rabanus-Wallace et. al	Flag leaf, Complete Spike, Whole aerial organs
PRJNA540081	Thinopyrum elongatum Genome Sequencing and Assembly	Horizontal gene transfer of Fhb7 from fungus underlies Fusarium head blight resistance in wheat.	Illumina HiSeq 4000	Thinopyrum elongatum (syn. Agropyron elongatum or Lophopyrum elongatum) is a grass of the Triticeae family with a diploid E genome (2n = 2X = 14) that is native to Eurasia and which is thought to be the basic genome donor for various tetra-, hexa-, and even deca-ploid species in the Thinopyrum genus. We sequenced and assembled the genome of Th. elongatum using a combination of technologies, which resulted in a 4.63 Gb assembly with a contig N50 size of 2.15 Mb and a scaffold N50 size of 73.24 Mb.	Leaf
PRJEB12520	Seeds of a rye (Secale cereale L.) self-fertile inbred line 7415 with and without Bs were grown under long-day conditions (16 h light, 22°C day/16°C night), and all experimental materials from different tissues were collected during this period. Illumina paired-end RNAseq reads obtained from generative (anther) and vegetative (root and leave) tissues with (4B) and without (0B) B chromosomes.	Rye B chromosomes encode a functional Argonaute-like protein with in vitro slicer activities similar to its A chromosome paralog	Illumina HiSeq 2000	Comparative transcriptome analysis (RNAseq) confirmed that B chromosomes of rye (Secale cereal) contribute to the transcriptome. In total, 1,954 and 1,218 B-derived transcripts with an open reading frame were expressed in generative and vegetative tissues, respectively. Beside B derived transposable element transcripts a high percentage of short transcripts without detectable similarity to known proteins and gene fragments from A chromosomes were found (41.2% and 54.4% in generative and vegetative tissue, respectively) suggesting an ongoing gene erosion process. 15.8% of the transcripts that derived from anthers and 20.3% that derived from vegetative tissues showed similarities with potential protein coding genes from the Bs. Thus, we conclude that rye B chromosomes carry functional genes and B- derived transcripts provide an additional layer of genetic complexity in combination with their related A-located genes.	Anther, root and leave
PRJDB2278	Construction of a rye (Secale cereale L.) reference transcriptome	Identification and characterization of rye genes not expressed in allohexaploid triticale.	454 GS FLX Titanium	As a test case for building a complete reference transcriptome for a eukaryotic species with a large un-sequenced genome, more than 5.6 million high quality 454 pyrosequencing cDNA reads from rye (Secale cereale) were generated and assembled. A novel post de novo assembly sequence analysis program, BLAST-based post-assembly process (BbPAP), was designed to eliminate redundancy, maximize contig length, and correct erroneous assemblies by recognizing and eliminating alternatively spliced transcripts and error-rich termini regions while integrating EST and genome sequence information from related species. A rye reference transcriptome consisting of 56,091 sequences with an average median length value of 1,301 nucleotides was obtained. It includes 41,567 coding loci, covering more than 90% of the hypothetical gene loci. More than 80% of the identified genes have complete coding regions representing the most complete gene index available in any Triticeae species. In addition, we identified that approximately 20% of the genes had putative alternative splicing sites. A minimum expansion of rye genes of 17% was calculated based upon comparison with orthologous single copy genes from Brachypodium. 4,461 novel rye or Triticeae-specific transcripts were identified and half of these were subjected to purification selection thus indicating their important functions in the formation of the Triticeae species. none provided	Head, Crown, anther, pistil, stem, root, seedling

Stress and Treatment

Project ID	Title	Related Publication	Sequencing Type	Description	Notes
PRJNA564622	Rye Sequence Data	Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential	Illumina HiSeq 2500	A reference quality assembly of the rye genome along with annotated gene features, miRNAs, and repetitive elements is used to investigate Triticeae evolution, focusing on the influence of transposable elements (TEs) and gross structural variations (CVs) to determine genome architectural features.	Temperature
PRJNA427159	Transcriptomics study of three Blumeria graminis formae speciales	Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen.	Illumina HiSeq 2000	We analyzed the gene expression and especially the expression of effector candidate genes in wheat and rye powdery mildews. Overall design: mRNA of wheat, rye and triticale infected with 3 wheat, 2 rye and 2 triticale powdery mildew isolates, respectively. 3 biological replicates of each infection were collected 48 hours after infection.	B.g. secalis

Mutant and Experimental Genetic Population

Project ID	Title	Related Publication	Sequencing Type	Description	Notes
PRJNA371298	Analysis of mutations disrupting the formation of the wax layer in rye, and assessment of their impact on morphological, biochemical and physiological traits	The GAMYB gene in rye: sequence, polymorphisms, map location, allele-specific markers, and relationship with α-amylase activity	Illumina HiSeq 1500	"The main aim of the grant is to analyze four mutations disrupting the formation of a correct wax layer on the green parts of rye plants. Basic research material consists of four pairs of near-isogenic lines (NIL). Three pairs are different in terms of another recessive mutation. It is planned to detect studied genes, identify their sequences, compare expression levels and determine the location in the genome. In addition, an attempt will be made to determine whether the studied genes show pleiotropic effects by analyzing the differences of various morphological and physiological traits. The extent to which the wax cover provides protection against water loss in optimum conditions and reduced soil moisture will be assessed.Four pairs of NIL will be characterized using molecular, biochemical and physiological methods. Molecular studies will include the analysis of mRNA performed using RNA-Seq method and q-PCR. Three different mapping populations will be characterized using GBS technique and different markers based on PCR (STS, SCAR, RAPD, ISSR, SSR). Mapping procedure will be carried out using JoinMap package. The sequence analysis of selected markers is planned by a capillary sequencer (Sanger method) and based on NGS methods.Some physiological characteristics will be evaluated, such as gas exchange, water balance, assimilation pigments content (chlorophyll and carotenoids) and photochemical activity of PSII. Gas exchange parameters will be measured with the use of gas analyzer and porometer. Pigments content will be determined by a spectrophotometric method and chlorophyll a fluorescence kinetics will be assessed by a fluorymetric method. Water balance will be evaluated on the basis of the ratio of the relative water content (RWC) and water saturation deficit ratio (WSD). The water impairment test and the weight of cut-off leaves test will be carried out (RWL).The chemical composition and amount of wax will be determined using capillary gas chromatography (GC) and ultra-high performance liquid chromatography (UHPLC).Comparing to other crops, i.e. barley (Hordeum vulgare) and wheat (Triticum aestivum), rye (Secale cereale) is not well known in terms of its nucleotide sequences. The resulting data will supply the complete set of mRNA sequences of four pairs of inbred lines, expanding the knowledge about rye transcriptome and providing information about the new SNP and SSR markers.By characterizing the three genes involved in the control of wax biosynthesis, our research will contribute to a better understanding of the molecular mechanism of this complex substance biosynthesis in plants. The mapping results will complement the knowledge on the genetic base of a waxy coat formation on the leaves, stems and spikes."	GAMYB