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The genome sequencing of Sitopsis species provide insights into its contribution to the B subgenome in Triticum aestivum

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Triticum aestivum Aegilops speltoides Triticum dicoccoides Aegilops longissima Aegilops bicornis Amblyopyrum muticum Aegilops searsii Aegilops sharonensis

PROVIDER: GSE197593 | GEO | 2023/08/22

REPOSITORIES: GEO

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The genome sequencing of Sitopsis species provide insights into its contribution to the B subgenome in Triticum aestivum [WES]

Project description:To reveal the origin of the wheat B sub-genome, we performed the whole genome sequencing of sitopsis species. Besides, we also conducted the RNA seq of Ae.speltoides and hexaploid wheat Chinese Spring.

2023-08-22 | GSE197464 | GEO

The genome sequencing of Sitopsis species provide insights into its contribution to the B subgenome in Triticum aestivum [RNA-seq]

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The genome sequencing of Sitopsis species provide insights into its contribution to the B subgenome in Triticum aestivum

Project description:The genome sequencing of Sitopsis species provide insights into its contribution to the B subgenome in Triticum aestivum

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The genome sequencing of Sitopsis species provide insights into its contribution to the B subgenome in Triticum aestivum [WES]

Project description:The genome sequencing of Sitopsis species provide insights into its contribution to the B subgenome in Triticum aestivum [WES]

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The genome sequencing of Sitopsis species provide insights into its contribution to the B subgenome in Triticum aestivum [RNA-seq]

Project description:The genome sequencing of Sitopsis species provide insights into its contribution to the B subgenome in Triticum aestivum [RNA-seq]

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Genome sequence of the progenitor of wheat A subgenome Triticum urartu.

Project description:Triticum urartu (diploid, AA) is the progenitor of the A subgenome of tetraploid (Triticum turgidum, AABB) and hexaploid (Triticum aestivum, AABBDD) wheat1,2. Genomic studies of T. urartu have been useful for investigating the structure, function and evolution of polyploid wheat genomes. Here we report the generation of a high-quality genome sequence of T. urartu by combining bacterial artificial chromosome (BAC)-by-BAC sequencing, single molecule real-time whole-genome shotgun sequencing 3 , linked reads and optical mapping4,5. We assembled seven chromosome-scale pseudomolecules and identified protein-coding genes, and we suggest a model for the evolution of T. urartu chromosomes. Comparative analyses with genomes of other grasses showed gene loss and amplification in the numbers of transposable elements in the T. urartu genome. Population genomics analysis of 147 T. urartu accessions from across the Fertile Crescent showed clustering of three groups, with differences in altitude and biostress, such as powdery mildew disease. The T. urartu genome assembly provides a valuable resource for studying genetic variation in wheat and related grasses, and promises to facilitate the discovery of genes that could be useful for wheat improvement.

| S-EPMC6784869 | biostudies-literature

Whole-genome resequencing of the wheat A subgenome progenitor Triticum urartu provides insights into its demographic history and geographic adaptation.

Project description:Triticum urartu is the progenitor of the A subgenome in tetraploid and hexaploid wheat. Uncovering the landscape of genetic variations in T. urartu will help us understand the evolutionary and polyploid characteristics of wheat. Here, we investigated the population genomics of T. urartu by genome-wide sequencing of 59 representative accessions collected around the world. A total of 42.2 million high-quality single-nucleotide polymorphisms and 3 million insertions and deletions were obtained by mapping reads to the reference genome. The ancient T. urartu population experienced a significant reduction in effective population size (Ne) from ∼3 000 000 to ∼140 000 and subsequently split into eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations during the Younger Dryas period. A map of allelic drift paths displayed splits and mixtures between different geographic groups, and a strong genetic drift towards hexaploid wheat was also observed, indicating that the direct donor of the A subgenome originated from northwestern Syria. Genetic changes were revealed between the eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations in genes orthologous to those regulating plant development and stress responses. A genome-wide association study identified two single-nucleotide polymorphisms in the exonic regions of the SEMI-DWARF 37 ortholog that corresponded to the different T. urartu ecotype groups. Our study provides novel insights into the origin and genetic legacy of the A subgenome in polyploid wheat and contributes a gene repertoire for genomics-enabled improvements in wheat breeding.

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proteome sequencing of Triticum aestivum L

Project description:The 15 DAP and 20 DAP endosperm samples from WT and lgp1 seeds were used for tandem mass tag (TMT) proteasome analysis. Three biological replicates were used for each genotype

2021-08-01 | PXD027683 |

High-throughput sequencing of small RNAs in Triticum aestivum

Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Triticum aestivum tissues (including leaves and spiklets infected with Fusarium and control). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the genome under study.

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Subgenome chromosome walking in wheat: a 450-kb physical contig in Triticum monococcum L. spans the Lr10 resistance locus in hexaploid wheat (Triticum aestivum L.).

Project description:For many agronomically important plant genes, only their position on a genetic map is known. In the absence of an efficient transposon tagging system, such genes have to be isolated by map-based cloning. In bread wheat Triticum aestivum, the genome is hexaploid, has a size of 1.6 x 10(10) bp, and contains more than 80% of repetitive sequences. So far, this genome complexity has not allowed chromosome walking and positional cloning. Here, we demonstrate that chromosome walking using bacterial artificial chromosome (BAC) clones is possible in the diploid wheat Triticum monococcum (A(m) genome). BAC end sequences were mostly repetitive and could not be used for the first walking step. New probes corresponding to rare low-copy sequences were efficiently identified by low-pass DNA sequencing of the BACs. Two walking steps resulted in a physical contig of 450 kb on chromosome 1A(m)S. Genetic mapping of the probes derived from the BAC contig demonstrated perfect colinearity between the physical map of T. monococcum and the genetic map of bread wheat on chromosome 1AS. The contig genetically spans the Lr10 leaf rust disease resistance locus in bread wheat, with 0.13 centimorgans corresponding to 300 kb between the closest flanking markers. Comparison of the genetic to physical distances has shown large variations within 350 kb of the contig. The physical contig can now be used for the isolation of the orthologous regions in bread wheat. Thus, subgenome chromosome walking in wheat can produce large physical contigs and saturate genomic regions to support positional cloning.

| S-EPMC27242 | biostudies-literature

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