Durum wheat (Triticum turgidum L. ssp. durum) is a major cereal and staple in the semi-arid regions of the Mediterranean Basin. It originates fr BBAA wild tetraploid domesticated in Neolithic era, later evolving domesticated emmer and then to up to 11T. turgidum subspecies, including durum wheat landraces and modern cultivars. Tetraploid wheat is the donor of the A and B genomes of hexaploid bread wheat (DDAABB), represent therefore a valuable source of genetic variability and beneficial alleles for both durum and bread wheat breeding. The reference durum wheat genome (cv Svevo) was previously sequenced an assembled using a short-read sequencing approach (Maccaferri et al., 2009), representing an important milestone for wheat genomics. In an effort to improve this release, an international consortium was established to produce a platinum-quality reference genome, that accomplish with the Contiguity, Completeness, Correctness ultimate RefSeq2.0 requirements. PACBIO HiFi long read 35X sequencing was coupled to BIONANO O Mapping, producing 259 Hybrid scaffolds (N50 = 112.3 Mb) ordered by Hi- data in a 10.4 Gb assembly. A complete and accurate gene prediction w then obtained by coupling Illumina RNASeq and Nanopore Isoseq sequencing of 30 plant samples representative of a range of tissues and development stages grown in normal growth condition and of 28 samples obtained under biotic, abiotic and nutrient stress conditions. The expression of 68,154 high confidence genes will be integrated in transcriptome atlas, together with more than 100,000 low confidence, TE-related or long no coding genes. Gene regulatory networks associated to spike and seed development are under investigation and will be associate with the chromatin accessib obtained by ATAC-Seq assays from the same samples, providing an exceptional starting point to study how enhancers, promoters, transcription facto binding cooperatively regulate gene expression during development. Finally, the preliminary results coming from the sequencing of 24 tetraploid wheat (representative of wild emmer, domesticated emmer, turgidum and turanicum subspecies, durum wheat landraces and modern varieties) pangenome will be presented. Genomic and transcriptomic data coming from this project will allow to fully explore the huge tetraploi genome diversity available for the identification of beneficial allel enhancing both durum and bread wheat resilience to abiotic stresses disease resistance.
UPGRADING THE DURUM WHEAT GENOMIC RESOURCES: FROM THE PLATINUM- QUALITY SVEVO GENOME ASSEMBLY AND ANNOTATION TO THE TETRAPLOID WHEAT PANGENOME
PIRONA R;CERIOTTI A;
2023
Abstract
Durum wheat (Triticum turgidum L. ssp. durum) is a major cereal and staple in the semi-arid regions of the Mediterranean Basin. It originates fr BBAA wild tetraploid domesticated in Neolithic era, later evolving domesticated emmer and then to up to 11T. turgidum subspecies, including durum wheat landraces and modern cultivars. Tetraploid wheat is the donor of the A and B genomes of hexaploid bread wheat (DDAABB), represent therefore a valuable source of genetic variability and beneficial alleles for both durum and bread wheat breeding. The reference durum wheat genome (cv Svevo) was previously sequenced an assembled using a short-read sequencing approach (Maccaferri et al., 2009), representing an important milestone for wheat genomics. In an effort to improve this release, an international consortium was established to produce a platinum-quality reference genome, that accomplish with the Contiguity, Completeness, Correctness ultimate RefSeq2.0 requirements. PACBIO HiFi long read 35X sequencing was coupled to BIONANO O Mapping, producing 259 Hybrid scaffolds (N50 = 112.3 Mb) ordered by Hi- data in a 10.4 Gb assembly. A complete and accurate gene prediction w then obtained by coupling Illumina RNASeq and Nanopore Isoseq sequencing of 30 plant samples representative of a range of tissues and development stages grown in normal growth condition and of 28 samples obtained under biotic, abiotic and nutrient stress conditions. The expression of 68,154 high confidence genes will be integrated in transcriptome atlas, together with more than 100,000 low confidence, TE-related or long no coding genes. Gene regulatory networks associated to spike and seed development are under investigation and will be associate with the chromatin accessib obtained by ATAC-Seq assays from the same samples, providing an exceptional starting point to study how enhancers, promoters, transcription facto binding cooperatively regulate gene expression during development. Finally, the preliminary results coming from the sequencing of 24 tetraploid wheat (representative of wild emmer, domesticated emmer, turgidum and turanicum subspecies, durum wheat landraces and modern varieties) pangenome will be presented. Genomic and transcriptomic data coming from this project will allow to fully explore the huge tetraploi genome diversity available for the identification of beneficial allel enhancing both durum and bread wheat resilience to abiotic stresses disease resistance.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
