Unknown,Transcriptomics,Genomics,Proteomics

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GBS-based identification of Triticum timopheevii introgressions in a wheat pre-breeding population

ABSTRACT: A wheat × T. timopheevii pre-breeding population was analyzed using Genotyping-by-sequencing (GBS) combined with a skim-seq pipeline to identify and characterize T. timopheevii introgressions. Read coverage analysis based on a combined T. aestivum–T. timopheevii reference genome enabled high-resolution detection of major chromosomal introgressions and copy-number changes. Sequencing reads were aligned to this combined assembly, and chromosome identity and physical position could be extracted. An \"in silico wheat × T. timopheevii hybrid\" reference genome was constructed by combining the reference sequences of the donor and the recipient species. To identify wheat-T. timopheevii introgressions, we combined the Chinese Spring reference genome (IWGSC RefSeq v1.0) (IWGSC, 2018) with the draft genome assembly of T. timopheevii (GCA_963921465.1) (Grewal et al., 2024). During the assembly process, unique identifiers were assigned to all chromosomes or pseudomolecules to maintain distinctiveness. Prior to alignment, the Illumina short reads from 42 lines, along with the previously described control genotypes, were demultiplexed and adapter-trimmed with Stacks v2.68 (Rochette et al., 2019). The processed paired-end reads were then mapped separately to the combined reference genome using HISAT v2.1.0 (Kim et el., 2019) with the – no-spliced-alignment and – no-unal parameters. Following alignment, concordant unique reads were retrieved by filtering the sequence alignment map (SAM) outputs for the YT:Z:CP and NH:i:1 tags.

INSTRUMENT(S): NextSeq 2000

ORGANISM(S): Triticum timopheevii

SUBMITTER: Balázs Kalapos

PROVIDER: E-MTAB-17094 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Aegilops tauschii is the donor of the wheat D subgenome and an important genetic resource for wheat. The assembly of Ae. tauschii acc. AL8/78 reference genome sequence Aet v4.0 was therefore an important milestone for wheat biology and breeding. The combination of the > 4.2 Gb size of the Ae. tauschii genome and > 84% of recently evolved repeated sequences make sequencing this genome challenging. Here, we report further advances in the development of the Ae. tauschii acc. AL8/78 genome sequence. Two new genome-wide optical maps were constructed and employed in the revision of pseudomolecules and estimations of gap lengths. Gaps were closed with contigs of single-molecule Pacific Biosciences reads. The number of gaps in Aet v5.0 decreased by 38,899 compared to Aet v4.0. Transposable elements and protein-coding genes were reannotated. The number of high-confidence genes was reduced from 38,886 in Aet v4.0 to 32,980 in Aet v5.0. A nonredundant set of 478 biologically important genes including many of known function in wheat was manually annotated. Sixty-one microRNA precursor and 60 phasiRNA loci were discovered, annotated, and their expression was characterized. Also characterized was expression of other small RNAs, such as hc-siRNAs and tRFs. This upgraded genome sequence will facilitate the use of Ae. tauschii in wheat breeding and biological research. Aegilops tauschii is the donor of the wheat D subgenome and an important genetic resource for wheat. The assembly of Ae. tauschii acc. AL8/78 reference genome sequence Aet v4.0 was therefore an important milestone for wheat biology and breeding. The combination of the > 4.2 Gb size of the Ae. tauschii genome and > 84% of recently evolved repeated sequences make sequencing this genome challenging. Here, we report further advances in the development of the Ae. tauschii acc. AL8/78 genome sequence. Two new genome-wide optical maps were constructed and employed in the revision of pseudomolecules and estimations of gap lengths. Gaps were closed with contigs of single-molecule Pacific Biosciences reads. The number of gaps in Aet v5.0 decreased by 38,899 compared to Aet v4.0. Transposable elements and protein-coding genes were reannotated. The number of high-confidence genes was reduced from 38,886 in Aet v4.0 to 32,980 in Aet v5.0. A nonredundant set of 478 biologically important genes including many of known function in wheat was manually annotated. Sixty-one microRNA precursor and 60 phasiRNA loci were discovered, annotated, and their expression was characterized. Also characterized was expression of other small RNAs, such as hc-siRNAs and tRFs. This upgraded genome sequence will facilitate the use of Ae. tauschii in wheat breeding and biological research. Aegilops tauschii is the donor of the wheat D subgenome and an important genetic resource for wheat. The assembly of Ae. tauschii acc. AL8/78 reference genome sequence Aet v4.0 was therefore an important milestone for wheat biology and breeding. The combination of the > 4.2 Gb size of the Ae. tauschii genome and > 84% of recently evolved repeated sequences make sequencing this genome challenging. Here, we report further advances in the development of the Ae. tauschii acc. AL8/78 genome sequence. Two new genome-wide optical maps were constructed and employed in the revision of pseudomolecules and estimations of gap lengths. Gaps were closed with contigs of single-molecule Pacific Biosciences reads. The number of gaps in Aet v5.0 decreased by 38,899 compared to Aet v4.0. Transposable elements and protein-coding genes were reannotated. The number of high-confidence genes was reduced from 38,886 in Aet v4.0 to 32,980 in Aet v5.0. A nonredundant set of 478 biologically important genes including many of known function in wheat was manually annotated. Sixty-one microRNA precursor and 60 phasiRNA loci were discovered, annotated, and their expression was characterized. Also characterized was expression of other small RNAs, such as hc-siRNAs and tRFs. This upgraded genome sequence will facilitate the use of Ae. tauschii in wheat breeding and biological research.

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GBS-based identification of Triticum timopheevii introgressions in a wheat pre-breeding population

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