Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation

Authors: WANG, LE - University Of California, Davis; ZHU, TINGTING - University Of California, Davis; RODRIGUEZ, JUAN - University Of California, Davis; DEAL, KARIN - University Of California, Davis; DUBCOVSKY, JORGE - University Of California, Davis; MCGUIRE, PATRICK - University Of California, Davis; LUX, THOMAS - Helmholtz Centre; SPANNAGL, MANUEL - Helmholtz Centre; MAYER, KLAUS - Helmholtz Centre; BALDRICH, PATRICIA - Donald Danforth Plant Science Center; MEYERS, BLAKE - University Of Missouri; Huo, Naxin; Gu, Yong; ZHOU, HONGYE - University Of Georgia; DEVOS, KATRIEN - University Of Georgia; BENNETZEN, JEFFREY - University Of Georgia; UNVER, TURGAY - Ficus Biotechnology; BUDAK, HIKMET - Montana Bioagriculture Inc; GULICK, PATRICK - Concordia University; GALIBA, GABOR - Hungarian University Of Agriculture And Life Science; KALAPOS, BALAZS - Eotvos Lorand University; NELSON, DAVID - University Of Tennessee; LI, PINGCHUAN - Agriculture And Agri-Food Canada; YOU, FRANK - Agriculture And Agri-Food Canada; MING-CHENG, LUO - University Of California, Davis; DVORAK, JAN - University Of California, Davis

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/31/2021
Publication Date: 9/13/2021
Citation: Wang, L., Zhu, T., Rodriguez, J.C., Deal, K.R., Dubcovsky, J., McGuire, P.E., Lux, T., Spannagl, M., Mayer, K.F., Baldrich, P., Meyers, B.C., Huo, N., Gu, Y.Q., Zhou, H., Devos, K.M., Bennetzen, J.L., Unver, T., Budak, H., Gulick, P.J., Galiba, G., Kalapos, B., Nelson, D.R., Li, P., You, F.M., Ming-Cheng, L., Dvorak, J. 2021. Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation. G3, Genes/Genomes/Genetics. 11(12). Article jkab325. https://doi.org/10.1093/g3journal/jkab325.
DOI: https://doi.org/10.1093/g3journal/jkab325

Interpretive Summary: Aegilops tauschii is wild species closely related to wheat species. In fact, it is the donor of the wheat D subgenome, representing an important genetic resource for wheat. Therefore, a high-quality genome sequence of the diploid Ae. tauschii is a very useful resource for wheat improvement as it possesses many important traits that can be integrated into wheat breeding program to enhance quality, yield, and resistance to disease and abiotic stresses. In this work, the genome sequence of Ae. tauschii accession AL8/78 was significantly improved using two optimal genome maps and PacBio long read sequences. The improved sequence version was used to analyze and understand its genetic information including transposable element contents and protein-coding genes etc. The improved genome sequence and updated annotation will enhance the utility of the Ae. tauschii genome sequence for wheat research and breeding.

Technical Abstract: Aegilops tauschii is the donor of the wheat D subgenome and an important genetic resource for wheat. The reference quality genome sequence Aet v4.0 for Ae. tauschii acc. AL8/78 was therefore an important milestone for wheat biology and breeding. Further advances in sequencing AL8/78 and release of Aet v5.0 sequence assembly are reported here. Two optical maps were constructed and used in the revision of pseudomolecules. Gaps were closed with Pacific Biosciences long read contigs, decreasing the gap number by 38,899. Transposable elements (TEs) and protein-coding genes were reannotated. The number of annotated high-confidence genes was reduced from 39,635 in Aet v4.0 to 32,885 in Aet v5.0. Biologically important genes, including those affecting plant phenology, grain quality, and tolerance of abiotic stresses in wheat were manually annotated in the Aet v5.0 assembly. A total of 1,921 disease resistance gene analogues (RGAs) were annotated by a dedicated pipeline. RGAs encoding nucleotide-binding site domain, receptor-like protein kinases, and receptor-like proteins were preferentially located in distal chromosome regions, whereas those encoding transmembrane coiled-coil protein RGAs were dispersed along the chromosomes. Discovery, annotation, and expression analyses of microRNA (miRNA) precursors, mature miRNAs, and phasiRNAs are reported, including miRNA target genes. Other small RNAs, such as hc-siRNAs and tRFs, were characterized. Greater sequence contiguity resulting in greater number of intact genes and TEs and revised positioning of two scaffolds will enhance the utility of the Ae. tauschii genome sequence for wheat research and breeding.