Optical maps refine the bread wheat Triticum aestivum vc. Chinese Spring genome assembly

Authors: ZHU, TINGTING - University Of California, Davis; WANG, LE - Clermont Universite, Universite D'Auvergne, Unite De Nutrition Humaine; RIMBERT, HELENE - Clermont Universite, Universite D'Auvergne, Unite De Nutrition Humaine; RODRIGUEZ, JUAN - University Of California, Davis; DEAL, KARIN - University Of California, Davis; DE OLIVEIRA, ROMAIN - Clermont Universite, Universite D'Auvergne, Unite De Nutrition Humaine; CHOULET, FREDERIC - Clermont Universite, Universite D'Auvergne, Unite De Nutrition Humaine; KEEBLE-GAGNERE, GABRIEL - Agribio, Centre For Agribioscience; TIBBITS, JOSQUIN - Agribio, Centre For Agribioscience; ROGERS, JANE - International Wheat Genome Sequencing Consortium (IWGSC); EVERSOLE, KELLYE - International Wheat Genome Sequencing Consortium (IWGSC); APPELS, RUDI - Agribio, Centre For Agribioscience; Gu, Yong; MASCHER, MARTIN - Leibniz Institute Of Plant Genetics And Crop Plant Research; DVORAK, JAN - University Of California, Davis; LUO, MING-CHENG - University Of California, Davis

Submitted to: The Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/19/2021
Publication Date: 4/22/2021
Citation: Zhu, T., Wang, L., Rimbert, H., Rodriguez, J., Deal, K.R., De Oliveira, R., Choulet, F., Keeble-Gagnere, G., Tibbits, J., Rogers, J., Eversole, K., Appels, R., Gu, Y.Q., Mascher, M., Dvorak, J., Luo, M. 2021. Optical maps refine the bread wheat Triticum aestivum vc. Chinese Spring genome assembly. The Plant Journal. 107(1):303-314. https://doi.org/10.1111/tpj.15289.
DOI: https://doi.org/10.1111/tpj.15289

Interpretive Summary: Wheat provides about one-fifth of the calories and proteins consumed by humans and is annually planted on an area larger than any other crop. The improved genome sequence and updated annotation will enhance the utility of the Ae. tauschii genome sequence for wheat research and breeding. The development of genomic resources, including a reference-quality genome sequence, is critical for accelerating genetic improvement of wheat. Due to the large size of wheat genome (16 Gb) and polyploid nature, sequencing wheat genome to generate a reference-quality genome assembly has been challenging. The first reference sequence for bread wheat cv. Chinese Spring (RefSeq v1.0) was published in 2018. Here, we report a new release of the bread wheat reference genome assembly (RefSeq v2.1). RefSeq v2.1 was generated by refining the RefSeq v1.0 using the BioNano optical mapping technology and Pacific Biosciences long reads. This improved wheat genome assembly is a major advance for applied and basic application.

Technical Abstract: Until recently, achieving a reference-quality genome sequence for bread wheat was long thought beyond the limits of genome sequencing and assembly technology, primarily due to the large genome size and > 80% repetitive sequence content. The release of the chromosome scale 14.5-Gb IWGSC RefSeq v1.0 genome sequence of bread wheat cv. Chinese Spring (CS) was, therefore, a milestone. Here, we used a direct label and stain (DLS) optical map of the CS genome together with a prior nick, label, repair, and stain (NLRS) optical map, and sequence contigs assembled with Pacific Biosciences long reads, to refine the v1.0 assembly. Inconsistencies between the sequence and maps were reconciled and gaps were closed. Gap filling and anchoring of 279 unplaced scaffolds increased the total length of pseudomolecules by 168 Mb (excluding Ns). Positions and orientations were corrected for 233 and 354 scaffolds, respectively, representing 10% of the genome sequence. The accuracy of the remaining 90% of the assembly was validated. As a result of the increased contiguity, the numbers of transposable elements (TEs) and intact TEs have increased in IWGSC RefSeq v2.1 compared with v1.0. In total, 98% of the gene models identified in v1.0 were mapped onto this new assembly through development of a dedicated approach implemented in the MAGAAT pipeline. The numbers of high-confidence genes on pseudomolecules have increased from 105,319 to 105,534. The reconciled assembly enhances the utility of the sequence for genetic mapping, comparative genomics, gene annotation and isolation, and more general studies on the biology of wheat.