Chinese Spring genome near-complete assembly (CS-CAU)

Chinese Spring (CS) is a landrace from China and a crucial cultivar used for genetic studies of wheat worldwide. Since the release of the CS-IWGSC genome assembly, it has been the most widely used reference genome for wheat worldwide and has greatly promoted various forms of basic and applied research in wheat. However, there are numerous gaps in the globally used wheat Chinese Spring (CS) genome. Here, we generated a 14.46 Gb near-completed assembly of the CS genome (CS-CAU), with a contig N50 over 266 Mb and an overall base accuracy of 99.9963%, which fills almost all gaps in CS-IWGSC genome assembly. The CS-CAU genome will serve as a valuable resource for the research and breeding of wheat as well as its related species.

Chinese Spring genome near-complete assembly and annotation

First, A total of 4,100.33 Gb (283.56× coverage) of ultralong Oxford Nanopore Technology (ONT) data, 420.60 Gb (29.01× coverage) of PacBio HiFi data, and 928.82 Gb (64.06× coverage) of MGI next-generation sequencing (NGS) data were generated for assembly of the wheat CS genome. The final wheat CS near-complete genome (CS-CAU) consisted of 14.46 Gb, with a contig N50 of 266.44 Mb. The assembled sizes of the A, B, and D subgenomes were 5.01, 5.37 and 4.07 Gb, respectively. The assemblies of four chromosomes (chr1D, chr3D, chr4D and chr5D) of the D subgenome are gap-free, including chr1D and chr5D, which are fully resolved from telomere to telomere. Among the 290 remaining gaps, 26, 257 and 7 were harbored in the A, B and D subgenomes, respectively. Except for the centromere of chr1B, which has a gap associated with superlong GAA repeat arrays, the centromeric sequences of all of the remaining 20 chromosomes were completely assembled.

Gene annotation of the CS assembly was performed using PASA and Mikado with RNA-seq evidence and GeMoMa with protein homology evidence, complemented by ab initio predictions using Fgenesh3. In total, 274,018 protein-coding genes were annotated, including 151,405 HC genes, and 59,180 HC genes were newly annotated here compared with the currently widely used annotation of the CS genome (the IWGSC v1.0 annotation).