Abstract
Triticum urartu (diploid, AA) is the progenitor of the A subgenome of tetraploid (Triticum turgidum, AABB) and hexaploid (Triticum aestivum, AABBDD) wheat1,2. Genomic studies of T. urartu have been useful for investigating the structure, function and evolution of polyploid wheat genomes. Here we report the generation of a high-quality genome sequence of T. urartu by combining bacterial artificial chromosome (BAC)-by-BAC sequencing, single molecule real-time whole-genome shotgun sequencing3, linked reads and optical mapping4,5. We assembled seven chromosome-scale pseudomolecules and identified protein-coding genes, and we suggest a model for the evolution of T. urartu chromosomes. Comparative analyses with genomes of other grasses showed gene loss and amplification in the numbers of transposable elements in the T. urartu genome. Population genomics analysis of 147 T. urartu accessions from across the Fertile Crescent showed clustering of three groups, with differences in altitude and biostress, such as powdery mildew disease. The T. urartu genome assembly provides a valuable resource for studying genetic variation in wheat and related grasses, and promises to facilitate the discovery of genes that could be useful for wheat improvement.
Highlights
Triticum urartu is the progenitor of the A subgenome of tetraploid (Triticum turgidum, AABB) and hexaploid (Triticum aestivum, AABBDD) wheat[1,2]
These results showed an earlier burst of Gypsy retrotransposition than of Copia retrotransposition in the T. urartu (Tu) genome; both bursts occurred after the divergence of the A and B genomes[11]
By comparing transcription factors in the Tu genome with those of the six sequenced grass genomes in the iTAK14 collection, including Brachypodium, rice, sorghum, maize, Aegilops tauschii (Aet)[15] and Ta7,16, we found that the number of reproductive meristem (REM) subfamily genes in the transcription factor B3 family[17] was amplified in the genomes of Tu, Aet and Triticum aestivum (Ta) (Supplementary Data 3, Extended Data Fig. 4c, Supplementary Information S1.1)
Summary
To evaluate the quality of our assembly, we compared the Tu genome to 12 previously published BAC sequences (Extended Data Fig. 2a) from the T. urartu G1812 genome downloaded from NCBI The mRNAs and ESTs of monocot species other than wheat were used as cross-species evidence; these were downloaded from NCBI and filtered to remove redundant sequences with a cutoff of 90% for both identity and coverage, which resulted in 548,604 cDNAs and 978,696 ESTs. RNA-seq data from 243 samples (2.47 Tb) of T. urartu and bread wheat were downloaded from NCBI and were assembled into contigs using SOAPdenovo-trans v1.03 (http://soap.genomics.org.cn/SOAPdenovo-Trans.html). We computationally identified gene insertions and deletions on Tu3 relative to Ta3B by combining data from B. distachyon (Bdistachyon_283_v2.1), rice (IRGSP1.0) and sorghum (http://phytozome.jgi.doe.gov/pz/portal.html) They are grass relatives of wheat that have well-sequenced and annotated genomic data.
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