Triticum turgidum Assembly and Gene Annotation

About Triticum turgidum

Durum wheat with a total production of about 35 million tons is the 10th most important crops worldwide. It is an integral component of the Mediterranean diet and one of the historical foods that followed the birth of civilization, likely to be one of the first domesticated crops in the Fertile Crescent. Durum is a tetraploid wheat with a genome of about 12 Gb, domesticated from wild emmer in the Fertile Crescent about 10,000 years ago. Further, it is an integral component of the Mediterranean diet and it is the historical food that followed the birth of civilization in the Fertile Crescent. From here it expanded to Europe, Africa, Asia, and the Americas, and it is today cultivated across the globe. The domestication process and the subsequent breeding activity have selected the modern durum wheat fixing the typical domestication traits (e.g. brittle rachis, naked seeds and threshability), agronomic traits (e.g. short straw and disease resistances) as well as specific pasta quality traits (grain hardness, pigment content, protein content).[1]

Assembly

The Svevo genome sequence was assembled de novo using protocols previously used for wild Emmer Wheat [2]. After sequencing and assembly, the scaffolds (length of the shortest contig needed to cover 50% of the genome (N50) = 6.0 megabases (Mb)) were ordered and oriented using the Svevo × Zavitan genetic map [3]. Thereafter, chromosome conformation capture sequencing (Hi-C) resulted in a set of pseudomolecules (9.96 Gb) corresponding to the 14 chromosomes of the genome and one group of unassigned scaffolds (499 Mb). The pseudomolecules encompass 95.3% of the assembled sequences and have 90% of the scaffolds oriented [1].

Annotation

Annotation of the Svevo genome led to the identification of 66,559 high confidence (HC) genes, 90.5% of which exhibited detectable evidence of expression in at least one of the 21 RNA-seq datasets listed here.

Ensembl Plants display the HC genes alongside 303,404 low confidence genes (LC) marked as alternative genes on the website.

Variation

Variation data was loaded from these variation sets:

35K: 60391 SNPs

820K: 1496076 SNPs

90K: 182507 SNPs

TabW280K: 241969 SNPs

References

1. Durum wheat genome highlights past domestication signatures and future improvement targets.
   Marco Maccaferri, Neil S. Harris, Sven O. Twardziok, Raj K. Pasam, Heidrun Gundlach, Manuel Spannagl, Danara Ormanbekova, Thomas Lux, Verena M. Prade, Sara G. Milner et al. 2019. Nature Genetics. 51:885895.
2. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication.
   Raz Avni, Moran Nave, Omer Barad, Kobi Baruch, Sven O. Twardziok, Heidrun Gundlach, Iago Hale, Martin Mascher, Manuel Spannagl, Krystalee Wiebe et al. 2017. Science. 357:93-97.
3. Ultra-dense genetic map of durum wheat wild emmer wheat developed using the 90K iSelect SNP genotyping assay.
   Raz Avni, Moran Nave, Tamar Eilam, Hanan Sela, Chingiz Alekperov, Zvi Peleg, Jan Dvorak, Abraham Korol, Assaf Distelfeld. 2014. Molecular Breeding. 34:15491562.

More information

General information about this species can be found in Wikipedia.