Triticum turgidum Assembly and Gene Annotation

Durum wheat (DW), Triticum turgidum L. ssp. durum (Desf.) Husn., genome BBAA, is a cereal grain mainly used for pasta production and evolved from domesticated emmer wheat (DEW), T. turgidum ssp. dicoccum Thell. DEW itself derived from wild emmer wheat (WEW), T. turgidum ssp. dicoccoides Thell., in the Fertile Crescent about 10,000 years ago [1].

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 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.

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.

Statistics

Summary

Assemblysvevo, INSDC Assembly GCA_900231445, Apr 2019
Database version98.1
Base Pairs10,463,058,104
Golden Path Length10,463,058,104
Genebuild bySVEVO
Genebuild methodImport
Data sourceCREA

Gene counts

Coding genes66,559
Gene transcripts196,153

About this species