| Analysis Name | Eragrostis tef Salk_teff_dabbi_3.0 Assembly & Annotation |
| Sequencing technology | PacBio RSII; Illumina HiSeq |
| Assembly method | Canu v. 1.4; 3D-DNA v. 180922 |
| Release Date | 2022-08-03 |
VanBuren R, Man Wai C, Wang X, Pardo J, Yocca AE, Wang H, Chaluvadi SR, Han G, Bryant D, Edger PP, Messing J, Sorrells ME, Mockler TC, Bennetzen JL, Michael TP. Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff. Nat Commun. 2020 Feb 14;11(1):884. doi: 10.1038/s41467-020-14724-z.
AbstractTeff (Eragrostis tef) is a cornerstone of food security in the Horn of Africa, where it is prized for stress resilience, grain nutrition, and market value. Here, we report a chromosome-scale assembly of allotetraploid teff (variety Dabbi) and patterns of subgenome dynamics. The teff genome contains two complete sets of homoeologous chromosomes, with most genes maintaining as syntenic gene pairs. TE analysis allows us to estimate that the teff polyploidy event occurred ~1.1 million years ago (mya) and that the two subgenomes diverged ~5.0 mya. Despite this divergence, we detect no large-scale structural rearrangements, homoeologous exchanges, or biased gene loss, in contrast to many other allopolyploids. The two teff subgenomes have partitioned their ancestral functions based on divergent expression across a diverse expression atlas. Together, these genomic resources will be useful for accelerating breeding of this underutilized grain crop and for fundamental insights into polyploid genome evolution.
Assembly statistics
| Genome size | 575.1 Mb |
| Total ungapped length | 574.4 Mb |
| Number of chromosomes | 20 |
| Number of scaffolds | 874 |
| Scaffold N50 | 27.1 Mb |
| Scaffold L50 | 9 |
| Number of contigs | 1,541 |
| Contig N50 | 1.4 Mb |
| Contig L50 | 121 |
| GC percent | 45.5 |
| Genome coverage | 73.0x |
| Assembly level | Chromosome |
The Eragrostis tef Salk_teff_dabbi_3.0 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | Eragrostis_tef.faa.gz |
The Eragrostis tef Salk_teff_dabbi_3.0 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | Eragrostis_tef.gff.gz |
| CDS sequences (FASTA file) | Et_cds.fa.gz |
| Protein sequences (FASTA file) | Et_pep.fa.gz |
Functional annotation for the Eragrostis tef Salk_teff_dabbi_3.0 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Eragrostis_tef.Pfam.tsv.gz |
Summary
| Query | Chromosome | Size(bp) | Coordinates | tBLASTn Hit | tBLASTn %ID | Domain |
| DUF247I-S1Ψ | 2A | 35425885 | 16547076-16548158 | Pvirgatum | 64 | DUF247 |
| DUF247I-S2 | 2B | 30633641 | 13934951-13936612 | Pvirgatum | 65 | DUF247 |
| DUF247II-SΨ | 2A | 35425885 | 16556070-16556345 | Pvirgatum | 62 | DUF247 |
| HPS10-S1 | 2A | 35425885 | 16548994-16549123,16549350-16549459 | Pvirgatum | 60 | - |
| HPS10-S2 | 2B | 30633641 | 13941664-13941826,13941942-13942048 | Pvirgatum | 59 | - |
| DUF247I-Z1 | 7A | 26459500 | 2638547-2640109 | LpZDUF247-I_chromosome2 | 58 | DUF247 |
| DUF247I-Z2 | 7B | 23383462 | 2307379-2308995 | LpZDUF247-I_chromosome2 | 58 | DUF247 |
| DUF247II-Z1 | 7A | 26459500 | 2634780-2636447 | Shybrid | 57 | DUF247 |
| DUF247II-Z2Ψ | 7B | 23383462 | 2302636-2303658 | Efulvus | 63 | DUF247 |
| HPS10-Z1 | 7A | 26459500 | 2637270-2637370,2637456-2637606 | LpsZ_contig4538 | 59 | - |
| HPS10-Z2 | 7B | 23383462 | 22621978-22622084,22622151-22622289 | LpsZ_chromosome2 | 59 | - |
Nucleotide
Protein