Eragrostis curvula Assembly and Gene Annotation

About Eragrostis curvula

Weeping lovegrass (Eragrostis curvula) is a C4 perennial grass member of the Poaceae family, Chloridoideae subfamily. The E. curvula complex has a basic chromosome number of x = 10 and includes cytotypes with different ploidy levels (from 2x to 8x) that may undergo sexual reproduction and facultative or obligate apomixis. Its drought tolerance and capacity to grow in sandy soils make it highly valued, especially for cattle feed in semiarid regions.

Assembly

The cultivar selected was a sexual diploid (620 Mb haplotype) originated from in vitro culture of inflorescences of the apomictic cv. Tanganyika (2n=4x=40). The sequencing was done with the PacBio Sequel platform. After a preliminary assembly one Dovetail Chicago and one Dovetail Hi-C library were added, obtaining chromosomes size contigs covering 95% of the diploid genome. The final assembly N50 was 43.41 Mb and the number of scaffolds 1,143. The final BUSCO results were 96.4% (80.3% single copy and 16.1% were duplicated).

Annotation

Gene annotation was performed using an ab initio prediction algorithm combined with data from ESTs and RNA-seq databases from different tissues of E. curvula and from proteins of related species. After three iterations of the MAKER software, near 56K gene models were obtained with an average size of 1,424 bp and 93.4% of the complete BUSCO genes.

Repeats were annotated with the Ensembl Genomes repeat feature pipeline. There are: 703004 Low complexity (Dust) features, covering 18 Mb (3.0% of the genome); 279122 RepeatMasker features (with the REdat library), covering 102 Mb (16.9% of the genome); 5846 RepeatMasker features (with the RepBase library), covering 1 Mb (0.1% of the genome); 242601 Tandem repeats (TRF) features, covering 26 Mb (4.3% of the genome); Repeat Detector repeats length 224Mb (37.2% of the genome).

References

1. A high-quality genome of Eragrostis curvula grass provides insights into Poaceae evolution and supports new strategies to enhance forage quality.
   Carballo J, Santos BACM, Zappacosta D. et al.. 2019. Scientific Reports. 9: 10250.

Picture credit: Forest & Kim Starr CC BY 3.0

More information

General information about this species can be found in Wikipedia.