All data is publicly available on NCBI (PRJNA343128). Below are the specific links for each datasets used in this project:
- Data used for genome assembly (WGS):
- Paired-end (180 bp insert size) SRR4249670
- Mate-pair (9 Kb insert size) SRR4249671
- Mate-pair (11 Kb insert size) SRR4249672)
- RNA-seq data used for annotation and DE (single-end):
- anther 3.0 mm (rep1 and re2): SRR12490853, SRR12490852
- anther 1.5 mm (rep1 and rep2): SRR4249671, SRR12490854
- External RNA-seq data used for annotation (paired-end):
- Young Leaf: SRR3233339
- miRNA-seq datasets
- 4.0 mm Anther, SRR12490849
- 3.0 mm Anther, SRR12490850
- 0.5 mm Anther,SRR12490851
- sRNA datasets
- Leaf sRNA, SRR12490857
- Pistil sRNA, SRR12490858
- PARE datasets
- Leaf PARE, SRR12490856
- Pistil PARE, SRR12490859
- Anther PARE, SRR12490860
The genome assembly and annotations are also available under the same BioProject and can be accessed using the links below (not active yet):
- The shared Box folder contains assembly, annotations and related files.
- These files are also available in CyVerse Data Commons, at this location
- Project/collaboration related questions: Matt Hufford, Toby Kellogg, Blake Meyers, Lynn Clark
- Assembly, annotation, datasets, general queries regarding scripts and workflows: Arun Seetharam
- Phylogenetic methods and related scripts/issues: Yunqing Yu
- PARE/sRNA/miRNA related questions and issues: Sébastien Belanger
If you use the genome or annotations or scripts from this repository in your research, please cite this publication:
Arun Seetharam†, Yunqing Yu†, Sébastien Belanger, Lynn G. Clark, Blake C. Meyers, Elizabeth A. Kellogg*, Matthew B. Hufford*.
The Streptochaeta genome and the evolution of the grasses.
Frontiers in Plant Science, vol. 12, p2165, 2021.
