Nov 2019 Updates – Reference genomes
Pilot species information: https://www.genomicsforaustralianplants.com/reference-genome/
1) Reference genome – Acacia
- Extraction | Completed
- Optimising HMW extractions for long read sequencing | Time frame: 7 months
- Sequencing approaches and Data availability | In progress
- Illumina short read | AGRF | Available Jul 2019
- MinION long read | AGRF | Available Aug 2019
- PromethION long read | AGRF | Available Sep 2019
- 10X | AGRF | Available Sep 2019
- Scaffolding – Hi-C | Currently investigating possibility of generating Hi-C library and sequence data to scaffold contigs into chromosome scale assemblies.
- RNA sequencing will be performed on freshly collected leaf, bud, and flower material in order to assemble transcripts for genome annotation.
- Bioinformatics | In progress
- QC, trimming, k-mer analyses (genome size and heterozygosity), read correction have been run.
- Preliminary testing of assembly software to determine effectiveness of tools, compute, and parameters completed.
- Preliminary workflows being tested on NCI to put together our long reads from Nanopore sequencing (MinION and PromethION), and polishing using short Illumina reads; complementary analyses being run at RBGV.
2) Reference genome – Telopea
- Extraction | Ongoing
- Optimising extractions for long read sequencing. This has been very challenging, extractions have been on-going since Jan.
- Currently trying a different extraction method on a sample of Alloxylon (closest relative of Telopea). If it works well, the extraction method will used on the waratah individual
- Sequencing approaches and Data availability | In progress
- 10X – Sample submitted, passed QC, sequencing in progress
- Hi-C – Currently monitoring the mountain waratahs. Once new leaves are available, these will be flash freeze for Hi-C.
3) Reference genome – Areocleome
- Plant growth and Extraction | Ongoing
- Plant growth has been slow. Initially trial with live plants – died due to cold weather. Currently growing plants in tissue culture.
- Currently optimising extractions for long read sequencing.
- Planned sequencing approaches
- Long read – Oxford Nanopore or PacBio
- Scaffolding – Hi-C