Nov 2019 Updates – Reference genomes

Pilot species information:

1) Reference genome – Acacia

  • Extraction | Completed
    1. Optimising HMW extractions for long read sequencing | Time frame: 7 months
  • Sequencing approaches and Data availability | In progress
    1. Illumina short read | AGRF | Available Jul 2019
    2. MinION long read | AGRF | Available Aug 2019
    3. PromethION long read | AGRF | Available Sep 2019
    4. 10X | AGRF | Available Sep 2019   
    5. Scaffolding – Hi-C | Currently investigating possibility of generating Hi-C library and sequence data to scaffold contigs into chromosome scale assemblies.
    6. RNA sequencing will be performed on freshly collected leaf, bud, and flower material in order to assemble transcripts for genome annotation.
  • Bioinformatics | In progress
    1. QC, trimming, k-mer analyses (genome size and heterozygosity), read correction have been run.
    2. Preliminary testing of assembly software to determine effectiveness of tools, compute, and parameters completed.
    3. 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
    1. Optimising extractions for long read sequencing. This has been very challenging, extractions have been on-going since Jan.
    2. 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
    1. 10X – Sample submitted, passed QC, sequencing in progress
    2. 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
    1. Plant growth has been slow. Initially trial with live plants – died due to cold weather. Currently growing plants in tissue culture.
    2. Currently optimising extractions for long read sequencing.   

  • Planned sequencing approaches
    1. Long read – Oxford Nanopore or PacBio
    2. Scaffolding – Hi-C