Feb 2020 updates

Conservation genomics update

The conservation genomics Expression of Interest (EOI) has been drafted and is currently under review. This will be circulated in the coming weeks.

Phylogenomics update

  1. Pilot – We are organising the reagents and logistics for the phylogenomics pilot.
  2. Stage 1 of the GAP Australian Angiosperm Tree of Life (AAToL) Expression of Interest is still open. Please submit your responses by the closing date on 13 March 2020. More details: here.

Reference genome – Acacia

  1. Data: llumina short read | MinION long read | PromethION long read | 10X
  2. Scaffolding – Hi-C | Currently investigating the possibility of generating Hi-C library and sequence data to scaffold contigs into chromosome scale assemblies.
  3. Bioinformatics update:
    • 10X data been assembled using SuperNova (both in-house at RBGV, and on Flashlite).
    • The Supernova assembly has been scaffolded using ARCS.
    • Combined MinION and PromethION data, together with the Illumina short read data, is currently being assembled using a hybrid approach with the software MaSuRCA, on Flashlite.
    • Combined MinION and PromethION data are currently being assembled using the software Canu, on the RBGV server.
    • The long-read Promethion data has been assembled with Flye.

Reference genome – Telopea/Waratah

  1. Data: 10X data and MinION is now available at the Data Portal.
  2. Scaffolding – Hi-C | Our attempt with a phase genomics kit failed, possibly due to the age of the leaves.  Unfortunately, the plant has perished in the bushfires. One possibility might be to perform Hi-C using a different individual from the same lineage, provided a large number of rearrangements are not expected.
  3. Bioinformatics update:
    • Initial Chromium 10 X assemblies looking quite good. We have run supernova with a few slightly different parameterizations, with N50 up to ~1.3Mb. This seems to represent a pretty good platform for building upon with long reads and Hi-C.

Reference genome – Areocleome

No updates at this stage.