Royal Botanic Gardens Victoria Annual Report 2018-19

Genomics for Australian Plants
(GAP) Project
A large national sequencing project,
Genomics for Australian Plants, is now
underway due to a significant five-year
grant from The Ian Potter Foundation
through its Science Committee. This
exciting project—initiated by RBGV with
BioPlatforms Australia and a consortium
of researchers from Australian State
and National Herbaria, Botanic Gardens
and Universities—aims to use genomic
information (DNA) to better understand
and conserve Australia’s flora. Initial
work sees researchers sequencing the
genomes of iconic Australian plants, and
resident staff Dr Anna Syme and Dr Chris
Jackson are directly involved in producing
the pilot genome assembly of the golden
wattle, Acacia pycnantha. Future project
goals include additional whole genome
assemblies of other taxa, a phylogenomic
analysis that incorporates all Australian
plant genera, and the application of new
genomic knowledge to inform biodiversity
management.
Truffle Genome Project
Dr Teresa Lebel, Senior Mycologist, and
Dr Tom May, Senior Research Scientist
(Mycology), have been working with
Dr Chris Jackson (Research Scientist
Bioinformatics) on the truffle genome
project (Joint Genome Institute 2017–
2020 (JCI)) data that is being released by
the JGI genomic data processing pipeline.
Three truffle and two mushroom genomes
and RNA in two different lineages are
being researched, while a further eight
truffle and nine mushroom genomes are
expected to become available soon.
Dr Jackson has written a series of
functional and analytical computer
scripts that will enable comparison of the
genomes, and drive trials of various types
of analysis for genes of interest, making
it easier to investigate the data arising
from newly added genomes as they
become available. Dr Lebel met with the
project leader Professor David Catcheside
(Flinders University) in June to conduct
successful field work to collect four of the
missing taxa, and to plan further analyses
and publications.
Fungal barcoding
Dr Teresa Lebel has finalised the last
60–80 taxa to be indexed as part of the
Fungal Barcode Project (FB) carried
out with the aid of Dr Gareth Holmes
(Research Assistant), Molly Bloomfield
(University of Melbourne), and citizen
mycotaxonomists (trained through the
‘Improving Fungal Literacy’ project),
Fran Guard (QLD) and Katie Syme (WA).
Guard has described a new species of
Marasmius, currently in press, while Syme
will shortly publish another new species
Asproinocybe lyophylloides, as well as a
new record for the genus Asproinocybe
in Australasia.
Dr Lebel and Dr Naveed Davoodian, Post
Doctoral Fellow(Mycology), continue
work on the ABRS truffle grant, with the
aid of two international students, Olivia
Asher and Pooja Singh (USA), residents
for a two-month internship. The total
number of sequences achieved so
far is just over 2,300 (for truffles and
macrofungi). The next priority for both
projects is to initiate more in-depth
analyses across all genera and to publish
descriptions of the new taxa identified by
this work.
Publications and citations
The Institute for Scientific Information
(ISI) indexed journals are maintained by
Clarivate Analytics as an authoritative
source of bibliographic data used to
assess the impact of research. In 2018,
Royal Botanic Gardens Victoria staff
published 35 ISI-indexed peer-reviewed
papers and garnered 1,601 citations from
published research.
PROVIDING PLANT
INFORMATION
Soaring VicFlora usage
VicFlora, a plant biodiversity knowledge
database, provides identification tools
and information on all Victorian plants.
It allows land and natural resource
managers to detect new weed incursions,
identify new records of plant biodiversity
in natural settings, and manage assets
under their control. VicFlora is continually
updated by Science staff in response
to taxonomic revisions, as well as the
discovery of new species in Victoria.
Parallel work focuses on supplementing
the written information with photographs
of the diagnostic features of every species
referenced by the database.
VicFlora now contains more than 20,900
images covering approximately 77 per cent
of Victoria’s plant species of which 58
per cent are represented by photographs
and 19 per cent by line drawings. Work
to procure images of the remaining 23
per cent of species continues. Selected
images of diagnostic characters from
exemplar Herbarium specimens of
eucalypts were recently incorporated into
the new multi-access key to eucalypts.
Meanwhile, the resources of the
Victorian Conservation Seedbank were
used by staff and volunteers to include
photographs of seeds from more than
850 Victorian species—the first time some
of these images were publicly available.
These visible improvements to the
provision of diagnostic plant data,
coupled with effective indexing of the site
by search engines, markedly increased
traffic to the website, which grew by
41 per cent over the previous financial
year, with an 84 per cent increase in the
number of unique users. The product
continues to be well-regarded by users
and fellow botanical institutions, and
several ‘power users’ provide regular
constructive feedback, allowing the
Biodiversity Services team to rectify
issues as they arise and further engage
with the community.
ROYAL BOTANIC GARDENS BOARD VICTORIA — ANNUAL REPORT 2018–19 35