Laboratories

Molecular systematics laboratory

The laboratory is located at the National Herbarium of NSW on the Sydney Gardens site. The laboratory opened in 1982 as a general laboratory with facilities for plant histology, chromosome analysis, and general laboratory techniques. Molecular systematic work commenced in 1991. The laboratory was enlarged and upgraded in 1996 and is now used primarily for research on phylogenetic and population studies based on DNA sequencing and the use of molecular markers.

Within the Science and Public Programs Branch of the Royal Botanic Gardens & Domain Trust, the Laboratory supports researchers working in the fields of Plant Diversity research and Evolutionary Ecology research.

The lab is equipped for

Extraction and storage of DNA from plant tissue
Gel electrophoresis and digital documentation
PCR amplification of DNA
E. coli cloning of target DNA segments
DNA fingerprinting principally using microsatellite markers
DNA sequencing and genotyping (in collaboration with external facilities)
Analysis of DNA sequences including the reconstruction of phylogenetic trees

A full list of users and projects is available in the current Plant Sciences Annual Report.

Our team

Carolyn Connelly (Molecular Laboratory Coordinator, Senior Technical Officer)
Dr Adam Marchant (Senior Technical Officer)

Staff performing molecular research within the Molecular Systematics Laboratory

Margaret Heslewood (Scientific Officer)
Dr Hannah McPherson (Scientific Officer)
Katie Thurlby (Technical Officer)
Dr Marlien van der Merwe (Scientific Officer)

Students and honoraries performing molecular research within the Molecular Systematics Laboratory

Scientific visitors

Permission must be sought from the Manager Plant Diversity to utilise the Herbarium Laboratory. Additionally, please make arrangements well in advance with the Laboratory Manager as a laboratory safety induction must be completed prior to commencing any lab work.

Molecular Laboratory 2010-2011

Carolyn Connelly - Molecular Laboratory Coordinator

The Laboratory currently supports approximately 20 researchers in Plant Diversity and Evolutionary Ecology research. The molecular data obtained in the laboratory is used for taxonomic projects and describing broader geographic patterns from plant population studies.

Carolyn Connelly took on a new role as the acting Laboratory Manager in September. Two current focus areas are rationalising storage and safety. Storage, curation and retrieval of plant tissue and genomic DNA samples held in the laboratory freezers are being reviewed.

Scientific volunteers - curation of the frozen tissue collection: January saw the commencement of a new project for scientific volunteers; to curate the valuable frozen preserved leaf material collected for DNA research. Principally this involves sorting dried leaf material from silica gel. Initially, samples were collected directly into plastic bags containing silica to dry them in the field. Meticulous sorting is required to separate the samples from the silica as the silica needs regular replacement. Samples are repackaged into envelopes then stored over fresh silica gel. The first volunteer, Daria Sosna, a student at USYD repackaged samples collected by Niko Strieber during her PhD studies in 2001. Curated samples are planned to be databased, linked in the Herbarium database to voucher specimens.

New Research Projects

Climatic gradients in Waratahs (Telopea; Proteaceae): From August 2010, Paul Rymer with Cathy Offord, Chris Allen, Katie Thurlby, Peter Weston and Maurizio Rossetto worked to determine the plastic and adaptive response to climatic gradients in Waratahs. This work integrates field, glasshouse and laboratory experiments with molecular analyses (nuclear microsatellites and RNA sequencing). The relative importance of plastic and adaptive responses has direct implications for population resilience to future climate scenarios. In February, Paul (now at University of Western Sydney, Hawkesbury) continued the collaborative research as an Honorary Research Associate (HRA).

Evolutionary history of Helicia (Proteaceae): Sarah Fayed (UTAS) visited from January to March, learning molecular laboratory techniques whilst commencing the molecular systematics component of her PhD project on the interesting evolutionary history of Helicia, the only genus of tropical Proteaceae to speciate and spread extensively and rapidly.

Systematics of the Australian Utricularia (Lentibulariaceae): Richard Jobson commenced work in the laboratory in February. He will be sequencing chloroplast markers trnL-F and rps16, with particular emphasis on subgenus Polypompholyx. A robust phylogenetic hypothesis will provide a framework for understanding the evolutionary and biogeographic history of this lineage. In addition, using sequence and microsatellite data, Richard will also examine phylogeographic patterns and taxonomic limits in the diverse Utricularia dichotoma complex.

Matt Renner commenced a three year ABRS funded Post Doctorate looking at the systematics and phylogeny of bryophytes: Australasian Radula (Radulaceae; Jungermanniopsida).

Completed Projects

A phylogeny of the Australian Lauraceae: Marlien van der Merwe, Paul Rymer and Katie Thurlby worked on assembling a nuclear gene phylogeny of the Australian Lauraceae with focus on the Cryptocarya group. The resultant partial RPBii gene phylogeny includes over 130 sequences representing over 75 species. Katie and Marlien also finalised the cpDNA phylogeny of the Lauraceae. Over 90% of the Australian woody Lauraceae are now included in the cpDNA phylogeny.

Australian Lomatia (Proteaceae): Emma McIntosh (USYD) carried out an Honours project titled 'Promiscuous Proteaceae: Natural hybridisation between Australian Lomatia species'. The research work will be presented in a poster at the IBC in Melbourne.

Technical Officer, Katie Thurlby departed in May after three and a half years in the molecular laboratory. Initially her research work was on Syzygium for an Honours Degree and employed part-time on Telopea population studies. On completion of Honours she assisted with various projects in Evolutionary Ecology.

Ongoing Projects

Australian Restionaceae: Barbara Briggs and Adam Marchant continued studies, developing a more comprehensively sampled data-set of chloroplast gene sequences for subfamily Leptocarpoideae. Analyses of the data-set will assist in determining an appropriate classification of the genera.

Project Camellia (Theaceae): George Orel (Honorary Research Associate), Anthony Curry (Richmond College of TAFE), Adam Marchant and Peter Wilson continue to conduct a multi-disciplinary study on material collected in Viet Nam, Cambodia and Laos including morphological analyses, molecular assessment and environmental appraisals to facilitate the publication of taxonomic papers and conference presentations.

Bicentenary Plant Diversity Program: In July 2010 Hannah McPherson, Paul Rymer and Katie Thurlby prepared DNA samples of 14 rainforest species from 11 different plant families to send to Southern Cross University for sequencing on the Solexa Illumina Next Generation Sequencing (NGS) platform. Thirteen samples were successfully sequenced in either multiplexed or individual runs. For eight of these there is data from the Sydney region and Northern NSW.

Hannah McPherson, Marlien van der Merwe and Paul Rymer have been analysing the data using CLC Genomics Workbench on the new high end PCs. They have constructed whole chloroplast sequences for the eight rainforest species occurring in two different geographic areas and are beginning to explore the data for areas of variation for use in a landscape-level study of rainforest diversity and phylogeography.

Hannah McPherson, Katie Thurlby, Carolyn Connelly and two students on student placement from the Australian Catholic University, Nick Weston and Juelian Siow, prepared approximately 2500 leaf samples for DNA extraction at AGRF in South Australia. The samples comprise population samples from more than 100 rainforest plant species from three distinct geographic areas: Dorrigo, Nightcap and the Border Ranges in Northern NSW. DNA will be used to explore phylogeographic patterns and the signal of landscape-level responses to the climatic cycles of the Quaternary.

Continuing Students

Endymion Cooper has conducted research on the phylogeny and biogeography of family Lepidoziaceae subfamily Lepidozioideae and a revision of Lepidozia and Telaranea. He has completed the sequencing component of his PhD project and will be submitting his thesis later this year. The first chapter of the thesis has been published in Molecular Phylogenetics and Evolution.

Rohan Mellick has conducted research comparing and contrasting molecular and fossil data in Podocarpus elatus, and is currently writing a PhD thesis.

Margaret Heslewood has conducted research on the historical biogeography and phylogeography of the family Cunoniaceae (Oxalidales) in Australasia, and is also currently writing a PhD thesis.

New Equipment

Two new high end computers are now housed on level 3 of the Herbarium. Each machine has a 64 bit dual processor and 48GB of RAM. CLC Genomics Workbench and Geneious have been installed on one machine and will primarily be for processing information from sequence data generated by next generation sequencing. The other has various analysis software installed and is available for analysis of large or complex datasets that would be time-consuming on the regular PCs. (IT budget)
May - replacement of the laboratory refrigerator, due to ongoing equipment breakdown.
June - purchase of a dedicated PCR workstation for RNA research work. Equipment used for RNA work has to be completely free of (contaminating) DNA.
Also new into the laboratory is a microplate mixer, purchased to ensure the solutions prepared for DNA amplification in a PCR plate are mixed effectively, increasing the success rate of these reactions.

Horticulture laboratories

Situated at the Australian Botanic Garden, Mount Annan, the horticultural research facility focuses on the ex situ conservation of rare and threatened species. The research laboratory was established in 1989 with a tissue culture laboratory the dominant design feature.

Tissue culture laboratory

The tissue culture laboratory is used for maintaining parental material in vitro, bulking up of commercial lines and providing a support function for the Mount Annan Botanic Garden�s nursery and the needs of our other Gardens. In addition the laboratory is used to develop protocols for species found to be difficult to vegetatively propagate and/or germinate from seed. The tissue culture laboratory plays an essential role in assisting the NSW Seedbank meet its conservation objectives.

The research area is divided into clean and dirty laboratories with a walk-in controlled environment room, allowing for the high standard of cleanliness required for tissue culture sterility.

Our team

Dr Cathy Offord (Manager Horticultural Research)
John Siemon (Science Facilities Coordinator)
John Silk (Technical Officer)
Amanda Rollason (Horticulturist)

NSW Seedbank

In 1999 NSW Treasury provided capital funds for the redevelopment of the NSW Seedbank facility. This redevelopment included a seed drying room, walk-in coolroom and freezer, seed testing room and additional office space, making it one of the best seedbanks in Australia and the major repository for NSW threatened species. The storage of NSW threatened species is considered to be part of the Royal Botanic Gardens & Domain Trusts' core role.

The aim of the NSW Seedbank is to collect and store a genetically representative samples of seed from endangered and threatened species or populations of NSW flora. The seedbank facilities have been designed for the storage of orthodox species. For this reason the priorities will initially focus on orthodox species for which there is some knowledge of seed germination, i.e. in the plant families Fabaceae and Myrtaceae. This will allow the establishment and development of operational procedures.

Our team

Peter Cuneo (Manager - Natural Heritage)
Richard Johnstone (Seedbank Officer)
Graeme Errington (Seedbank Assistant)
Leah Seed (Seed Technology Officer)

Click here to find out about the role of the NSW Seedbank.

Plant Pathology laboratory

The Plant Pathology Laboratory is located in the Plant Pathology and Mycology Centre within the Central Depot of the Royal Botanic Garden, Sydney site. It services the essential functions of the Plant Disease Diagnostic Unit and the Plant Pathology Research Program within the Royal Botanic Gardens & Domain Trust Science and Public Programs Branch. These functions include plant disease diagnosis, plant pathogen detection and isolation, fungal identification, growth of fungal cultures, storage of fungal specimens and analysis of fungal DNA. The Laboratory is divided into four sub-laboratories: General Laboratory, Molecular Laboratory, Mycological Laboratory and Herbarium, and Diagnostic and Imaging Laboratory.

Current equipment includes

Light microscope (Olympus SZH10 stereo microscope) with camera attachment
Olympus BH2 with fluorescent attachment and camera attachment
Two laminar flow cabinets, 2 autoclaves, fungal culture and growth cabinets and shelves, -80^oC freezer
Equipment for extraction of DNA from fungal or plant tissues, agarose gel electrophoresis and gel digital photography, PCR DNA amplification, refrigerators and freezers