ICMP culture collection: M A N A A K I W H E N U A L A N D C A R E - PowerPoint PPT Presentation

P A G E 1 ICMP culture collection: M A N A A K I W H E N U A – L A N D C A R E R E S E A R C H Informatics and genomics Dr Bevan Weir , ICMP Curator & Director F e b r u ar y 1 9

P A G E 2 Host Institute of ICMP • Government Research Institute − Manaaki Whenua • Environmental Research − Greenhouse gasses T I T L E G O E S H E R E − Pest control − Soils research − Sustainable land use − Biological Systematics • Holds National Biological Collections • 40% Government funded F e b r u a r y 1 9

The ICMP culture collection • 21,000 cultures • 50:50 Fungi : Bacteria, since 1952 • Broad taxonomic diversity • Plant pathogens, ‘mushrooms’, beneficials e.g. rhizobia • Many cultures found only in NZ • Almost all bacterial plant pathogens • Database: Taxonomy, history, strain properties, GenBank links all online http://www.landcareresearch.co.nz/resources/collections/icmp

4

F e b r u ar y 1 9 M A N A A K I W H E N U A – L A N D C A R E R E S E A R C H P A G E 5

MA N A A K I W H E N U A – L A N D C A R E R E S E A R C H F e b r u a r y 1 9 P A G E 6 Biodiversity informatics PTA

P A G E 7 Biodiversity informatics • A single custom built software package for all collections − Expensive and slow to implement, but flexible and responsive to needs M A N A A K I W H E N U A – L A N D C A R E R E S E A R C H • Open data is a New Zealand government mandate − (almost) all data online and CC-BY 4.0 INT − Federated into GBIF and other platforms − All sequences in GenBank • GBIF − Publish to an IPT server weekly − Very useful for data quality metrics: geolocation and date errors − Download stats − Citable DOI datasets − Enables biodiversity science F e b r u ar y 1 9

MA N A A K I W H E N U A – L A N D C A R E R E S E A R C H F e b r u a r y 1 9 P A G E 8 Genomics

P A G E 9 Pseudomonas syringae genomes • First in-house genome November 2010 on 454 Jr M A N A A K I W H E N U A – L A N D C A R E R E S E A R C H − Psa disease of kiwifruit in New Zealand, effector genes • Recently sequenced with D. Guttman 391 ICMP P. syringae genomes (in press) − P. syringae species complex is subdivided into primary (agricultural) and secondary (environmental) − inter-phylogroup recombination is rare − This level of genetic cohesion and the shared plant-associated niche argues for considering the primary phylogroups as a true biological species. F e b r u ar y 1 9

1 0 Leotiomycetes phylogenetic classification • Leotiomycetes are ecologically diverse fungi, including mycorrhizas, endophytes, pathogens, and saprobes • Higher level classification based on morphologically defined taxa • Several known useful genes but hard to design working primers, no need with full genomes • Tree based on 3,156 genes from 51 selected genomes, 10 new ICMP genomes (in press) • A framework for enabling future taxonomically targeted studies using deliberate specimen selection

1 1 Epicoccum secondary metabolites • Secondary metabolites do interesting things • Epicoccum red pigment has anti fungal activity • Custom genome annotation pipelines for these biosynthetic gene clusters • Supports recently described Epicoccum species • Informs biodiscovery of new biological compounds

Our Land, Our Future Our Land, Our Future Tō tātou whenua, mō āpōpō Tō tātou whenua, mō āpōpō