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

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

ICMP culture collection: Informatics and genomics

Dr Bevan Weir, ICMP Curator & Director

F e b r u ar y 1 9 P A G E 1

F e b r u a r y 1 9 T I T L E G O E S H E R E P A G E 2

Host Institute of ICMP

• Government Research Institute

− Manaaki Whenua

• Environmental Research

− Greenhouse gasses − Pest control − Soils research − Sustainable land use − Biological Systematics

• Holds National Biological Collections
• 40% Government funded

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

F e b r u a r 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 P A G E 6

Biodiversity informatics

PTA

Biodiversity informatics

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 7

• A single custom built software package for all collections

− Expensive and slow to implement, but flexible and responsive to needs

• 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 a r 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 P A G E 8

Genomics

Pseudomonas syringae genomes

• First in-house genome November 2010
• n 454 Jr

− 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.

P A G E 9 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

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 0

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

1 1

Our Land, Our Future

Tō tātou whenua, mō āpōpō

Our Land, Our Future

Tō tātou whenua, mō āpōpō