NZ Rhizobia

GenBank from the NCBI is an amazing and invaluable resource for DNA sequences, and combined with the searching tool BLAST it is really easy to identify your unknown gene sequence.

The trouble is that many of the organism identifications of GenBank sequences are dubious, outdated, or just plain wrong. Identifying a sequence as the wrong species is just bad science no matter what your reason, but is especially important for regulatory agencies. The problem of incorrect identifications is a self-compounding problem as these incorrect identifications are used by other sequence submitters to name their sequences.

Dear Colletotrichum community, Some of us use molecular data to untangle the systematics of the economically important genus Colletotrichum and combine this with morphological features and host preferences, while others study infection strategies and look for explanations for pathogenicity by studying genomes and gene expression or screen control measures to reduce yield loss.

Agrobacterium is a well-known genus in bacteriology and molecular biology, but research has shown that it cannot easily be separated from the Rhizobium genus, thus all Agrobacterium species should be renamed as Rhizobium species (the earlier name). However there has been some opposition to renaming Agrobacterium, in this article I explain the research and taxonomy, and suggest a solution.

The recent revisions of Colletotrichum taxonomy have been fantastic for stabilising and modernising our concepts of this important plant pathogen. However, many of the new species are very difficult to distinguish by morphology alone, and multiple gene sequences are required.

Recently Lei Cai and I set up the International Subcommission on Colletotrichum Taxonomy (ISCT) to deal with recent changes in the ICN nomenclatural code. Our main objective is to produce lists of accepted and rejected names in Colletotrichum before the next IMC fungal conference.

The major publication of my postdoc is now out — all 65 pages of it — in Studies in Mycology. In this publication we review the taxonomy of the fungus commonly known as Colletotrichum gloeosporioides, and reveal that is a complex (or species aggregate) of 22 different species. We also recognise one subspecies, and informally recognise another “species” at the f. sp. level (pending further research).

From July this year I am now the curator of the International Collection of Microorganisms from Plants (ICMP) held by Landcare Research in Auckland, New Zealand. This is recognised as a “nationally significant collection” by the NZ government, and is registered as WDCM 589.

The ICMP has a large collection of Bacteria and Fungi isolated from plants and the natural environment. Many of these are important plant pathogens.

The ITS gene region has been selected as the official gene for fungal barcoding in a recent publication of the Proceedings of the National Academy of Sciences. Myself and two colleagues from Landcare Research are co-authors of the paper (as members of the Fungal Barcoding Consortium).

I am moving this website content over to a Drupal CMS format, there will be some broken links in the interim. The new CMS will allow me to do site updates much faster and easier. Update 9 April 2012: The entire site has been converted to Drupal, let me know if something is broken.