How to get good fungal and bacterial identifications from GenBank sequences

Submitted by Bevan Weir on 29 October, 2014 - 21:44

ncbi logoGenBank 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The trouble is that many of the organism identifications of GenBank sequences are dubious, outdated, or just plain wrong.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.

Colletotrichum SIG meeting at IMC10

Submitted by Bevan Weir on 17 April, 2014 - 16:18

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 or Rhizobium, which name to use?

Submitted by Bevan Weir on 27 April, 2013 - 16:59

agrobacteria gall on rootAgrobacterium 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 Colletotrichum gloeosporioides species complex

Submitted by Bevan Weir on 2 September, 2012 - 14:41

Fig. 2 from the paper, types of species within the complexThe 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).

Curator of the ICMP

Submitted by Bevan Weir on 15 August, 2012 - 22:15

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.

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