DNA sequencing for better identification of fungi

In the past, fungi were identified using morphology – what they look like. This included their shape, colour and size visible to the human eye, as well as features revealed by a microscope. Classifications were based on the characters that humans found the most useful to measure and observe. Fungi are also morphologically simple, meaning that classifications were based on only a few characters.

Now, DNA sequencing has completely changed the game. Suddenly fungal taxonomists have an almost unlimited number of characters to use to develop their classifications. Mycologists around the world are collectively developing new classifications that incorporate new knowledge about relationships provided by DNA sequences. Users of the classifications – such as plant pathologists, ecologists and biosecurity regulators – increasingly use DNA sequences rather than microscopes to identify their specimens.

One consequence of the switch from morphology to sequences is that most lists of fungal pathogens thought to be ‘present in New Zealand’ are based on the old, morphology-based classifications and identification methods. The question arises, can the old records be trusted? The ‘present in New Zealand’ lists need to be validated and accurate because they are the basis of managing New Zealand’s biosecurity. Whether or not a species already occurs here is the vital first step in assessing biosecurity risk at the border.

Manaaki Whenua is in a key position to undertake this validation by sequencing our collections of microorganisms and fungi that support the ‘present in New Zealand’ statements. We have now carried out validation studies on several groups of very important soil-borne plant/crop pathogens that were notoriously difficult to identify using morphology. These include the genera Fusarium (which causes, among other serious diseases, fusarium wilt in many vegetable crops and crown rot in cereal crops); Phoma (which causes black rot and leaf spot diseases in vegetable crops); and Verticillium (the cause of verticillium wilt in over 350 species of vegetables, fruit trees, flowers, field crops, and shade or forest trees).