Introducing the session "Recovering DNA"

Recovering DNA Barcodes from Degraded Genetic Material in Natural History Collections.

Natural history collections are invaluable resources of reference material, allowing field collected specimens to be linked to the established taxonomic framework.  Even older specimens of dubious appearance might contain useful genetic material, which obviously says a lot about the increase in the value of natural history collections that derive from ongoing improvements in technology.  However, there seems to be two main impediments to obtaining useful DNA sequence from this resource:  1. achieving successful PCR amplification; and 2. ensuring that sequences are derived from the correct specimen rather than a contaminating source, and are not chimeric or the result of post mortem DNA template damage. 

The focus of this session is the challenges that we all face in recovering DNA sequence from natural history reference collections.  Some of these challenges might be mostly specific to a particular set of organisms, and others are considered more widely.  The speakers in this session come from a variety of fields but are united by the same common goal of incorporating high quality barcodes from reference material.  Thus, the hope is that there will be much cross-fertilisation between fields in terms of general methodology, tips and tricks, and ultimately the general acceptance of minimum standards for publications. 

The presenters will speak on a wide variety of organisms, including fungi, plants, marine algae, insects, crustaceans and small vertebrates; relating experiences with standard and modified barcode primer sets; Sanger sequencing as well as next generation DNA sequencing approaches; and their efforts for quality assessment and database tools that can track barcoding success.  While the stated focus of the session is methodological, the resulting applications of the upcoming presentations are also diverse, from species identification and the estimation of levels of biodiversity, to the tracking of invasive species in time and space. 

In my own work, I have spent the past three years sequencing DNA from a variety of sample types from small terrestrial vertebrates at the Australian Centre for Ancient DNA using approaches developed in the field of ancient DNA.  This work has been undertaken in the context of taxonomic resolution rather than barcoding and species discovery, however the laboratory processes and considerations are obviously very similar.  Targeted sequences of sufficient length and quality were recovered from bone, teeth, feathers, dried skin, scales, muscle and fur, and in another unrelated metagenomics project, dried herbarium specimens.  Contamination levels were extremely low and the proportion of sequences recovered was dependent on small but important adjustments to standard protocols for DNA extraction and Sanger sequencing.

I think the variety of experiences that will be presented in the session will contain something for everyone - those working in relatively small labs designed for standard molecular analysis in botany and zoology, to those running or making use of larger facilities with higher throughput capacity.  There is good potential that relatively simple improvements and reorganisation to protocols and processes, as gleaned from this upcoming session, could improve dramatically the quality and rates of sequencing success for barcoding projects. 

At the end of the second half of the session will be a period of around 15 mins where everyone can participate in a general discussion on the theme of the session, or ask additional questions to presenters.  Come and listen to the talks and have your say. And enjoy our wonderful city of Adelaide during your visit - Welcome!

Kyle Armstrong, The University of Adelaide