Researchers have turned a decades old problem in genome sequence analysis on its head to uncover hidden information on how yeasts evolved, giving insights into evolutionary processes common to all of life.

Ascus (sexual spore-bearing cell) plus ascospores of the yeast Saccharomyces paradoxus

The National Collection of Yeast Cultures (NCYC) at the Institute of Food Research houses over 4,000 different strains of yeast. This represents a great source of biodiversity that could be exploited further for brewing and baking, as well as for new applications in biorefining, if the evolutionary relationships linking these strains were better understood.

To help understand how different yeast strains are related to one another, the researchers examined the part of their genomes that contains the instruction for making the ribosome – the molecular machinery responsible for converting genetic information into proteins. Ribosomal DNA (rDNA) is common to all cellular life, making it very useful for studying biodiversity at a number of different taxonomic levels. For example, in fungi it’s used as a DNA ‘barcode’ for species identification as well as to construct phylogenetic family trees.

Clock of Life

This sort of analysis relies on changes in the rDNA sequences that accumulate over time during evolution.  As ribosomes and their functions are so crucial, these changes were previously thought to be few in number.

“rDNA is like a molecular clock, ticking away in our cells” said Dr Ian Roberts, curator of NCYC, which is supported by the Biotechnology and Biological Sciences Research Council (BBSRC).

Identifying and contrasting changes to the rDNA that have occurred over time allows for very broad comparisons between diverse species, and even wider – ribosomal sequence was at the heart of classifying the Archaea as a separate domain of life.

However, one major problem associated with using rDNA for phylogenetic studies is the frequent presence of differences between the multiple adjacent copies of the rDNA within a single strain. These “micro-heterogeneities” , which have been observed in many species in the tree of life over the past few decades, can confuse phylogenetic analyses, which do not account for them.

However, Dr Jo Dicks and colleagues at the NCYC had a hunch that the rDNA micro-heterogeneities could be more than an inconvenience. And the Saccharomyces Genome Resequencing Project (SGRP) presented an opportunity to test this theory. Saccharomyces cerevisiae, or brewer’s/baker’s yeast, was the first eukaryote to have its genome sequenced. For some years now, the Wellcome Trust Sanger Institute has been leading a project to sequence, in greater detail than ever before, the genomes of 37 S. cerevisiae strains, as well as 26 strains of Saccharomyces paradoxus, a close wild relative.

The Norwich researchers’ strategy was to use the information from the resequencing project to characterise as much rDNA variation as they could find, also looking at parts of the rDNA usually ignored to find much greater quantities than anyone had thought existed.

“We turned the problem on its head,” said Dr Jo Dicks. “We used the very variation that had caused so many researchers headaches in creating phylogenetic trees to actually estimate those same trees.”

Over a period of four years, PhD student Claire West and NCYC researcher Dr Steve James went through the resequencing information coming out of the Sanger Institute, first by a specially created computer application and subsequently by hand, and the harder they looked the more variation they found. The problems previous researchers had had with the rDNA stemmed from the fact that they were only looking at a tiny proportion of it. By finding all, or close to all, of the variation, the NCYC team showed these problems simply went away.

Yeast culture crosses continents

“We found a signal in the noise” explains Dr Jo Dicks. “There is a huge amount of information in the rDNA, at multiple levels. For example, we were able to identify intercontinental hybridisation events among yeast strains.”

Saccharomyces cerevisiae – bakers’ yeast

The information contained in the rDNA gives more clues as to the origins of modern yeasts. Comparing the evolutionary information of S. cerevisiae and S. paradoxus shows how domestication and human activity have moulded the genome of the yeast we use in baking and brewing. The S. cerevisiae genome is like a mosaic, with its chromosomal make-up derived from ancestral strains found in different regions of the world (e.g. Africa, Europe, Malaysia and North America), reflecting human movement across the globe and how yeast has travelled with us.

The study is also providing new insights into how rDNA itself evolves, and in general the process of concerted evolution. Concerted evolution occurs when a gene is duplicated in the genome, but instead of the two copies evolving separately they influence each other and evolve together in a concerted manner. Across the whole of life, rDNA shows concerted evolution, so the new information derived from this study will be invaluable in getting a better understanding of this mechanism.

The analysis was made possible through the development of software, called TURNIP, which was designed to handle large repetitive sequences, such as the rDNA tandem repeats in Saccharomyces yeasts. The NCYC researchers are now planning further work with Dr Rob Davey, who developed the TURNIP software, and is now based at The Genome Analysis Centre (TGAC). IFR and TGAC are two institutes on the Norwich Research Park that receive strategic support from BBSRC.

Together they will analyse some of the 4,000+ yeast strains held in the collection, to look for strains with potential for use in biorefining. They will be looking for yeast strains that can ferment different carbon sources (e.g. xylose), or produce novel, valuable products, and then linking these back to the information contained within the genome. And the insights provided by this new study will help to unlock this genomic potential held in yeast’s vast biodiversity.

Reference:

Ribosomal DNA Sequence Heterogeneity Reflects Intra-Species Phylogenies and Predicts Genome Structure in Two Contrasting Yeast Species, West et al, Systematic Biology doi: 10.1093/sysbio/syu019

Find out more about the National Collection of Yeast Cultures at the IFR in this BBSRC video