Breakthrough in hybrid species science
Massey University scientists have discovered a universal law that explains how hybrid species survive and thrive.Computational biologist Professor Murray Cox and molecular biologist Dr Austen Ganley led the research that analysed what happens when a new species is formed. Their findings were published today in the Public Library of Science online journal,Genetics.“When two very different species suddenly merge together, a new species is created instantaneously that contains two different sets of machinery, or RNA (Ribonucleic acid) as it’s known,” Professor Cox says. “Some parts of this machinery won’t work together, so we asked the question, how does this hybrid survive?”
Professor Cox says hybrids are surprisingly common and can be seen in the cotton used to make bed-sheets, the wheat in bread and in New Zealand alpine plants.
His team used advanced computational biology methods to sequence and analyse hundreds of millions of RNA copies of a fungus found in grass. “This particularly fungus [epichloe endophyte] is one of the good guys,” he says. “The plant gives the fungus a place to live, and the fungus produces chemicals that kill insects that try to eat the grass. This hidden relationship is a key reason for the success of New Zealand’s multibillion dollar dairy industry.”
Professor Cox was amazed to find that the RNA levels in the grass fungus were almost identical to the patterns found in cotton – the only other hybrid species that has undergone similar analysis.
“These species are radically different, for starters, one is a plant, the other is a fungus,” he says. “Therefore we realised we had identified universal rules that dictate how gene expression has to behave in order for hybrid species to control their two sets of machinery [RNA], regardless of what exact species those hybrids are.”
These genetic rules revealed that the hybrid’s genes mimic one parent or the other. “The RNA levels showed one copy effectively gets turned off. It’s not simply an average of what its parents have. This pattern occurs in both fungi and plants — in other words, there are universal rules that control gene expression levels in hybrids across the tree of life.”
It is this final point that has generated the greatest interest in the scientific community and earned Professor Cox’s research a place in the PLOS Genetics publication.
Source: MASSEY
Citation: Cox MP, Dong T, Shen G, Dalvi Y, Scott DB, et al. (2014) An Interspecific Fungal Hybrid Reveals Cross-Kingdom Rules for Allopolyploid Gene Expression Patterns. PLoS Genet 10(3): e1004180. doi:10.1371/journal.pgen.1004180
Author Summary
Organisms are complex biological systems that must continue to function even as their genomes evolve. While evolution is usually gradual, the formation of new species by the hybridization of different parents—allopolyploidization—occurs nearly instantaneously. A key question is what happens to expression of the two parental gene copies following genome merger. To determine this, we focused on a fungal allopolyploid from a group that dominates many of the world's pastoral economies. To investigate the fate of gene expression in this system, we developed a novel pipeline to assign high throughput RNA sequence reads to the two parental gene copies, thus allowing quantification of expression. We found transcriptional responses to be predominantly conservative: most gene copies either inherit parental expression patterns, or if differentially expressed in the parents, that difference is lost in the hybrid. Moreover, we identified an extraordinary level of concordance in the fate of genome-wide allopolyploid gene expression with that seen in cotton. The very different nature of these two allopolyploids suggests that there is a set of universal rules for the transcriptional response to genome merger. We propose a mechanistic model whereby this conserved response reflects similarities in mutational processes that underlie gene regulatory evolution.
Abstract
Polyploidy, a state in which the chromosome complement has undergone an increase, is a major force in evolution. Understanding the consequences of polyploidy has received much attention, and allopolyploids, which result from the union of two different parental genomes, are of particular interest because they must overcome a suite of biological responses to this merger, known as “genome shock.” A key question is what happens to gene expression of the two gene copies following allopolyploidization, but until recently the tools to answer this question on a genome-wide basis were lacking. Here we utilize high throughput transcriptome sequencing to produce the first genome-wide picture of gene expression response to allopolyploidy in fungi. A novel pipeline for assigning sequence reads to the gene copies was used to quantify their expression in a fungal allopolyploid. We find that the transcriptional response to allopolyploidy is predominantly conservative: both copies of most genes are retained; over half the genes inherit parental gene expression patterns; and parental differential expression is often lost in the allopolyploid. Strikingly, the patterns of gene expression change are highly concordant with the genome-wide expression results of a cotton allopolyploid. The very different nature of these two allopolyploids implies a conserved, eukaryote-wide transcriptional response to genome merger. We provide evidence that the transcriptional responses we observe are mostly driven by intrinsic differences between the regulatory systems in the parent species, and from this propose a mechanistic model in which the cross-kingdom conservation in transcriptional response reflects conservation of the mutational processes underlying eukaryotic gene regulatory evolution. This work provides a platform to develop a universal understanding of gene expression response to allopolyploidy and suggests that allopolyploids are an exceptional system to investigate gene regulatory changes that have evolved in the parental species prior to allopolyploidization.
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