Genomics and conservation efforts - 07/03/2021
Professors Mike Bruford and Darren Griffin, from the Universities of Cardiff and Kent, discuss the meaning of “whole genome sequence” and its revolutionary impact on conservation efforts.
Targets of the United Nations Convention on Biological Diversity (2010) required signatory countries to minimise genetic erosion and conserve genetic diversity by 2020. To advance this goal, genome sequences of domesticated and wild animals, culturally/socio-economically valuable species and cultivated plants need to be generated. The aim is therefore to the revolutionise biological and evolutionary understanding, secure biodiversity and create new societal benefits.
Although whole-genome sequencing of microorganisms like the SARS-COV2 genome enabled rapid testing and contact-tracing, it is still a relatively new concept for more complex organisms like animals. Since the first sequencing attempts of organisms such as mammals and birds from 2001-2010, the genomes of innumerable microorganisms, fungi, plants and animals have been sequenced, at least to a certain extent.
Global loss of biodiversity is increasing and even more alarming, however efforts arising from genome sequencing are promising to slow this trend. Generation of quality genomic data, its subsequent analysis and application can revolutionise traditional conservation efforts. Nevertheless, finding solutions for conservation managers is challenging, as there is a gap between basic research and practical application.
Genomic studies have found that genetic exchange among species seems to be the rule, not the exception as previously believed, and possibly helps species to adapt. Populations protected by their 'species label' can benefit from comprehensive conservation measures, indicating that species identification has real impact. Furthermore, the importance of prioritising the conservation of organismal groups with an inherent genetic capacity to adapt to their environment has been demonstrated in cross-group genome analyses.
In this context, good quality genome sequences can accelerate conservation with viable practical solutions, whilst information of poorer quality is less valuable.
“Chromosome-level assemblies”
Modern DNA sequencing technology enables the generation of low-quality genomes in a simple and inexpensive manner. However, these circumstances can change when large sequence segments are allocated to an organism’s overall genomic “map”. This “map”, with all genes ordered and assigned to their correct position on chromosomes, is missing in most sequenced genomes. Furthermore, these gene patterns vary between species, and genome assemblies are little more than a “bag of DNA” without this species-specific organisation. Coupling the professors’ work with modern sequencing technologies, approaches are used to directly visualise the pattern of sequence segments from the available data. A "chromosome level assembly" is a comprehensive overview of this and the organised genome. This genomic analysis approach can therefore transform key areas of conservation genetics, including categories such as population viability, phylogenomics and genetic variation.
Chromosome level assemblies can identify the connection between the genome and the organism’s phenotype. This is particularly beneficial in agricultural selection and breeding, allowing for more efficient food production and improved food security, which have economic impacts too. For the conservation of many CITES-listed threatened/endangered species, such assemblies are vital as some hybrids may have advanced traits that could support their survival. These different genome organisations of species can be readily identified with a chromosome level assembly.
In conclusion, chromosome-level assemblies allow the visualisation of species-specific genomic sequences in regard to their organisation and position on chromosomes. This offers a viable approach to overcome the gap between basic research and practical application in conservation efforts of genetic diversity.