What is conservation genomics?

To understand genomic conservation and how it can help, we need to understand what DNA sequencing is. DNA is present in all living things, it is the genetic code of life, the instructions for building and operating an organism. Sequencing is a method used to decode these instructions, and can subsequently be used to assemble reference genomes. High-quality draft reference genomes can then be used to improve conservation efforts by answering a range of questions by providing information on species identity, genetic disease risk or how an organism has evolved.

ORG.one is supported by Oxford Nanopore Technologies who have developed a new generation of scalable, real-time sequencing devices.

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MinION in Peru
Studying genetic diversity

Studying genetic diversity

Genetic diversity provides the building blocks upon which evolution can act, equipping a species with the potential to adapt to any changes that come their way. Generally, the greater the genetic diversity within a population, the better its prospects are for thriving long into the future.

Genetic diversity can be assessed by sequencing specific regions of DNA, such as DNA microsatellites — highly repetitive sequences — or single nucleotide polymorphisms (SNPs). These regions of DNA often show greater variation amongst individuals within a diverse population. Another important method involves the identification of deleterious alleles, which are gene variants known or predicted to have a negatively impact an individual. These are often caused by mutations or structural variants (SVs).

Previous sequencing technologies have struggled to characterise SVs and microsatellites due to their size and repetitive nature. Long nanopore reads can span SVs and repetitive sequences, enabling unprecedented resolution of the genomic diversity and genomic health of endangered populations.

Assessing genomic health is not only vital for assessing a population's overall condition, but also serves as an early warning signal that a species might be beginning to decline, signalling the need for intervention.

High-resolution identification

The ability to delineate between populations and sub-populations is vital for effective monitoring and conservation strategies. In the past, this was done through comparing phenotypes (observable traits, such as fur colour) or DNA barcodes — small regions of standardised DNA present in almost all organisms genomes but divergent between different species.

Oxford Nanopore whole-genome sequencing simplifies this process by assembling an organism’s mitochondrial or chloroplast genome, or it's entire genome, instead of a few selected genes. In addition, long nanopore sequencing reads can assemble repetitive regions (as well as large SVs) often assembled incorrectly, or missed entirely by other sequencing technologies.

The long nanopore sequencing reads therefore provides greater resolution than other identification methods and can be used to refine taxonomy of species, as well as identify cryptic species, sub-species and even identify individuals in a population — see section "non-invasive monitoring" below for more information. Individual identification can be vital for conservation programs, such as those carrying out genetic rescue and management of breeding programs.

Long nanopore sequencing reads also reduce sequencing coverage requirements, as they cover a larger proportion of the genome per read. Lower sequencing coverage is not only more cost-effective than traditional methods, as less sequencing is required to identify the organism, but also reduces the time taken to result, speeding up the identification process.

Read length to coverage chart

Figure 1: Longer reads allow complete assembly from lower-coverage data.

Nanopore sequencing is uniquely positioned to decrease time to result even further. Unlike traditional methods where sequencing takes place in a lab and analysis can only be done once sequencing is complete, nanopore sequencing enables initial insights to be gathered in-real time.

Coupled with the portable MinION and PromethION 2 Solo devices, turn-around-time is reduced further by bringing the lab closer to the sample and eliminating transportation times. Taken together in situ low pass nanopore sequencing can provide rapid high-resolution identification of any species, anywhere.

Sequencing workflow

Figure 2: Nanopore sequencing workflow to enable real-time analysis and decreased time to result.

Joanna Malukiewicz and her team used portable nanopore sequencing to successfully determine the complete mitogenome of Brazil's endemic buffy-tufted-ear marmoset (Callithrix aurita) — one of the world’s most endangered primates.

Using mitogenomic data generated using the MinION device, they accurately identified different species and subspecies of marmoset, and confirmed breeding between different marmosets species was taking place (interspecific hybridisation) — noting that the hybrid marmosets tended to have a ‘koala bear’ appearance. Their data has provided evidence of ‘anthropogenic hybridisation’ — human-mediated changes in genomics between native and non-native taxa.

Joanna explains multiple factors are driving anthropogenic hybridisation of C. aurita: their natural habitat is disappearing due deforestation resulting in ecological competition (less space for different species to live), infectious diseases such as yellow fever (reducing intraspecific mating), and illegal trafficking of the common marmoset (C. jacchus) with subsequent release of this species into the wild. The ability to identify and monitor anthropogenic hybridisation, through accessible genomics, is therefore important as these irreversible effects on the genomics of the native Brazilian buffy-tufted-ear marmoset (C. aurita) population could eventually lead to its extinction but also can be avoided by intervening in the human activities which are driving these changes.

Non-invasive monitoring

DNA, or more specifically environmental DNA (eDNA), is being used as a non-invasive monitoring tool. eDNA is any DNA collected from environmental samples, such as soil, water or air. That DNA can originate from a range of sources, such as faeces, blood, skin cells, or mucus. The major advantage of eDNA is that it enables monitoring of an organism without physically having to capture it, therefore creating the opportunity to study rare or elusive organisms, many of which are endangered. However, before eDNA can be used as an effective monitoring tool, reference data — such as a draft reference quality genome — must be available to map the eDNA sequencing reads to. This is one of the reasons why ORG.one is supporting the de novo assembly of endangered species.

Reindert Nijland and his team have been supported in the sequencing and assembly of the European sturgeon’s (Acipenser sturio) genome. With their draft reference quality genome assembly, the team are developing an, eDNA based, real-time monitoring method, using the portable MinION device, to track the reintroduction of the European sturgeon in the rivers and estuaries in the Netherlands.

The kākāpō (Strigops habroptila) recovery programme have also set up an eDNA-based approach for monitoring the kākāpō population. They have even gone beyond just accurately detecting the presence of the species and have demonstrated they can identify individual kākāpōs from eDNA using Oxford Nanopore’s Adaptive sampling and whole-genome approach.

Improving the success of breeding programs

For breeding programs to be successful, it is imperative that mating partners are genetically diverse to avoid inbreeding. However, by definition, an endangered species is one facing an extremely high risk of extinction, and therefore there are a limited number of available mating partners. Sequencing can help to identify how closely related potential mating partners are, enabling managers to identify optimal pairings to minimise inbreeding and its subsequent consequences, loss of genetic diversity and inbreeding depression. This enables breeding programmes to maximise the retention of genetic diversity over time and maximise the potential of the program for supporting conservation efforts, such as returning a species back into the wild.

Selective breeding

Earlier sections highlighted how mutations and structural variants can lead to deleterious alleles, signalling poor genomic health. However, mutations and structural variants can also drive adaptation. With this information in mind, conservationists can enhance selective breeding programs by leveraging genomic data, rather than relying solely on phenotypic traits. By breeding individuals with beneficial alleles, such as those conferring drought or heat tolerance, or enhanced immune responses, or by excluding those carrying deleterious alleles, they can develop populations that are not only well-suited to current environmental conditions but also resilient to future changes.

Chick with MinION

Epidemiology and identification of pathogens

Inbreeding and loss of genetic diversity decreases the diversity of immune genes, increasing the risk of extinction through infectious disease. Sequencing can help to identify new pathogens present within an endangered population. With this information, conservationists can track and effectively treat these diseases. Portable, real-time, in situ, nanopore sequencing takes this one step further by bringing the sequencing lab into the field. Portable genomics enables researchers and conservationists to monitor a potential new disease in real-time, enabling them to act rapidly. In 2021, Lara Urban used the MinION device, for nanopore metagenomics, on a remote island in New Zealand, to detect Appergillus fumigatus — a fungus that has the potential to kill the critically endangered kākāpō. The system was put in place as an early warning system to ensure that if chicks were infected, action could be taken in time to save them.