Whole Genome Re-sequencing in the Conservation of Threatened Species

The swift decline of global biodiversity has spurred a growing focus on preserving biodiversity. Conservation genetics stands out as a crucial tool in safeguarding endangered species, significantly enriching our understanding across various aspects of conservation biology. Nonetheless, certain key scientific inquiries within conservation biology, such as the evolutionary trajectory of at-risk plants, the drivers and mechanisms behind endangerment, and the workings of adaptive evolution, remain subjects requiring deeper investigation.

In recent times, the integration of high-throughput sequencing technology with conservation genetics has given rise to conservation genomics. This emerging field introduces novel techniques and perspectives that delve into these pivotal inquiries with greater depth. A standout technique in conservation genomics, whole-genome resequencing, has achieved notable progress in exploring endangered plant phylogeny and population genetics. This technique delves into genome diversity, the evolutionary history of populations, adaptive evolution, and the decline of inbreeding. Through these explorations, insights into the taxonomic classification and conservation divisions of endangered species have emerged. Moreover, the studies have illuminated the species' evolutionary background, reasons for endangerment, and aspects of adaptive evolutionary history.

Classical conservation genetics studies have relied on methods such as allelic and microsatellite genotyping, as well as mitochondrial DNA sequencing, to yield valuable insights about natural populations. However, these approaches provided only limited genetic marker data. In the 21st century, the rapid advancement of sequencing technologies, particularly NGS and long-read sequencing, has paved the way for the birth of conservation genomics. Presently, the prevailing methods for genome conservation can be categorized into two main streams: reduced representation genome sequencing (RRGS) and whole-genome sequencing.

Reduced Representation Genome Sequencing

Reduced representation genome sequencing (RRGS), also known as partial genome sequencing, substantially simplifies the genome's complexity. As a result, it decreases both the sequencing expenses and computational demands. This approach offers several advantages, including cost-effectiveness, enhanced stability, simpler library construction procedures, shorter experimental periods, a substantial yield of single nucleotide polymorphisms (SNPs), and independence from the reference genome. Consequently, it finds extensive utility in safeguarding endangered plant and animal species. Hence, this technology plays a crucial role in the conservation efforts directed towards endangered flora and fauna.

RRGS encompasses various techniques, such as restriction site-associated DNA sequencing (RAD seq), RNA sequencing (RNA seq), and whole exome sequencing (WES). These methods share a common characteristic: they typically scrutinize only a fraction of the genome. However, due to the inherent incomplete coverage and occasional missing data, the data acquired through RRGS pose challenges for subsequent population genetics analyses. In contrast, the whole-genome resequencing method, reliant on a reference genome, offers a significant enhancement in the quantity and quality of obtained genetic markers. This advancement greatly refines the precision of acquired genetic markers when compared to the simplified genome sequencing methods.

Whole Genome Sequencing

Whole genome sequencing encompasses two primary categories: de novo whole genome sequencing and whole genome resequencing. De novo sequencing involves constructing an entirely new genome sequence from scratch. The complexity and success of this assembly process depend on factors such as genome size, intricacy, available computational resources, and expertise in bioinformatics. Currently, the process of de novo whole genome sequencing predominantly relies on three generations of sequencing technologies. These include single-molecule real-time sequencing (SMRT) and High Fidelity (HiFi) reads offered by Pacific Biosciences, as well as nanopore sequencing by Nanopore Technologies (ONT). Following sequencing, the application of Hi-C (high throughput chromosome conformation capture) aids in assembling the sequencing data into chromosomal contexts.

On the other hand, the objective of whole genome resequencing is to analyze genomic variations across individuals and populations. This involves using sequencing technology to generate numerous short reads, which are then compared against a reference genome. By doing so, population-level single nucleotide polymorphism (SNP) data can be acquired. Subsequent analyses in population genetics are conducted based on these SNP data.

Resequencing In the Preservation of Endangered Plants

  • Unraveling Phylogenetic Connections and Population Genetic Patterns
    The entirety of a species' evolutionary journey is encapsulated within whole genome data. This approach, contrasting with traditional methods focusing on a few genes, enables the creation of more robust phylogenetic connections. This innovation offers fresh avenues for recognizing closely related species and unveiling concealed ones. By harnessing genome resequencing data, we gain robust statistical backing for constructing phylogenetic relationships and characterizing population genetic arrangements. This method effectively resolves intricate phylogenetic interplays and population genetic configurations that elude traditional approaches. It facilitates precise identification of conservation priorities and units, lending profound significance to species preservation.
  • Evaluating Genomic Diversity
    Through whole genome resequencing, nearly all genetic data of a species can be acquired, empowering the assessment of its comprehensive genetic diversity, encompassing both individual entities and populations—a concept termed genomic diversity.
  • Unveiling Population History and Dynamics
    The history of population dynamics delves into the fluctuations of a species' population size and associated parameters across time. Investigating the historical dynamics of endangered plant populations—comprising shifts in effective population size, patterns of bottleneck formation, migration trends, and more—unveils the trajectory and reasons underlying their jeopardized status. While conventional conservation genetics relies on mitochondrial and chloroplast DNA fragments or microsatellite genetic markers for insights into historical population dynamics, such methods demand substantial sample sizes and only trace recent population changes. Whole-genome resequencing data, in contrast, comprehensively reconstruct historical population size changes across various temporal scales, offering novel perspectives on the influence of past events on present-day population size and genetic composition.
  • Detecting Signals of Natural Selection and Population Localization
    Long-term viability, population expansion potential, and risk of extinction in plants hinge on adaptive variation. Beyond assessing the genetic underpinnings of adaptive traits, resequencing-based conservation genomics identifies specific genes driving such diversity in natural populations. This approach enhances understanding of adaptive processes and potential. Furthermore, genome-wide association studies (GWAS) and similar methodologies illuminate the genetic origins of adaptive variation in natural populations. These strategies have unveiled candidate genes in numerous endangered species, elucidating their involvement in selection or endemic adaptations.
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