Overview of Genome Re-sequencing

Genome resequencing has emerged as a transformative technique in genomics, enabling comprehensive analyses of genetic variation within populations. This process involves sequencing the entire genome of species with known reference genomes, allowing for the identification of diverse genetic variants such as single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), and structural variations (SVs). Leveraging genome resequencing technology, researchers can rapidly conduct resource census screening, predict candidate genes for important traits, and offer personalized medical treatment in medicine. Additionally, this technique significantly enhances the efficiency of molecular breeding in agriculture. As a versatile tool, whole genome resequencing finds applications in both scientific research and clinical practice.

Know more possibilities by referring to our article Whole Genome Re-sequencing in the Conservation of Threatened Species.

Technical Advancements

• Sequencing Platforms
  The heart of whole genome resequencing lies in the availability of advanced sequencing platforms. Cutting-edge technologies like Illumina's high-throughput sequencers and the emerging long-read platforms from PacBio and Oxford Nanopore have revolutionized DNA sequencing. These platforms leverage diverse approaches, such as shotgun sequencing and single-molecule sequencing, to generate high-quality data with differing read lengths, accuracy, and throughput.
• Library Preparation
  Before sequencing, DNA samples must undergo library preparation, a critical step that involves fragmenting the DNA, attaching adapter sequences, and amplifying the fragments. This process impacts the sequencing coverage, read length, and overall data quality. Modern library preparation methods often incorporate unique molecular identifiers (UMIs) to mitigate errors and enhance accuracy.
• Bioinformatics Pipelines
  The analysis of massive sequencing datasets demands robust bioinformatics pipelines. These pipelines encompass alignment of sequenced reads to the reference genome, variant calling, and annotation. Leveraging algorithms that account for sequencing errors, mapping biases, and complex genomic features is crucial for accurate variant detection.

Technical Advantages

• Comprehensive Mutation Spectrum
  Whole genome resequencing enables the detection of high-frequency, low-frequency, and even rare mutations and structural variations across the entire genome. This provides a holistic understanding of the genetic landscape associated with phenotypes.
• Individual and Population Insights
  For individual samples, researchers can obtain a comprehensive genomic mutation spectrum. At the population level, this technique aids in studying evolutionary history, environmental adaptation, natural selection, and trait localization.
• Genetic Variation Discovery
  Through resequencing, the genome of an individual or a population can be sequenced and analyzed, yielding an abundance of genetic polymorphism data including SNPs, InDels, SVs, and CNVs. The establishment of genetic polymorphism databases lays the groundwork for exploring evolutionary relationships and identifying candidate genes for specific traits.
• Core Germplasm Resource Screening
  Re-sequencing core germplasm resources provides deep insights into genetic diversity at the gene and genotype levels. This informs the establishment of germplasm resource banks, facilitates germplasm exchange and utilization, and aids in targeted varietal protection. The data generated also contributes to the development of excellent varieties through molecular improvement.
• Genetic Evolution Analysis
  For species with reference genomes, whole genome resequencing enables the comparison of genomic information across subspecies. By identifying highly accurate genetic variants, including SNPs, InDels, CNVs, and SVs, researchers can delve into topics such as population genetic structure, domestication mechanisms, population history, and evolutionary dynamics. This molecular-level analysis sheds light on the species' evolutionary mechanisms, environmental adaptation, and related issues.
• Key Aspects of Genetic Evolution Analysis
  Origin and Migration: Analyzing materials from potential origin populations helps uncover species origin, migration routes, and evolutionary relationships.
  Domestication Mechanisms: Studying wild and domesticated types from different regions elucidates the mechanisms behind artificial domestication and identifies genes subjected to selection.
  Species Improvement: Materials from diverse regions and times aid in understanding species improvement mechanisms and the genes responsible.
  Adaptive Evolution: Collecting specimens with varying geographical and altitude distributions offers insights into adaptive evolution mechanisms and genes under selection.
  Family Line Classification: Materials from different family lines allow for the development of molecular markers and classification of family lines.
• Prediction of Trait Candidate Genes
  Whole-genome resequencing of species groups with known reference genomes involves detecting SNP markers distributed across the genome. By analyzing linkage disequilibrium with specific traits and employing statistical methods, researchers can predict candidate genes or genomic regions associated with those traits.