Description

Most diploid genome assemblies disregard differences between homologous chromosomes, assembling the genome into a pseudo-haploid sequence. This approach represents an artificial consensus of diploid assemblies. Such an artificial consensus may lead to inaccurate gene annotations and incorrect biological interpretations.

As research progresses, it has become clear that single-set genome data is insufficient to fully represent the comprehensive information of a species. The combination of different genetic loci between homologous chromosomes significantly affects biological phenotypes, such as heterosis in plants and animals, and hybrid sterility in some species. Differences between haplotype alleles have a significant impact on gene expression, function, and phenotype, with the advantageous phenotypes of most hybrid varieties being regulated by these allelic variations.

Haplotype analysis can lay an important foundation for understanding the genetic mechanisms underlying key traits in species. In population genetics, haplotypes can be used to analyze allelic differences, trace individual relationships, and understand migration patterns and evolutionary history. In agriculture, haplotypes can be used to identify superior allelic variations and explore theories of heterosis.

Technical Features

• Comparison of gene characteristics of assembled haplotype genomes
• Detection of structural variations between haplotype genomes
• Analysis of gene expression on haplotype genomes, studying allelic imbalance expression in combination with species tissue parts and developmental stages
• Analysis of gene expression in or adjacent to structural variations