Closing Human Reference Genome Gaps: Identifying and Characterizing Gap-Closing Sequences.

Area of Science:

• Genomics
• Human Genetics

Background:

• The human reference genome contains hundreds of gaps, representing about 5% of its total sequence length.
• Advancements in whole genome *de novo* assemblies, particularly from long-read sequencing, offer opportunities to resolve these gaps.

Purpose of the Study:

• To identify and characterize gap-closing sequences using *de novo* long-read assemblies.
• To assess the novelty and validation of these sequences against existing datasets and non-human primate genomes.
• To investigate the nature and potential biological significance of the newly identified sequences.

Main Methods:

• Comparative analysis of 17 *de novo* long-read sequencing assemblies against the human reference genome.
• Validation of identified gap-closing sequences using unmapped reads from the Simons Genome Diversity Project.
• Cross-species comparison with four non-human primate genomes.
• Sequence analysis to determine the content of repeats and satellite DNA.

Main Results:

• Identified 1,125 gap-closing sequences for 132 gaps, adding up to 2.2 Mb of novel sequence data.
• Over 90% of non-redundant novel sequences were validated by unmapped reads.
• 15.6% of non-reference sequences were found in non-human primate genomes.
• Identified high content of simple repeats and satellite sequences in the novel regions.
• Discovered that 32.6% of the closed gaps are polymorphic.

Conclusions:

• Long-read sequencing assemblies can effectively identify novel sequences to close gaps in the human reference genome.
• These novel sequences, including polymorphic regions, contribute significantly to understanding human genetic diversity and may hold important biological functions.