Journal Article

Perspectives and opportunities in forensic human, animal, and plant integrative genomics in the Pangenome era

He, Guanglin, Liu, Chao, Wang, Mengge

2025

Overview

The Human Pangenome Reference Consortium, the Chinese Pangenome Consortium, and other plant and animal pangenome projects have announced the completion of pilot work aimed at constructing high-quality, haplotype-resolved reference graph genomes representative of global ethno-linguistically different populations or different plant and animal species. These graph-based, gapless pangenome references, which are enriched in terms of genomic diversity, completeness, and contiguity, have the potential for enhancing long-read sequencing (LRS)-based genomic research, as well as improving mappability and variant genotyping on traditional short-read sequencing platforms. We comprehensively discuss the advancements in pangenome-based genomic integrative genomic discoveries across forensic-related species (humans, animals, and plants) and summarize their applications in variant identification and forensic genomics, epigenetics, transcriptomics, and microbiome research. Recent developments in multiplexed array sequencing have introduced a highly efficient and programmable technique to overcome the limitations of short forensic marker lengths in LRS platforms. This technique enables the concatenation of short RNA transcripts and DNA fragments into LRS-optimal molecules for sequencing, assembly, and genotyping. The integration of new pangenome reference coordinates and corresponding computational algorithms will benefit forensic integrative genomics by facilitating new marker identification, accurate genotyping, high-resolution panel development, and the updating of statistical algorithms. This review highlights the necessity of integrating LRS-based platforms, pangenome-based study designs, and graph-based pangenome references in short-read mapping and LRS-based innovations to achieve precision forensic science. •Global pangenome projects have built high-quality, haplotype-resolved reference genomes representing diverse populations.•Graph-based pangenome references enhance genomic diversity, benefiting long-read and short-read sequencing research.•Pangenome advances improve variant identification, forensic genomics, epigenetics, transcriptomics, and microbiome research.•MAS-seq addresses short forensic marker limitations by enabling optimal RNA and DNA fragment sequencing.•New pangenome coordinates and algorithms improve accurate genotyping, marker discovery, and forensic genomics innovations.

• Publisher: Elsevier B.V,Elsevier Limited
• Subject: Algorithms / Animal human relations / Animal species / Animals / Bias / Biomarkers / Consortia / DNA Fingerprinting / DNA sequencing / Drug resistance / Epigenetics / Forensic Genetics / Forensic integrative genomics / Forensic science / Gene sequencing / Genetic diversity / Genetic Markers / Genetic research / Genome / Genomes / Genomic diversity / Genomics / Genotyping / Haplotypes / High-Throughput Nucleotide Sequencing / Humans / Long-read third-generation sequencing / Microbiomes / Microbiota / Multiculturalism & pluralism / Pangenome reference / Paradigm shift / Population / Sequence Analysis, DNA / Technological change / Transcriptomics