Biology subjects

Suo, M.

Publications and source records attributed to Suo, M..

3 recordsLinked to original sources

bioRxiv2026

Hidden genetic diversity in 320 nearly-complete East Asian genome assemblies

East Asian populations, representing over 20% of the global population, remain critically underrepresented in human genomic studies, limiting our understanding of population-stratified genetic variation and its implications for health and disease. Here we present the first phase of the Asian Pan-Genome project (APG), comprising 320 nearly complete, fully phased haploid genome assemblies from 160 East Asian individuals. These assemblies achieve unprecedented quality, with an average contig N50 of 144.3 megabase pairs and an average quality value of 64.5. Leveraging these superior assemblies, we reveal previously uncharacterized diversity in human repeatome, including population-stratified patterns in centromere satellites and rDNA arrays. Compared to existing global human genome assemblies, the newly generated genomes supplement 152 million base pairs of novel sequences, 355 gene gains, 18,300 structural variation loci and 26 large euchromatic inversions missing from current human pangenomes. We perform population stratification analyses of structural variations, and further resolve the structural haplotypes of complex genomic regions such as Major Histocompatibility Complex and Survival Motor Neuron loci across global pangenomes, exemplifying tandem-duplicate and inversion-rich complex locus architectures in the human genome, respectively. This resource provides a critical foundation for human genetic studies, especially for East Asian populations, promoting more accurate variant discovery, reducing bias, and ultimately advancing the equity and efficacy of genomic medicine.

genomics↗

bioRxiv2026

Deciphering complete archaic introgression sequences in modern human genomes

Genetic introgression from archaic hominins has profoundly reshaped the genetic diversity and adaptive potential of modern humans, yet the full catalog of introgressed sequences, particularly those residing in structurally complex regions has remained elusive. Here, we present ASMaid (ASseMbly-based archaic introgression detector), a Hidden Markov Model-based framework that leverages haplotype-resolved pangenome assemblies to identify archaic-derived sequences with unprecedented completeness. By integrating both single-nucleotide genotype and structural variation (SV) signals, ASMaid captures significantly more intact archaic segments than conventional reference-based approaches. Applying ASMaid to a global panel of 610 phased human genome assemblies, we show that non-African individuals carry approximately 79.8 Mbp of Neanderthal and 8.3 Mbp of Denisovan sequences, representing substantial increases over previous estimates, respectively. Notably, we detected several centromere-spanning archaic segments, including EAS-specific calls on chromosomes 5 and 7. Our assembly-based approach uncovered 1,701 archaic-derived SVs, revealing a previously overlooked layer of archaic functional legacy. High-frequency introgressed loci are enriched in pathways associated with metabolism, immunity, and nervous system (e.g. CTNNA2 linked to early-onset schizophrenia risk), underscoring the fundamental role of introgression in modulating modern human traits. Notably, we identified dozens of loci potentially facilitating local adaptation, such as PRDM16 involved in adipocyte differentiation and cold tolerance, and CSGALNACT2 associated with chondroitin sulfate synthesis. Furthermore, our analysis delineates three distinct Denisovan introgression pulses in Eastern Eurasian genomes, in which the first two pulses are shared across East Eurasian and Oceanian populations, while the third remain primarily exclusive in East Asians. Reflecting these complex introgression events, 31 Denisovan-derived segments, including the TBX15-WARS2 locus, are inferred to have been introduced via at least two events. This comprehensive map of archaic introgression provides a fundamental resource for understanding how ancient gene flow continuously shapes human phenotypic diversity and adaptation.

evolutionary biology↗

bioRxiv2024

Genetic diversity and evolution of rice centromeres

AbstractUnderstanding the mechanisms driving centromere evolution is crucial for deciphering eukaryotic evolution and speciation processes. Despite their widely recognized characteristics of conserved function in cell division, the centromeres have showed high diversity in composition and structure between species. The mechanism underlying this paradox remain poorly understood. Here, we assembled 67 high-quality rice genomes from Oryza AA group, encompassing both Asian and African rice species, and conducted an extensive analysis of over 800 nearly complete centromeres. Through de novo annotation of satellite sequences and employing a progressive compression strategy, we quantified the local homogenization and multi-layer nested structures of rice centromeres and found that genetic innovations in rice centromeres primarily arise from internal structural variations and retrotransposon insertions, along with a certain number of non-canonical satellite repeats (sati). Despite these rapid structural alterations, the single-base substitution rate in rice centromeres appears relatively lower compared to the chromosome arms. Contrary to the KARMA model for Arabidopsis centromere evolution, our model (RICE) suggests that centrophilic LTRs contribute to the decline of progenitor centromeres composed of satellite repeats, and facilitate the formation of evolutionary neo-centromeres, which are enriched with extended CENH3 binding regions beyond the native satellite arrays in plant genomes. In summary, this study provides novel insights into genomic divergence and reproductive barriers among rice species and subspecies, and advances our understanding of plant centromere evolution.

genetics↗