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<p>Pangenome projects have enhanced our understanding of human genomic and genetic diversity, but repetitive regions are still challenging to assemble and yet medically important. Here we generate 20 near-complete haplotypes from 10 Japanese male individuals using three complementary long-read and long-range datasets and construct a pangenome graph from these haplotype-resolved assemblies. All haplotypes achieve an N50 value exceeding 100 Mbp for gapless contigs. We substantially improve the average reconstruction rate of complete haplotypes from 46.8% and 52.8% in two previous pangenome graphs to 91.2% within 30 segmentally duplicated complex regions. Furthermore, we identify complete minor haplotypes in the <i>KIR</i> and <i>SMN</i> regions that are absent in those previous pangenome graphs. We find putatively biased gene conversion events occurring in only one direction around the <i>SMN</i> and beta-defensin (<i>DEFB</i>) genes, implying non-random evolution in these regions. Our study contributes to the growing body of pangenomic data, offering a more refined view of human genomic diversity involving complex segmental duplications.</p>

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Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年5月27日

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  • Yoshihiko Suzuki,
  • Chie Owa,
  • Haruka Kobayashi,
  • Ryo Nakabayashi,
  • Brandy McNulty,
  • Ivo Violich,
  • Benedict Paten,
  • Karen H. Miga,
  • Shinichi Morishita

摘要

Pangenome projects have enhanced our understanding of human genomic and genetic diversity, but repetitive regions are still challenging to assemble and yet medically important. Here we generate 20 near-complete haplotypes from 10 Japanese male individuals using three complementary long-read and long-range datasets and construct a pangenome graph from these haplotype-resolved assemblies. All haplotypes achieve an N50 value exceeding 100 Mbp for gapless contigs. We substantially improve the average reconstruction rate of complete haplotypes from 46.8% and 52.8% in two previous pangenome graphs to 91.2% within 30 segmentally duplicated complex regions. Furthermore, we identify complete minor haplotypes in the KIR and SMN regions that are absent in those previous pangenome graphs. We find putatively biased gene conversion events occurring in only one direction around the SMN and beta-defensin (DEFB) genes, implying non-random evolution in these regions. Our study contributes to the growing body of pangenomic data, offering a more refined view of human genomic diversity involving complex segmental duplications.