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PubMed · 42372111

Revisiting the genome assembly of Lupinus species reveals differential diploidization after a shared whole-genome duplication.

Liying Yang·Yanju Shuai·Weiran Li·Junping Gao·Jianduo Zhang·Haomin Lyu·Songyi Ji·Mingli Chen
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Abstract

Accurate genome assemblies are essential for comparative genomics, yet Hi-C-guided scaffolding can introduce structural errors that misrepresent chromosome architecture and bias evolutionary inferences. Here, we identified pervasive scaffolding errors-including artificial fusions, internal inversions, and incomplete contig mounting-in 2 previously published Lupinus genomes (L. cosentinii and L. digitatus) using a segmentation method based on long terminal repeat (LTR) retrotransposon density. We reassembled both genomes, producing chromosome-level references of 472.7 Mb (16 chromosomes) and 427.2 Mb (21 chromosomes), with BUSCO completeness >98.5%. Synteny validation and reapplication of LTR profiling confirmed that all prior errors were resolved. Using these corrected genomes together with 4 additional Lupinus species and 2 outgroup legumes, we investigated postpolyploid evolution. Synonymous substitution rate (Ks) analysis revealed a genus-specific whole-genome duplication (WGD) event (Ks = 0.17) shared by all 6 Lupinus species. The proportion of WGD-derived genes varied markedly, from 60% in L. digitatus to only 36% in L. mutabilis, indicating differential diploidization. While all species retained a core set of WGD duplicates enriched in cytoskeleton organization, ion transport, and defense responses, each exhibited lineage-specific functional trajectories: cell wall modification in L. cosentinii and L. digitatus, nitrogen metabolism in L. albus and L. angustifolius, flower development in L. luteus, and stress/lipid metabolism in L. mutabilis. Our corrected assemblies provide optimal references for Lupinus comparative genomics, and our findings demonstrate that a shared WGD event can lead to both conserved and highly divergent postpolyploid fates, likely underpinning adaptive diversification within the genus.

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LupinusGenome, PlantGene DuplicationDiploidyGenomicsEvolution, MolecularRetroelementsSyntenyPhylogenyTerminal Repeat SequencesHi-C scaffoldinggene family expansiongenome assembly errorpostpolyploid evolution (diploidization)whole-genome duplication (WGD)Journal Article

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Liying Yang, Yanju Shuai, Weiran Li, Junping Gao, Jianduo Zhang, Haomin Lyu, Songyi Ji, Mingli Chen. 2026-09-02. Revisiting the genome assembly of Lupinus species reveals differential diploidization after a shared whole-genome duplication.. https://doi.org/10.1093/g3journal%2Fjkag171

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