The gap-free potato genome assembly reveals large tandem gene clusters of agronomical importance in highly repeated genomic regions

Article Biochemistry & Molecular Biology

Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity

Genevieve Hoopes et al.

Summary: Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars revealed extensive allelic diversity and structural variation, resulting in a complex transcriptome and predicted proteome. Wild species contribute to the allelic diversity in tetraploid cultivars. Understanding the complexity of the potato genome is key for precision breeding and hybridization.

MOLECULAR PLANT (2022)

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Article Genetics & Heredity

Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

Hequan Sun et al.

Summary: This study reports the reconstruction of the autotetraploid genome of potato based on high-quality long reads, single-cell sequencing, and Hi-C data, revealing the characteristics of genome similarity and structural rearrangements caused by recent inbreeding. Only a portion of the genes were present in all four haplotypes, and some genes may be regulated through allele-specific DNA methylation.

NATURE GENETICS (2022)

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Article Biochemistry & Molecular Biology

Genome architecture and tetrasomic inheritance of autotetraploid potato

Zhigui Bao et al.

Summary: In this study, a chromosome-scale, haplotype-resolved genome assembly of a cultivated potato was achieved using state-of-the-art sequencing technologies and polyploid graph binning. The study provides insights into the genomic architecture of autopolyploids and will guide their breeding.

MOLECULAR PLANT (2022)

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Article Multidisciplinary Sciences

Graph pangenome captures missing heritability and empowers tomato breeding

Yao Zhou et al.

Summary: Constructing a graph pangenome of tomato can improve the estimation of heritability for complex traits, identify more causal structural variants, and facilitate the identification of genetic factors underlying agronomically important traits. This study advances our understanding of the heritability of complex traits and demonstrates the power of the graph pangenome in crop breeding.

NATURE (2022)

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Article Multidisciplinary Sciences

Genome evolution and diversity of wild and cultivated potatoes

Die Tang et al.

Summary: This study assembles 44 high-quality diploid potato genomes to investigate the genome evolution and diversity of potatoes. The results show a substantial expansion of disease-resistance genes in the potato genome compared to related solanaceous crops, indicating the impact of tuber-based propagation strategies on potato genome evolution. The study also identifies a transcription factor that determines tuber identity and its interaction with an inductive signal.

NATURE (2022)

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Article Biotechnology & Applied Microbiology