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Evaluating two different models of peanut’s origin

Nature Genetics volume 52, pages 557–559 (2020)Cite this article

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Matters Arising to this article was published on 11 May 2020

The Original Article was published on 01 May 2019

arising from W. Zhuang et al. Nature Genetics https://doi.org/10.1038/s41588-019-0402-2 (2019)

Multiple lines of evidence indicate a recent (<10,000 years ago) origin of peanut (Arachis hypogaea) and provide a foundation for understanding the evolution of this important crop1,2. However, recently, a manuscript presented results incompatible with this understanding, reporting much older polyploidization (~450,000 years ago) and, furthermore, questioning the species identity of one of the diploid ancestors3. By performing new chromosome-scale comparisons, we identify the inappropriate parameter, thus falsifying the model of older polyploidization. Our analyses confirm both the age of polyploidization as <10,000 years and the identity of the two peanut ancestral species as Arachis duranensis and Arachis ipaensis.

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Fig. 1: Visualizations of divergence between the B genomes of diploid and tetraploid Arachis.
Fig. 2: Comparison of Ks curves from the Shitouqi manuscript and this study.

Data availability

The genome assemblies and annotations of A. hypogaea cv. Tifrunner, A. duranensis and A. ipaensis are available at PeanutBase (https://peanutbase.org/peanut_genome) and at NCBI (GenBank accession numbers CM009801–CM009820). The genome of A. ipaensis is available at PeanutBase and in GenBank under assembly accession GCA_000816755.1. The genome assembly of A. hypogaea cv. Shitouqi is available at GenBank under accession number PRJNA480120.

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Author information

Authors and Affiliations

  1. Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA

    David J. Bertioli, Brian Abernathy & Josh Clevenger

  2. Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA

    David J. Bertioli & Josh Clevenger

  3. Department of Crop and Soil Science, University of Georgia, Athens, GA, USA

    David J. Bertioli & Josh Clevenger

  4. Instituto de Botánica del Nordeste (CONICET- UNNE), Corrientes, Argentina

    Guillermo Seijo

  5. FACENA, Universidad Nacional del Nordeste, Corrientes, Argentina

    Guillermo Seijo

  6. Corn Insects and Crop Genetics Research Unit, US Department of Agriculture–Agricultural Research Service, Ames, IA, USA

    Steven B. Cannon

Authors
  1. David J. Bertioli
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  2. Brian Abernathy
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  3. Guillermo Seijo
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  4. Josh Clevenger
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  5. Steven B. Cannon
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Contributions

Chromosome-scale DNA comparisons: B.A. and D.J.B.; Ks analyses: S.B.C. Biogeography: G.S. Critical evaluation: D.J.B., S.B.C., J.C., G.S. and B.A. The manuscript was written by D.J.B., S.B.C., J.C. and G.S.

Corresponding authors

Correspondence to David J. Bertioli or Steven B. Cannon.

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The authors declare no competing interests.

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Extended data

Extended Data Fig. 1 Frequency curve for SNP densities, in 100,000 bp blocks between Arachis ipaensis and the B subgenome of A. hypogaea.

Extended Data Figure 1. Frequency curve for SNP densities, in 100,000 bp blocks between Arachis ipaensis and the B subgenome of A. hypogaea. The alignments covered more then 96% of the genomes.

Extended Data Fig. 2 Visualizations of divergence between the A genomes of diploid and tetraploid Arachis.

Extended Data Figure 2. Visualizations of divergence between the A genomes of diploid and tetraploid Arachis. Frequencies of DNA divergencies (in 10,000 bp tiles) between A. duranensis and the A. hypogaea A subgenomes (cultivars Tifrunner and Shitouqi; a and b respectively). Modal divergences are ~2.5 differences per 1,000 bp respectively. Dot plots using 400 bp (=1,000/2.5) word lengths of A. duranensis chromosome A01 with the homologous chromosomes of A. hypogaea (cultivars Tifrunner and Shitouqi; c and d respectively). The diagonal lines, formed from dots indicating identical spans of 400 bp, run through evolutionarily dynamic pericentromeric regions. (also see Extended Data Figure 3).

Extended Data Fig. 3 Intraspecific chromosome comparisons using dot plots of two common bean varieties.

Extended Data Figure 3. Intraspecific chromosome comparisons using dot plots of two common bean varieties (Phaseolous vulgaris, one Andean, one MesoAmerican chromosomes 1 used for plots). These dot plots are intended to give the reader a basis for comparison of the interspecific Arachis plots (Figure 1 main manuscript and Extended Data Figure 2) which use the same word lengths (a, 400 bp ; b 4,000 bp). (b) The almost complete absence of signal shows there are almost no spans of identity of 4,000 bp between the chromosomes.

Supplementary information

Reporting Summary

Supplementary Data 1

Frequency distribution curves for whole-genome divergence (in 10,000-bp tiles) and divergence at synonymous codon sites in paired genes (Ks curves). Eight pairwise comparisons of diploid and tetraploid Arachis genomes.

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Bertioli, D.J., Abernathy, B., Seijo, G. et al. Evaluating two different models of peanut’s origin. Nat Genet 52, 557–559 (2020). https://doi.org/10.1038/s41588-020-0626-1

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