Reply to: Evaluating two different models of peanut’s origin

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Fig. 1: Ks values for collinear orthologous and homeologous gene pairs.
Fig. 2: Identity distributions of 10-kb windows in paired comparisons of Shitouqi and two wild species.

Data availability

The genome assembly and annotation of A. hypogaea cv. Shitouqi are available at http://peanutgr.fafu.edu.cn and at GenBank under accession number PRJNA480120 and CP030983CP031002, respectively. The genome assemblies and annotations of A. hypogaea cv. Tifrunner and diploid A. duranensis and A. ipaensis are available at https://peanutbase.org/peanut_genome.

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Acknowledgements

The work reported in this publication was supported by grants from the NSF of China (U1705233, 31601337 and 31701463) to W.Z., H.C. and C.Z., respectively, and the Ministry of Science and Technology of China (2016YFD0101001) to X.W. R.K.V. thanks the CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC) for partially supporting this study. ICRISAT is part of the CGIAR consortium.

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Contributions

W.Z., R.K.V. and X.W. designed or supervised the research. W.Z., X.W. and A.H.P. guided the analysis. X.W., M.Y., P.S., H.C. and C.Z. were responsible for Ks analyses. W.Z., X.W., H.C., C.Z., Y.Z., L.W., W.X., W.C. and H.F. made critical evaluations, performed analysis and prepared materials. W.Z., X.W., R.K.V. and A.H.P. wrote and finalized the manuscript.

Corresponding authors

Correspondence to Weijian Zhuang or Xiyin Wang or Rajeev K. Varshney.

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The authors declare no competing interests.

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Extended data

Extended Data Fig. 1 Ks distribution of linked alignments of homologous genes.

Ks values estimated from five linked alignments of randomly selected homologous gene pairs between A. duranensis genome and Shitoqi A subgenome a, A. ipaensis genome and Shitoqi B subgenome b, A. duranensis genome and Tifrunner A subgenome c, A. ipaensis genome and Tifrunner B subgenome d. Ks peaks are 0.028, 0.015, 0.014 and 0.01, respectively for Ad-At, Bd-Bt, Ad-At and Bd-Bt.

Extended Data Fig. 2 Comparisons of Ks patterns between Medicago and three groups of peanut orthologs.

Ks patterns of Mt and three groups of Ad (Mt-Ad) orthologs with Ks=0, 0<Ks<0.1, and Ks >=0.1 in Ad-At (Shitoqi) genomes a, Mt-Ad in Ad-At (Tifrunner) genomes b, Mt-At in Ad-At (Shitoqi) genomes c, Mt-At in Ad-At (Tifrunner) genomes d, Mt-Bd in Bd-Bt (Shitoqi) genomes e, Mt-Bd in Bd-Bt (Tifrunner) genomes f, and Mt-Bt in Bd-Bt (Shitoqi) genomes g, and Mt-Bt in Bd-Bt (Tifrunner) genomes h.

Extended Data Fig. 3 K values of colinear and bidirectional best hit LTR homologs between subgenomes.

K distribution patterns between A. duranensis genome and Shitoqi A subgenome a, e, A. duranensis genome and Tifrunner A subgenome b, f, A. ipaensis genome and Shitoqi B subgenome c, g, A. ipaensis genome and Tifrunner B subgenome d, h. The upper 4 subfigures are for LTR homologs with matched regions > 500 bp, and the lower 4 > 1000 bp. Here, similar to the definition of Ks, K is defined as K=−3/4*Ln(1–4(1-p)/3), where p is the identity between colinear and bi-directional-best-hit LTR homologs from peanut subgenomes.

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Supplementary Information

Supplementary Table 1 and Supplementary Data 1 and 2

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Zhuang, W., Wang, X., Paterson, A.H. et al. Reply to: Evaluating two different models of peanut’s origin. Nat Genet 52, 560–563 (2020). https://doi.org/10.1038/s41588-020-0627-0

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