Reply to “Subgenome-aware analyses suggest a reticulate allopolyploidization origin in three Papaver genomes”

Nature Communications, vol. 14, pp. 2203

Abstract

We assembled genomes of three Papaver species, P. somniferum, P. rhoeas and P. setigerum , and revealed two-round whole genome duplication (WGD) events and the punctuated patchwork evolution of morphinan and noscapine biosynthesis pathway based on comparative genomic analyses of collinearity, phylogenetic tree, and synonymous substitution rate ( Ks ) at species level 1 . Recently, Zhang et al. reanalyzed our three Papaver genomes based on the subgenome-phasing analysis by their newly published tool SubPhaser 2 . They confirmed the two WGDs we previously detected, but provide strong evidence that the WGDs were likely allopolyploidy events. We consider the subgenome-phasing analysis from Zhang et al. to be an important research development building on our original study 1 , promoting the illuminating the evolutionary history of Papaver species.

Authors 6

1. Xiaofei Yang

   First Affiliated Hospital of Xi'an Jiaotong University · Xi'an Jiaotong University

   Affiliation as printed

   Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, China

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, China

   School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, China

2. Shenghan Gao

   Xi'an Jiaotong University

   Affiliation as printed

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, China

3. Tun Xu

   Xi'an Jiaotong University

   Affiliation as printed

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, China

4. Bo Wang

   Xi'an Jiaotong University

   Affiliation as printed

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, China

5. Yanyan Jia

   Xi'an Jiaotong University

   Affiliation as printed

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, China

6. Kai Ye corresponding Aachen Faculty of Science, Leiden University

   Leiden University · First Affiliated Hospital of Xi'an Jiaotong University · Xi'an Jiaotong University

   Affiliation as printed

   Faculty of Science, Leiden University, 2311 EZ, Leiden, The Netherlands. kaiye@xjtu.edu.cn

   Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, China. kaiye@xjtu.edu.cn

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, China. kaiye@xjtu.edu.cn

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, China. kaiye@xjtu.edu.cn

   School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, China. kaiye@xjtu.edu.cn

   School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, China. kaiye@xjtu.edu.cn

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, Shaanxi, China