Open AccessThe complex genome and adaptive evolution of polyploid Chinese pepper ( Zanthoxylum armatum and Zanthoxylum bungeanum )
Author(s) -
Hu Lisong,
Xu Zhongping,
Fan Rui,
Wang Guanying,
Wang Fuqiu,
Qin Xiaowei,
Yan Lin,
Ji Xunzhi,
Meng Minghui,
Sim Soonliang,
Chen Wei,
Hao Chaoyun,
Wang Qinghuang,
Zhu Huaguo,
Zhu Shu,
Xu Pan,
Zhao Hui,
Lindsey Keith,
Daniell Henry,
Wendel Jonathan F.,
Jin Shuangxia
Publication year - 2023
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1111/pbi.13926
Subject(s) - biology , genome , zanthoxylum , polyploid , genome evolution , genomics , genetics , evolutionary biology , botany , gene
Summary Zanthoxylum armatum and Zanthoxylum bungeanum , known as ‘Chinese pepper’, are distinguished by their extraordinary complex genomes, phenotypic innovation of adaptive evolution and species‐special metabolites . Here, we report reference‐grade genomes of Z. armatum and Z. bungeanum . Using high coverage sequence data and comprehensive assembly strategies, we derived 66 pseudochromosomes comprising 33 homologous phased groups of two subgenomes, including autotetraploid Z. armatum . The genomic rearrangements and two whole‐genome duplications created large (~4.5 Gb) complex genomes with a high ratio of repetitive sequences (>82%) and high chromosome number (2 n = 4 x = 132). Further analysis of the high‐quality genomes shed lights on the genomic basis of involutional reproduction, allomones biosynthesis and adaptive evolution in Chinese pepper, revealing a high consistent relationship between genomic evolution, environmental factors and phenotypic innovation. Our study provides genomic resources and new insights for investigating diversification and phenotypic innovation in Chinese pepper, with broader implications for the protection of plants under severe environmental changes.