Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis

被引：24

作者：

Chen, Weikai ^{[1
]}

Wang, Xiangfeng ^{[1
]}

Sun, Jie ^{[1
]}

Wang, Xinrui ^{[1
]}

Zhu, Zhangsheng ^{[1
,2
]}

Ayhan, Dilay Hazal ^{[1
]}

Yi, Shu ^{[1
]}

Yan, Ming ^{[1
]}

Zhang, Lili ^{[1
,3
]}

Meng, Tan ^{[1
]}

Mu, Yu ^{[1
]}

Li, Jun ^{[1
]}

Meng, Dian ^{[1
]}

Bian, Jianxin ^{[1
]}

Wang, Ke ^{[1
,4
]}

Wang, Lu ^{[1
]}

Chen, Shaoying ^{[1
]}

Chen, Ruidong ^{[1
]}

Jin, Jingyun ^{[1
]}

Li, Bosheng ^{[1
]}

Zhang, Xingping ^{[1
]}

Deng, Xing Wang ^{[1
,5
]}

He, Hang ^{[1
,5
]}

Guo, Li ^{[1
]}

机构：

[1] Peking Univ, Inst Adv Agr Sci, Shandong Lab Adv Agr Sci Weifang, Shandong Lab Adv Agr Sci Weifang, Weifang 261325, Peoples R China

[2] South China Agr Univ, Coll Hort, Guangzhou 510642, Peoples R China

[3] Weifang Inst Technol, Coll Modern Agr & Environm, Weifang 262500, Peoples R China

[4] Shandong Agr Univ, Coll Life Sci, Tai An 271018, Peoples R China

[5] Peking Univ, Peking Tsinghua Ctr Life Sci, Beijing 100871, Peoples R China

来源：

NATURE COMMUNICATIONS | 2024年 / 15卷 / 01期

关键词：

HI-C; PHYLOGENETIC ANALYSIS; PROVIDES INSIGHTS; READ ALIGNMENT; PUNGENCY; ACCURATE; SEQUENCE; DNA; IDENTIFICATION; ALIGNER;

D O I：

10.1038/s41467-024-48643-0

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Chili pepper (Capsicum) is known for its unique fruit pungency due to the presence of capsaicinoids. The evolutionary history of capsaicinoid biosynthesis and the mechanism of their tissue specificity remain obscure due to the lack of high-quality Capsicum genomes. Here, we report two telomere-to-telomere (T2T) gap-free genomes of C. annuum and its wild nonpungent relative C. rhomboideum to investigate the evolution of fruit pungency in chili peppers. We precisely delineate Capsicum centromeres, which lack high-copy tandem repeats but are extensively invaded by CRM retrotransposons. Through phylogenomic analyses, we estimate the evolutionary timing of capsaicinoid biosynthesis. We reveal disrupted coding and regulatory regions of key biosynthesis genes in nonpungent species. We also find conserved placenta-specific accessible chromatin regions, which likely allow for tissue-specific biosynthetic gene coregulation and capsaicinoid accumulation. These T2T genomic resources will accelerate chili pepper genetic improvement and help to understand Capsicum genome evolution.

引用

页数：14

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