背景回顾：Humans have domesticated diverse species from across the plant kingdom, however our current understanding of plant domestication is largely founded on major cereal crops. 

主要研究：Here, we examine the evolutionary processes and genetic basis underlying the domestication of water caltrop (Trapa spp., Lythraceae), a traditional, yet presently-underutilized non-cereal crop that sustained early Chinese agriculturalists.

结果1-基因组：We generated a chromosome-level genome assembly of tetraploid T. natans, and then divided the allotetraploid genome into two subgenomes. 

结果2-重测序揭示驯化：Based on resequencing data from 57 accessions, representing cultivated diploid T. natans, wild T. natans (2x and 4x) and diploid T. incisa, we showed that water caltrop was likely first domesticated in the Yangtze River Valley as early as 6,300 yr BP, and experienced a second improvement c. 800 years ago. 

结果3-异源多倍体起源：We also provided strong support for an allotetraploid origin of T. natans within the past 230,000–310,000 years. 

结果4-驯化相关基因：By integrating selective sweep and transcriptome profiling analyses, we identified a number of genes potentially selected and/or differentially expressed during domestication, some of which likely contributed not only to larger fruit sizes but also to a more vigorous root system, facilitating nutrient uptake, environmental stress response, and underwater photosynthesis. 

结论：Our results shed light on the evolutionary and domestication history of water caltrop, one of the earliest domesticated crops in China. This study has implications for genomic-assisted breeding of this presently underutilized aquatic plant, and improves our general understanding of plant domestication.

 摘 要 

人类驯化了植物界很多不同的植物物种，但是目前我们对于植物驯化的理解大多是基于谷类作物的基础上。本文中，作者报道了菱角的演化进程和遗传基础，菱角是一个传统的、目前还未能充分利用的非谷类作物，早期却作为中国农业工作者的粮食。作者报道了四倍体菱角（Trapa natans）的染色体级别基因组组装，并将菱角的异源四倍体基因组分成了两套基因组。通过对包含二倍体栽培种菱角、野生菱角（包含二倍体和四倍体）以及二倍体野菱在内的57份材料重测序数据分析，作者发现6300年前菱角首先在长江流域被驯化，而后约在800年前经历了第二次改良。另外，作者发现四倍体菱角的异源多倍化事件大概发生在距今二十三到三十一万年前。通过结合选择清除和转录图谱分析，作者鉴定到了一些在驯化中受到选择或是差异表达的基因，其中某些基因可能不仅作用于更大的果实，还作用于增强菱角根系的活力，从而加强营养吸收、环境胁迫响应以及水下光合。本文的研究结果揭示了中国最早驯化作物之一菱角的演化和驯化历史。这项研究对目前未充分利用的水生植物的基因组辅助育种具有重要意义，并增加了我们对植物驯化的理解。