Genome sequencing and transcriptome analyses provide insights into the origin and domestication of water caltrop (Trapa spp., Lythraceae)

Abstract

Humans have domesticated diverse species from across the plant kingdom; however, our current understanding of plant domestication is largely founded on major cereal crops. 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. We generated a chromosome-level genome assembly of tetraploid T. natans, and then divided the allotetraploid genome into two subgenomes. 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 6300 yr BP, and experienced a second improvement c. 800 years ago. We also provided strong support for an allotetraploid origin of T. natans within the past 230 000-310 000 years. 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. 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.

A high-quality Buxus austro-yunnanensis (Buxales) genome provides new insights into karyotype evolution in early eudicots

“…Within rosids, the main conflicts with previous phylogenetic analyses related to the position of Myrtales and the phylogenetic relationships within clade II. Our results indicated that Myrtales are sister to other rosids, which is consistent with most analyses [37,[45][46][47][48][49][50][51][52][53]56] but not with an analysis of 1000 transcriptomes that suggests that Myrtales are nested within other malvids [27]. Within rosid clade II, our results support the hypothesis that Fagales are sister to the other species and Cucurbitales are sister to Fabales, whereas previous studies have concluded that Fagales and Fabales cluster together and Cucurbitales and Rosales are sister clades [27,43,50].…”

Water wisteria genome reveals environmental adaptation and heterophylly regulation in amphibious plants

“…In addition, WUSCHEL-related homeobox (WOX) genes are also involved in leaf development and they regulates the expression of CIN class TCPs (Jha et al, 2020; Wang et al, 2020). Many aquatic species have evolved to be polyploid during species differentiation (Albert and Renner, 2020; Lu et al, 2021; Prancl et al, 2014), and polyploid was verified to be one of the strategies for plants to expand their ranges and invade new environments by endowing polyploid progenies with novel traits (Cheng et al, 2021a). In addition, gene expansion (especially TFs) is important for plant evolution (Feller et al, 2011; Mathew and Agarwal, 2018).…”

“…Amphibious plants are those that can grow in both terrestrial and submerged conditions and evolved unique advantages between different environments (Agarie et al, 1997). Profound investigations have been performed on terrestrial plants, and a few genomic data of aquatic plants were also recently reported (Lu et al, 2021; Shi et al, 2022). However, genomic data of amphibious plants are still lacking.…”

From comparative gene content and gene order to ancestral contigs, chromosomes and karyotypes

“…We wished to include as many orders as possible in our study, ideally with access to at least six genomes with high quality, preferably chromosome-level, assemblies, distributed among at least three different families. At the time of data collection, we could obtain suitable data from three fabid orders, Fagales [20–27], Cucurbitales [28–33], Malpighiales [34–39]; three malvid orders, Myrtales [40–44], Malvales [45–50] and Sapindales [51–61]; one campanulid order, Asterales [62–68]; and three lamiid orders, Gentianales [69–75], Lamiales [76–82] and Solanales [83–88], plus Ericales [89–94]. Other orders with sufficient genomes available were not selected, such as Fabales, because representative genomes from only one or two families were available, or Brassicales, which is the subject of a concurrent publication.…”