Genome of plant watercress (<i>Nasturtium officinale</i> R. Br.) illuminates genomic basis for marine-incursions adaptation in the Mediterranean area

Watercress (Nasturtium officinale R. Br.), an herbaceous plant in the cruciferous family, has a long history of use as a vegetable. In this report, we present a high-quality assembly of the watercress genome, based primarily on PacBio and Hi-C sequencing data. The assembled genome of watercress was 337.51 Mb in size, with a contig N50 length of 3.26 Mb and a scaffold N50 length of 5.85 Mb. Approximately 49.15% (165.88 Mb) of the assembled genome was annotated as repetitive sequences, with long terminal repeats (LTRs) being the most abundant, representing 41.96% of the genome. About 96.6% of the assembly was anchored onto 16 pseudo-chromosomes using Hi-C data. Analyses of the syntenic relationships within and between species collectively indicated that watercress underwent an additional whole-genome duplication (WGD) event after divergence from Arabidopsis. The time of the watercress-specific WGD was estimated to be around 4.7 to 12.6 million years ago (Mya), which coincided with the Zanclean flood about 5.33 Mya. After the WGD, a total of 14,353 homologous gene pairs, including 22,476 genes were retained, accounting for 57.71% of all genes in the watercress genome. From the perspective of the watercress genome, we found that watercress might adapt to various abiotic stresses caused by the Zanclean flood through two mechanisms: one is enhancing tolerance to various abiotic stresses, and the other is escaping various abiotic stresses by floating growth. The watercress genome and transcriptome presented here provide useful information for subsequent molecular breeding and understanding how watercress adapted to an aquatic environment.