Salt stress is an important environmental limiting factor. Water dropwort (Oenanthe javanica) is an important vegetable in East Asia; however, its phenotypic and physiological response is poorly explored. For this purpose, 48 cultivars of water dropwort were grown hydroponically and treated with 0, 50, 100, and 200 mm NaCl for 14 days. Than their phenotypic responses were evaluated, afterward, physiological studies were carried out in selected sensitive and tolerant cultivars. In the present study, the potential tolerant (V11E0022) and sensitive (V11E0135) cultivars were selected by screening 48 cultivars based on their phenotype under four different levels of salt concentrations (0, 50, 100, and 200 mm). The results depicted that plant height, number of branches and leaves were less effected in V11E0022, and most severe reduction was observed in V11E0135 in comparison with others. Than the changes in biomass, ion contents, accumulation of reactive oxygen species, and activities of antioxidant enzymes and non-enzymatic antioxidants were determined in the leaves and roots of the selected cultivars. The potential tolerant cultivar (V11E0022) showed less reduction of water content and demonstrated low levels of Na⁺ uptake, malondialdehyde, and hydrogen peroxide (H₂O₂) in both leaves and roots. Moreover, the tolerant cultivar (V11E0022) showed high antioxidant activities of ascorbate peroxidase (APX), superoxide dismutase, peroxidase, catalase (CAT), reduced glutathione (GSH), and high accumulation of proline and soluble sugars compared to the sensitive cultivar (V11E0135). These results suggest the potential tolerance of V11E0022 cultivar against salt stress with low detrimental effects and a good antioxidant defense system. The observations also suggest good antioxidant capacity of water dropwort against salt stress. The findings of the present study also suggest that the number of branches and leaves, GSH, proline, soluble sugars, APX, and CAT could serve as the efficient markers for understanding the defense mechanisms of water dropwort under the conditions of salt stress.

The chloroplast genome is important for plant development and plant evolution. Nelumbo nucifera is one member of relict plants surviving from the late Cretaceous. Recently, a new sequencing platform PacBio RS II, known as `SMRT (Single Molecule, Real-Time) sequencing’, has been developed. Using the SMRT sequencing to investigate the chloroplast genome of N. nucifera will help to elucidate the plastid evolution of basal eudicots. The sizes of the de novo assembled complete chloroplast genome of N. nucifera were 163,307 bp, 163,747 bp and 163,600 bp with average depths of coverage of 7×, 712× and 105× sequenced by Sanger, Illumina MiSeq and PacBio RS II, respectively. The precise chloroplast genome of N. nucifera was obtained from PacBio RS II data proofread by Illumina MiSeq reads, with a quadripartite structure containing a large single copy region (91,846 bp) and a small single copy region (19,626 bp) separated by two inverted repeat regions (26,064 bp). The genome contains 113 different genes, including four distinct rRNAs, 30 distinct tRNAs and 79 distinct peptide-coding genes. A phylogenetic analysis of 133 taxa from 56 orders indicated that Nelumbo with an age of 177 million years is a sister clade to Platanus, which belongs to the basal eudicots. Basal eudicots began to emerge during the early Jurassic with estimated divergence times at 197 million years using MCMCTree. IR expansions/contractions within the basal eudicots seem to have occurred independently. Because of long reads and lack of bias in coverage of AT-rich regions, PacBio RS II showed a great promise for highly accurate `finished’ genomes, especially for a de novo assembly of genomes. N. nucifera is one member of basal eudicots, however, evolutionary analyses of IR structural variations of N. nucifera and other basal eudicots suggested that IR expansions/contractions occurred independently in these basal eudicots or were caused by independent insertions and deletions. The precise chloroplast genome of N. nucifera will present new information for structural variation of chloroplast genomes and provide new insight into the evolution of basal eudicots at the primary sequence and structural level.

Summary: Sacred lotus (Nelumbo nucifera) is an ornamental plant that is also used for food and medicine. This basal eudicot species is especially important from an evolutionary perspective, as it occupies a critical phylogenetic position in flowering plants. Here we report the draft genome of a wild strain of sacred lotus. The assembled genome is 792 Mb, which is approximately 85–90% of genome size estimates. We annotated 392 Mb of repeat sequences and 36 385 protein‐coding genes within the genome. Using these sequence data, we constructed a phylogenetic tree and confirmed the basal location of sacred lotus within eudicots. Importantly, we found evidence for a relatively recent whole‐genome duplication event; any indication of the ancient paleo‐hexaploid event was, however, absent. Genomic analysis revealed evidence of positive selection within 28 embryo‐defective genes and one annexin gene that may be related to the long‐term viability of sacred lotus seed. We also identified a significant expansion of starch synthase genes, which probably elevated starch levels within the rhizome of sacred lotus. Sequencing this strain of sacred lotus thus provided important insights into the evolution of flowering plant and revealed genetic mechanisms that influence seed dormancy and starch synthesis.

Abiotic stress, such as drought and salinity, severely affect the growth and yield of many plants. Oenanthe javanica (commonly known as water dropwort) is an important vegetable that is grown in the saline-alkali soils of East Asia, where salinity is the limiting environmental factor. To study the defense mechanism of salt stress responses in water dropwort, we studied two water dropwort cultivars, V11E0022 and V11E0135, based on phenotypic and physiological indexes. We found that V11E0022 were tolerant to salt stress, as a result of good antioxidant defense system in the form of osmolyte (proline), antioxidants (polyphenols and flavonoids), and antioxidant enzymes (APX and CAT), which provided novel insights for salt-tolerant mechanisms. Then, a comparative transcriptomic analysis was conducted, and Gene Ontology (GO) analysis revealed that differentially expressed genes (DEGs) involved in the carbohydrate metabolic process could reduce oxidative stress and enhance energy production that can help in adaptation against salt stress. Similarly, lipid metabolic processes can also enhance tolerance against salt stress by reducing the transpiration rate, H₂O₂, and oxidative stress. Furthermore, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEGs involved in hormone signals transduction pathway promoted the activities of antioxidant enzymes and reduced oxidative stress; likewise, arginine and proline metabolism, and flavonoid pathways also stimulated the biosynthesis of proline and flavonoids, respectively, in response to salt stress. Moreover, transcription factors (TFs) were also identified, which play an important role in salt stress tolerance of water dropwort. The finding of this study will be helpful for crop improvement under salt stress.