Accumulation of unfolded and misfolded proteins in endoplasmic reticulum (ER) elicits a well-conserved response called the unfolded protein response (UPR), which triggers the upregulation of downstream genes involved in protein folding, vesicle trafficking, and ER-associated degradation (ERAD). Although dynamic transcriptomic responses and the underlying major transcriptional regulators in ER stress response in Arabidopsis have been well established, the proteome changes induced by ER stress have not been reported in Arabidopsis. In the current study, we found that the Arabidopsis Landsberg erecta (Ler) ecotype was more sensitive to ER stress than the Columbia (Col) ecotype. Quantitative mass spectrometry analysis with Tandem Mass Tag (TMT) isobaric labeling showed that, in total, 7439 and 7035 proteins were identified from Col and Ler seedlings, with 88 and 113 differentially regulated (FC > 1.3 or <0.7, p < 0.05) proteins by ER stress in Col and Ler, respectively. Among them, 40 proteins were commonly upregulated in Col and Ler, among which 10 were not upregulated in bzip28 bzip60 double mutant (Col background) plants. Of the 19 specifically upregulated proteins in Col, as compared with that in Ler, components in ERAD, N-glycosylation, vesicle trafficking, and molecular chaperones were represented. Quantitative RT-PCR showed that transcripts of eight out of 19 proteins were not upregulated (FC > 1.3 or <0.7, p < 0.05) by ER stress in Col ecotype, while transcripts of 11 out of 19 proteins were upregulated by ER stress in both ecotypes with no obvious differences in fold change between Col and Ler. Our results experimentally demonstrated the robust ER stress response at the proteome level in plants and revealed differentially regulated proteins that may contribute to the differed ER stress sensitivity between Col and Ler ecotypes in Arabidopsis.

Houttuynia cordata, also known as Yuxingcao in Chinese, is a perennial herb in the Saururaceae family. It is highly regarded for its medicinal properties, particularly in treating respiratory infections and inflammatory conditions, as well as boosting the human immune system. However, a lack of genomic information has hindered research on the functional genomics and potential improvements of H. cordata. In this study, we present a near-complete assembly of H. cordata genome and investigate the biosynthetic pathway of flavonoids, specifically quercetin, using genomics, transcriptomics, and metabolomics analyses. The genome of H. cordata diverged from that of Saururus chinensis around 33.4 million years ago; it consists of 2.24 Gb with 76 chromosomes (4n = 76) and has undergone three whole-genome duplication (WGD) events. These WGDs played a crucial role in shaping the H. cordata genome and influencing the gene families associated with its medicinal properties. Through metabolomics and transcriptomics analyses, we identified key genes involved in the β-oxidation process for biosynthesis of houttuynin, one of the volatile oils responsible for the plant's fishy smell. In addition, using the reference genome, we identified genes involved in flavonoid biosynthesis, particularly quercetin metabolism, in H. cordata. This discovery has important implications for understanding the regulatory mechanisms that underlie production of active pharmaceutical ingredients in traditional Chinese medicine. Overall, the high-quality genome assembly of H. cordata serves as a valuable resource for future functional genomics research and provides a solid foundation for genetic improvement of H. cordata for the benefit of human health.