Targeting of KOR by famotidine promotes OPC maturation differentiation and CNS remyelination via STAT3 signaling pathway.

This study aims to identify FDA-approved drugs that can target the kappa-opioid receptor (KOR) for the treatment of demyelinating diseases. Demyelinating diseases are characterized by myelin sheath destruction or formation that results in severe neurological dysfunction. Remission of this disease is largely dependent on the differentiation of oligodendrocyte precursor cells (OPCs) into mature oligodendrocytes (OLGs) in demyelinating lesions. KOR is an important regulatory protein and drug target for the treatment of demyelinating diseases. However, no drug targeting KOR has been developed due to the long clinical trials for drug discovery. Here, a structure-based virtual screening was applied to identify drugs targeting KOR among 1843 drugs of FDA-approved drug libraries, and famotidine was screen out by its high affinity cooperation with KOR as well as the clinical safety. We discovered that famotidine directly promoted OPC maturation and remyelination using the complementary in vitro and in vivo models. Administration of famotidine was not only effectively enhanced CNS myelinogenesis, but also promoted remyelination. Mechanically speaking, famotidine promoted myelinogenesis or remyelination through KOR/STAT3 signaling pathway. In general, our study provided evidence of new clinical applicability of famotidine for the treatment of demyelinating diseases for which there is currently no effective therapy.

Pseudorabies virus manipulates mitochondrial tryptophanyl-tRNA synthetase 2 for viral replication.

The pseudorabies virus (PRV) is identified as a double-helical DNA virus responsible for causing Aujeszky's disease, which results in considerable economic impacts globally. The enzyme tryptophanyl-tRNA synthetase 2 (WARS2), a mitochondrial protein involved in protein synthesis, is recognized for its broad expression and vital role in the translation process. The findings of our study showed an increase in both mRNA and protein levels of WARS2 following PRV infection in both cell cultures and animal models. Suppressing WARS2 expression via RNA interference in PK-15 â€‹cells led to a reduction in PRV infection rates, whereas enhancing WARS2 expression resulted in increased infection rates. Furthermore, the activation of WARS2 in response to PRV was found to be reliant on the cGAS/STING/TBK1/IRF3 signaling pathway and the interferon-alpha receptor-1, highlighting its regulation via the type I interferon signaling pathway. Further analysis revealed that reducing WARS2 levels hindered PRV's ability to promote protein and lipid synthesis. Our research provides novel evidence that WARS2 facilitates PRV infection through its management of protein and lipid levels, presenting new avenues for developing preventative and therapeutic measures against PRV infections.

Is histological healing more clinically valuable than endoscopic healing in Crohn's disease?

OBJECTIVES: Small bowel (SB) endoscopic healing has not been well explored in patients with Crohn's disease (CD). This study aimed to assess the clinical utility of SB endoscopic mucosal and histological healing in patients with CD. METHODS: In total, 99 patients with CD in clinical-serological remission were retrospectively followed after they underwent colonoscopy and double-balloon enteroscopy. Time until clinical relapse (CD activity index of >150 with an increase of >70 points) and serological relapse (abnormal elevation of C-reactive protein levels) constituted the primary endpoints. RESULTS: Of the 99 patients, 75 (74.7%) exhibited colonoscopic healing and 43 (43.4%) exhibited SB endoscopic healing. Clinical relapse, serological relapse, hospitalization, and surgery occurred in 8 (18.6%), 11 (25.6%), 11 (25.6%), and 2 (4.6%) patients, respectively. Of the 43 patients who exhibited SB endoscopic healing, 21 (48.8%) achieved histological healing. Clinical relapse, serological relapse, hospitalization, and surgery occurred in 4 (19.0%), 7 (33.3%), 7 (33.3%), and 1 (4.8%) patient, respectively. There was no statistically significant difference in the number of patients who relapsed, were hospitalized, or underwent surgery between those who exhibited histological healing and those who did not. CONCLUSION: A substantial number of patients who were in clinical-serological remission did not undergo SB endoscopic healing, and the lesions increased their risk of clinical relapse. Thus, endoscopic healing may be of greater clinical value than histological healing when evaluating the remission of patients with CD.

Development of an inducible Cas9 nickase and PAM-free Cas12a platform for bacterial diagnostics.

Rapid, efficient, specific and sensitive diagnostic techniques are critical for selecting appropriate treatments for drug-resistant bacterial infections. To address this challenge, we have developed a novel diagnostic method, called the Dual-Cas Tandem Diagnostic Platform (DTDP), which combines the use of Cas9 nickase (Cas9n) and Cas12a. DTDP works by utilizing the Cas9n-sgRNA complex to create a nick in the target strand's double-stranded DNA (dsDNA). This prompts DNA polymerase to displace the single-stranded DNA (ssDNA) and leads to cycles of DNA replication through nicking, displacement, and extension. The ssDNA is then detected by the Cas12a-crRNA complex (which is PAM-free), activating trans-cleavage and generating a fluorescent signal from the fluorescent reporter. DTDP exhibits a high sensitivity (1 CFU/mL or 100 ag/µL), high specificity (specifically to MRSA in nine pathogenic species), and excellent accuracy (100%). The dual RNA recognition process in our method improves diagnostic specificity by decreasing the limitations of Cas12a in detecting dsDNA protospacer adjacent motifs (PAMs) and leverages multiple advantages of multi-Cas enzymes in diagnostics. This novel approach to pathogenic microorganism detection has also great potential for clinical diagnosis.

Exonuclease III Can Efficiently Cleave Linear Single-Stranded DNA: Reshaping Its Experimental Applications in Biosensors.

Exonuclease III (Exo III) has been generally used as a double-stranded DNA (dsDNA)-specific exonuclease that does not degrade single-stranded DNA (ssDNA). Here, we demonstrate that Exo III at concentrations above 0.1 unit/µL can efficiently digest linear ssDNA. Moreover, the dsDNA specificity of Exo III is the foundation of many DNA target recycling amplification (TRA) assays. We demonstrate that with 0.3 and 0.5 unit/µL Exo III, the degradation of an ssDNA probe, free or fixed on a solid surface, was not discernibly different, regardless of the presence or absence of target ssDNA, indicating that Exo III concentration is critical in TRA assays. The study has expanded the Exo III substrate scope from dsDNA to both dsDNA and ssDNA, which will reshape its experimental applications.

Mucilage secretion by aerial roots in sorghum (Sorghum bicolor): sugar profile, genetic diversity, GWAS and transcriptomic analysis.

Aerial root mucilage can enhance nitrogen fixation by providing sugar and low oxygen environment to the rhizosphere microbiome in Sierra Mixe maize. Aerial root mucilage has long been documented in sorghum (Sorghum bicolor), but little is known about the biological significance, genotypic variation, and genetic regulation of this biological process. In the present study, we found that a large variation of mucilage secretion capacity existed in a sorghum panel consisting of 146 accessions. Mucilage secretion occurred primarily in young aerial roots under adequately humid conditions but decreased or stopped in mature long aerial roots or under dry conditions. The main components of the mucilage-soluble were glucose and fructose, as revealed by sugar profiling of cultivated and wild sorghum. The mucilage secretion capacity of landrace grain sorghum was significantly higher than that of wild sorghum. Transcriptome analysis revealed that 1844 genes were upregulated and 2617 genes were downregulated in mucilage secreting roots. Amongst these 4461 differentially expressed genes, 82 genes belonged to glycosyltransferases and glucuronidation pathways. Sobic.010G120200, encoding a UDP-glycosyltransferase, was identified by both GWAS and transcriptome analysis as a candidate gene, which may be involved in the regulation of mucilage secretion in sorghum through a negative regulatory mechanism.

TMEM41B Is an Interferon-Stimulated Gene That Promotes Pseudorabies Virus Replication.

Pseudorabies virus (PRV) is a double-stranded DNA virus that causes Aujeszky's disease and is responsible for economic loss worldwide. Transmembrane protein 41B (TMEM41B) is a novel endoplasmic reticulum (ER)-localized regulator of autophagosome biogenesis and lipid mobilization; however, the role of TMEM41B in regulating PRV replication remains undocumented. In this study, PRV infection was found to upregulate TMEM41B mRNA and protein levels both in vitro and in vivo. For the first time, we found that TMEM41B could be induced by interferon (IFN), suggesting that TMEM41B is an IFN-stimulated gene (ISG). While TMEM41B knockdown suppressed PRV proliferation, TMEM41B overexpression promoted PRV proliferation. We next studied the specific stages of the virus life cycle and found that TMEM41B knockdown affected PRV entry. Mechanistically, we demonstrated that the knockdown of TMEM41B blocked PRV-stimulated expression of the key enzymes involved in lipid synthesis. Additionally, TMEM41B knockdown played a role in the dynamics of lipid-regulated PRV entry-dependent clathrin-coated pits (CCPs). Lipid replenishment restored the CCP dynamic and PRV entry in TMEM41B knockdown cells. Together, our results indicate that TMEM41B plays a role in PRV infection via regulating lipid homeostasis. IMPORTANCE PRV belongs to the alphaherpesvirus subfamily and can establish and maintain a lifelong latent infection in pigs. As such, an intermittent active cycle presents great challenges to the prevention and control of PRV disease and is responsible for serious economic losses to the pig breeding industry. Studies have shown that lipids play a crucial role in PRV proliferation. Thus, the manipulation of lipid metabolism may represent a new perspective for the prevention and treatment of PRV. In this study, we report that the ER transmembrane protein TMEM41B is a novel ISG involved in PRV infection by regulating lipid synthesis. Therefore, our findings indicate that targeting TMEM41B may be a promising approach for the development of PRV vaccines and therapeutics.

Genome-wide identification, evolutionary and functional analyses of KFB family members in potato.

BACKGROUND: Kelch repeat F-box (KFB) proteins play vital roles in the regulation of multitudinous biochemical and physiological processes in plants, including growth and development, stress response and secondary metabolism. Multiple KFBs have been characterized in various plant species, but the family members and functions have not been systematically identified and analyzed in potato. RESULTS: Genome and transcriptome analyses of StKFB gene family were conducted to dissect the structure, evolution and function of the StKFBs in Solanum tuberosum L. Totally, 44 StKFB members were identified and were classified into 5 groups. The chromosomal localization analysis showed that the 44 StKFB genes were located on 12 chromosomes of potato. Among these genes, two pairs of genes (StKFB15/16 and StKFB40/41) were predicted to be tandemly duplicated genes, and one pair of genes (StKFB15/29) was segmentally duplicated genes. The syntenic analysis showed that the KFBs in potato were closely related to the KFBs in tomato and pepper. Expression profiles of the StKFBs in 13 different tissues and in potato plants with different treatments uncovered distinct spatial expression patterns of these genes and their potential roles in response to various stresses, respectively. Multiple StKFB genes were differentially expressed in yellow- (cultivar 'Jin-16'), red- (cultivar 'Red rose-2') and purple-fleshed (cultivar 'Xisen-8') potato tubers, suggesting that they may play important roles in the regulation of anthocyanin biosynthesis in potato. CONCLUSIONS: This study reports the structure, evolution and expression characteristics of the KFB family in potato. These findings pave the way for further investigation of functional mechanisms of StKFBs, and also provide candidate genes for potato genetic improvement.

Genome-wide identification of PEBP gene family members in potato, their phylogenetic relationships, and expression patterns under heat stress.

BACKGROUND: The phosphatidylethanolamine-binding protein (PEBP) gene family is involved in regulating many plant traits. Genome-wide identification of PEPB members and knowledge of their responses to heat stress may assist genetic improvement of potato (Solanum tuberosum). METHODS AND RESULTS: We identified PEBP gene family members from both the recently-updated, long-reads-based reference genome (DM v6.1) and the previous short-reads-based annotation (PGSC DM v3.4) of the potato reference genome and characterized their heat-induced gene expression using RT-PCR and RNA-Seq. Fifteen PEBP family genes were identified from DM v6.1 and named as StPEBP1 to StPEBP15 based on their locations on 6 chromosomes and were classified into FT, TFL, MFT, and PEBP-like subfamilies. Most of the StPEBP genes were found to have conserved motifs 1 to 5. Tandem or segmental duplications were found between StPEBP genes in seven pairs. Heat stress induced opposite expression patterns of certain FT and TFL members but involving different members in leaves, roots and tubers. CONCLUSION: The long-reads-based genome assembly and annotation provides a better genomic resource for identification of PEBP family genes. Heat stress tends to decrease FT gene activities but increases TFL gene activities, but this opposite expression involves different FT/TFL pairs in leaves, roots, and tubers. This tissue-specific expression pattern of PEBP members may partly explain why different potato organs differ in their sensitivities to heat stress. Our study provides candidate PEBP family genes and relevant information for genetic improvement of heat tolerance in potato and may help understand heat-induced responses in other plants.

EGCG Restricts PRRSV Proliferation by Disturbing Lipid Metabolism.

Porcine reproductive and respiratory syndrome virus (PRRSV) infection leads to late-term reproductive failure and respiratory illness that affect the global swine industry. Epigallocatechin gallate (EGCG) is a polyphenolic compound from green tea that exerts antiviral activity against diverse viruses. This study aimed to report an uncharacterized mechanism of how EGCG restricted PRRSV proliferation. EGCG showed no significant effects on cell viability, cell cycle progression, and apoptosis in porcine alveolar macrophages and MARC-145 cells. The treatment of cells with EGCG attenuated the replication of both highly pathogenic and less pathogenic PRRSV in vitro. The viral life cycle analysis demonstrated that EGCG affected PRRSV replication and assembly, but not viral attachment, entry, or release. Interestingly, EGCG treatment abrogated the increased lipid droplets formation and lipid content induced by PRRSV infection. We further demonstrated that EGCG blocked PRRSV-stimulated expression of the key enzymes in lipid synthesis. In addition, EGCG attenuated PRRSV-induced autophagy that is critical for PRRSV proliferation. The supplementation of oleic acid restored PRRSV replication and assembly under EGCG treatment. Together, our results support that EGCG inhibits PRRSV proliferation through disturbing lipid metabolism. IMPORTANCE Porcine reproductive and respiratory syndrome virus (PRRSV) is an enveloped single-positive-stranded RNA virus that causes acute respiratory distress in piglets and reproductive failure in sows, resulting in huge economic losses to the global swine industry. Several lines of evidence have suggested the crucial roles of lipids in PRRSV proliferation. Our previous report demonstrated that PRRSV activated lipophagy to facilitate viral replication through downregulating the expression of N-Myc downstream-regulated gene 1. The manipulation of lipid metabolism may be a new perspective to prevent PRRSV spread. In the present study, we reported that epigallocatechin-3-gallate (EGCG), the major component of green tea catechins, significantly attenuated PRRSV infection through inhibiting lipid synthesis and autophagy. Given that natural products derived from plants have helped in the prevention and treatment of various infectious diseases, EGCG has a great potential to serve as a safe and environmentally friendly natural compound to treat PRRSV infection.

Heat-stress-induced sprouting and differential gene expression in growing potato tubers: Comparative transcriptomics with that induced by postharvest sprouting.

Crops face increased risk from heat stress due to climate change. Potato (Solanum tuberosum L.) tubers grown in hot summers often have defects including pre-harvest sprouting ("heat sprouts"). We have used 18 potato cultivars to investigate whether heat stress (HS) conditions alone could cause heat sprouting and dormancy changes in tubers. We also examined transcriptomic responses of potato to HS and whether these responses are like those induced by postharvest sprouting. We demonstrated that HS alone caused heat sprouts and shortened postharvest dormancy period, heat-sprouted tubers became dormant after harvest, and cultivars varied substantially for producing heat spouts but there was no clear association with cultivar maturity earliness. Cultivar Innovator did not show any heat sprouts and still had long dormancy. Dormancy-associated genes (DOG1 and SLP) were downregulated in HS tubers like in postharvest sprouting tubers. We have identified 1201 differentially expressed genes, 14 enriched GO terms and 12 enriched KEGG pathways in response to HS in growing tubers of 'Russet Burbank'. Transcriptomic response of 'Russet Burbank' to HS showed significant similarities to that of postharvest non-HS sprouted tubers. Gibberellin biosynthesis pathway was enriched in heat-stressed tubers and was likely involved in heat sprouting and dormancy release. Heat sprouting and postharvest sprouting shared common candidate genes and had significant similarity in gene expression. Our study has significance for selecting potato cultivars for farming, planning storage and utilization of heat-stressed tubers, identifying sprouting-related genes, understanding heat-stress biology, and breeding heat-tolerant potato cultivars, especially for sustainable potato production under climate change.

Potato Response to Drought Stress: Physiological and Growth Basis.

Drought poses a major challenge to the production of potatoes worldwide. Climate change is predicted to further aggravate this challenge by intensifying potato crop exposure to increased drought severity and frequency. There is an ongoing effort to adapt our production systems of potatoes through the development of drought-tolerant cultivars that are appropriately engineered for the changing environment. The breeding of drought-tolerant cultivars can be approached through the identification of drought-related physiological and biochemical traits and their deployment in new potato cultivars. Thus, the main objective of this study was to develop a method to identify and characterize the drought-tolerant potato genotypes and the related key traits. To achieve this objective, first we studied 56 potato genotypes including 54 cultivars and 2 advanced breeding lines to assess drought tolerance in terms of tuber yield in the greenhouse experiment. Drought differentially reduced tuber yield in all genotypes. Based on their capacity to maintain percent tuber yield under drought relative to their well-watered controls, potato genotypes differed in their ability to tolerate drought. We then selected six genotypes, Bannock Russet, Nipigon, Onaway, Denali, Fundy, and Russet Norkotah, with distinct yield responses to drought to further examine the physiological and biochemical traits governing drought tolerance. The drought-induced reduction in tuber yield was only 15-20% for Bannock Russet and Nipigon, 44-47% for Onaway and Denali, and 83-91% for Fundy and Russet Norkotah. The tolerant genotypes, Bannock Russet and Nipigon, exhibited about a 2-3-fold increase in instantaneous water-use efficiency (WUE) under drought as compared with their well-watered controls. This stimulation was about 1.8-2-fold for moderately tolerant genotypes, Onaway and Denali, and only 1.5-fold for sensitive genotypes, Fundy, and Russet Norkotah. The differential stimulation of instantaneous WUE of tolerant and moderately tolerant genotypes vs. sensitive genotypes was accounted for by the differential suppression of the rates of photosynthesis, stomatal conductance, and transpiration rates across genotypes. Potato genotypes varied in their response to leaf protein content under drought. We suggest that the rates of photosynthesis, instantaneous WUE, and leaf protein content can be used as the selection criteria for the drought-tolerant potato genotypes.

Preliminary prediction of the control reproduction number of COVID-19 in Shaanxi Province, China.

OBJECTIVES: Firstly, according to the characteristics of COVID-19 epidemic and the control measures of the government of Shaanxi Province, a general population epidemic model is established. Then, the control reproduction number of general population epidemic model is obtained. Based on the epidemic model of general population, the epidemic model of general population and college population is further established, and the control reproduction number is also obtained. METHODS: For the established epidemic model, firstly, the expression of the control reproduction number is obtained by using the next generation matrix. Secondly, the real-time reported data of COVID-19 in Shaanxi Province is used to fit the epidemic model, and the parameters in the model are estimated by least square method and MCMC. Thirdly, the Latin hypercube sampling method and partial rank correlation coefficient (PRCC) are adopted to analyze the sensitivity of the model. CONCLUSIONS: The control reproduction number remained at 3 from January 23 to January 31, then gradually decreased from 3 to slightly greater than 0.2 by using the real-time reports on the number of COVID-19 infected cases from Health Committee of Shaanxi Province in China. In order to further control the spread of the epidemic, the following measures can be taken: (i) reducing infection by wearing masks, paying attention to personal hygiene and limiting travel; (ii) improving isolation of suspected patients and treatment of symptomatic individuals. In particular, the epidemic model of the college population and the general population is established, and the control reproduction number is given, which will provide theoretical basis for the prevention and control of the epidemic in the colleges.

The celery genome sequence reveals sequential paleo-polyploidizations, karyotype evolution and resistance gene reduction in apiales.

Celery (Apium graveolens L. 2n = 2x = 22), a member of the Apiaceae family, is among the most important and globally grown vegetables. Here, we report a high-quality genome sequence assembly, anchored to 11 chromosomes, with total length of 3.33 Gb and N50 scaffold length of 289.78 Mb. Most (92.91%) of the genome is composed of repetitive sequences, with 62.12% of 31 326 annotated genes confined to the terminal 20% of chromosomes. Simultaneous bursts of shared long-terminal repeats (LTRs) in different Apiaceae plants suggest inter-specific exchanges. Two ancestral polyploidizations were inferred, one shared by Apiales taxa and the other confined to Apiaceae. We reconstructed 8 Apiales proto-chromosomes, inferring their evolutionary trajectories from the eudicot common ancestor to extant plants. Transcriptome sequencing in three tissues (roots, leaves and petioles), and varieties with different-coloured petioles, revealed 4 and 2 key genes in pathways regulating anthocyanin and coumarin biosynthesis, respectively. A remarkable paucity of NBS disease-resistant genes in celery (62) and other Apiales was explained by extensive loss and limited production of these genes during the last ~10 million years, raising questions about their biotic defence mechanisms and motivating research into effects of chemicals, for example coumarins, that give off distinctive odours. Celery genome sequencing and annotation facilitates further research into important gene functions and breeding, and comparative genomic analyses in Apiales.

Paleo-polyploidization in Lycophytes.

Lycophytes and seed plants constitute the typical vascular plants. Lycophytes have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed plants. Here, genomic analyses including the homologous gene dot plot analysis detected multiple paleo-polyploidization events, with one occurring approximately 13-15 million years ago (MYA) and another about 125-142 MYA, during the evolution of the genome of Selaginella moellendorffii, a model lycophyte. In addition, comparative analysis of reconstructed ancestral genomes of lycophytes and angiosperms suggested that lycophytes were affected by more paleo-polyploidization events than seed plants. Results from the present genomic analyses indicate that paleo-polyploidization has contributed to the successful establishment of both lineages-lycophytes and seed plants-of vascular plants.

Transcriptome analysis of heat stress response genes in potato leaves.

Heat stress has a severe impact on potato growth and tuberization process, always resulting in the decrease of tuber yield and quality. Therefore, it is of great significance for potato breeding to illuminate the mechanism of heat stress on potato and explore heat resistant genes. In this study, two cDNA libraries from normal potato leaves (20 °C day/18 °C night) and potato leaves with 3 days of heat treatment (35 °C day/28 °C night) were constructed respectively. Totally, 1420 differentially expressed genes (DEGs) were identified. The expression patterns of 12 randomly selected genes detected using droplet digital PCR agreed with the sequencing data. Gene ontology analysis showed that these DEGs were clustered into 49 different GO types, reflecting the functional diversity of the heat stress response genes. The results of KEGG pathway enrichment showed the potential biological pathways in which the DEGs were involved, indicating that these pathways may be involved in heat tolerance regulation. Most potato heat transcription factors (StHsfs) and heat shock proteins (StHsps) were not expressed efficiently based on expression profile of these DEGs. StHsp26-CP and StHsp70 were markedly increased after 3 days of heat treatment. These data will be useful for further understanding the molecular mechanisms of potato plant tolerance to heat stress and provide a basis for breeding heat-tolerance varieties.

Coriander Genomics Database: a genomic, transcriptomic, and metabolic database for coriander.

Coriander (Coriandrum sativum L.), also known as cilantro, is a globally important vegetable and spice crop. Its genome and that of carrot are models for studying the evolution of the Apiaceae family. Here, we developed the Coriander Genomics Database (CGDB, http://cgdb.bio2db.com/) to collect, store, and integrate the genomic, transcriptomic, metabolic, functional annotation, and repeat sequence data of coriander and carrot to serve as a central online platform for Apiaceae and other related plants. Using these data sets in the CGDB, we intriguingly found that seven transcription factor (TF) families showed significantly greater numbers of members in the coriander genome than in the carrot genome. The highest ratio of the numbers of MADS TFs between coriander and carrot reached 3.15, followed by those for tubby protein (TUB) and heat shock factors. As a demonstration of CGDB applications, we identified 17 TUB family genes and conducted systematic comparative and evolutionary analyses. RNA-seq data deposited in the CGDB also suggest dose compensation effects of gene expression in coriander. CGDB allows bulk downloading, significance searches, genome browser analyses, and BLAST searches for comparisons between coriander and other plants regarding genomics, gene families, gene collinearity, gene expression, and the metabolome. A detailed user manual and contact information are also available to provide support to the scientific research community and address scientific questions. CGDB will be continuously updated, and new data will be integrated for comparative and functional genomic analysis in Apiaceae and other related plants.

Preferential gene retention increases the robustness of cold regulation in Brassicaceae and other plants after polyploidization.

Cold stress profoundly affects plant growth and development and is a key factor affecting the geographic distribution and evolution of plants. Plants have evolved adaptive mechanisms to cope with cold stress. Here, through the genomic analysis of Arabidopsis, three Brassica species and 17 other representative species, we found that both cold-related genes (CRGs) and their collinearity were preferentially retained after polyploidization followed by genome instability, while genome-wide gene sets exhibited a variety of other expansion mechanisms. The cold-related regulatory network was increased in Brassicaceae genomes, which were recursively affected by polyploidization. By combining our findings regarding the selective retention of CRGs from this ecological genomics study with the available knowledge of cold-induced chromosome doubling, we hypothesize that cold stress may have contributed to the success of polyploid plants through both increasing polyploidization and selectively maintaining CRGs during evolution. This hypothesis requires further biological and ecological exploration to obtain solid supporting evidence, which will potentially contribute to understanding the generation of polyploids and to the field of ecological genomics.

Deciphering the high-quality genome sequence of coriander that causes controversial feelings.

Coriander (Coriandrum sativum L. 2n = 2x = 22), a plant from the Apiaceae family, also called cilantro or Chinese parsley, is a globally important crop used as vegetable, spice, fragrance and traditional medicine. Here, we report a high-quality assembly and analysis of its genome sequence, anchored to 11 chromosomes, with total length of 2118.68 Mb and N50 scaffold length of 160.99 Mb. We found that two whole-genome duplication events, respectively, dated to ~45-52 and ~54-61 million years ago, were shared by the Apiaceae family after their split from lettuce. Unbalanced gene loss and expression are observed between duplicated copies produced by these two events. Gene retention, expression, metabolomics and comparative genomic analyses of terpene synthase (TPS) gene family, involved in terpenoid biosynthesis pathway contributing to coriander's special flavour, revealed that tandem duplication contributed to coriander TPS gene family expansion, especially compared to their carrot counterparts. Notably, a TPS gene highly expressed in all 4 tissues and 3 development stages studied is likely a major-effect gene encoding linalool synthase and myrcene synthase. The present genome sequencing, transcriptome, metabolome and comparative genomic efforts provide valuable insights into the genome evolution and spice trait biology of Apiaceae and other related plants, and facilitated further research into important gene functions and crop improvement.

Improving Potato Stress Tolerance and Tuber Yield Under a Climate Change Scenario - A Current Overview.

Global climate change in the form of extreme heat and drought poses a major challenge to sustainable crop production by negatively affecting plant performance and crop yield. Such negative impact on crop yield is likely to be aggravated in future because continued greenhouse gas emissions will cause further rise in temperature leading to increased evapo-transpiration and drought severity, soil salinity as well as insect and disease threats. This has raised a major challenge for plant scientists on securing global food demand, which urges an immediate need to enhance the current yield of major food crops by two-fold to feed the increasing population. As a fourth major food crop, enhancing potato productivity is important for food security of an increasing population. However, potato plant is highly prone to high temperature, drought, soil salinity, as well as insect and diseases. In order to maintain a sustainable potato production, we must adapt our cultivation practices and develop stress tolerant potato cultivars that are appropriately engineered for changing environment. Yet the lack of data on the underlying mechanisms of potato plant resistance to abiotic and biotic stress and the ability to predict future outcomes constitutes a major knowledge gap. It is a challenge for plant scientists to pinpoint means of improving tuber yield under increasing CO2, high temperature and drought stress including the changing patterns of pest and pathogen infestations. Understanding stress-related physiological, biochemical and molecular processes is crucial to develop screening procedures for selecting crop cultivars that can better adapt to changing growth conditions. Elucidation of such mechanism may offer new insights into the identification of specific characteristics that may be useful in breeding new cultivars aimed at maintaining or even enhancing potato yield under changing climate. This paper discusses the recent progress on the mechanism by which potato plants initially sense the changes in their surrounding CO2, temperature, water status, soil salinity and consequently respond to these changes at the molecular, biochemical and physiological levels. We suggest that future research needs to be concentrated on the identification and characterization of signaling molecules and target genes regulating stress tolerance and crop yield potential.