De novo assembly and analysis of the Pugionium cornutum (L.) Gaertn. transcriptome and identification of genes involved in the drought response

Comparative differences in maintaining membrane fluidity and remodeling cell wall between Glycine soja and Glycine max leaves under drought

Water shortage is one of the most important environmental factors limiting crop yield. In this study, we used wild soybean (Glycine soja Sieb. et Zucc.) and soybean (Glycinemax (L.) Merr.) seedlings as experimental materials, simulated drought stress using soil gravimetry, measured growth and physiological parameters, and analyzed differentially expressed genes and metabolites in the leaves of seedling by integrated transcriptomics and metabolomics techniques. The results indicate that under water deficit, Glycine soja maintained stable photosynthate by accumulating Mg2+, Fe3+, Mn2+, Zn2+ and B3+, and improved water absorption by increasing root growth. Notably, Glycine soja enhanced linoleic acid metabolism and plasma membrane intrinsic protein (PIP1) gene expression to maintain membrane fluidity, and increased pentose, glucuronate and galactose metabolism and thaumatin protein genes expression to remodel the cell wall, thereby increasing water-absorption to better tolerate to drought stress. In addition, it was found that secondary phenolic metabolism, such as phenylpropane biosynthesis, flavonoid biosynthesis and ascobate and aldarate metabolism were weakened, resulting in the collapse of the antioxidant system, which was the main reason for the sensitivity of Glycine max to drought stress. These results provide new insights into plant adaptation to water deficit and offer a theoretical basis for breeding soybean varieties with drought tolerance.

Physiological, transcriptome and gene functional analysis provide novel sights into cadmium accumulation and tolerance mechanisms in kenaf

Kenaf is considered to have great potential for remediation of heavy metals in ecosystems. However, studies on molecular mechanisms of root Cd accumulation and tolerance are still inadequate. In this study, two differently tolerant kenaf cultivars were selected as materials and the physiological and transcriptomic effects were evaluated under Cd stress. This study showed that 200 µmol/L CdCl2 treatment triggered the reactive oxygen species (ROS) explosion and membrane lipid peroxidation. Compared with the Cd-sensitive cultivar 'Z', the Cd-tolerant cultivar 'F' was able to resist oxidative stress in cells by producing higher antioxidant enzyme activities and increasing the contents of ascorbic acid (AsA) and glutathione (GSH). The root cell wall of 'F' exhibited higher polysaccharide contents under Cd treatment, providing more Cd-binding sites. There were 3,439 differentially expressed genes (DEGs) that were co-regulated by Cd treatment in two cultivars. Phenylpropanoid biosynthesis and plant hormone signal transduction pathways were significantly enriched by functional annotation analysis. DEGs associated with pectin, cellulose, and hemi-cellulose metabolism were involved in Cd chelation of root cell wall; V-ATPases, ABCC3 and Narmp3 could participated in vacuolar compartmentalization of Cd; PDR1 was responsible for Cd efflux; the organic acid transporters contributed to the absorption of Cd in soil. These genes might have played key roles in kenaf Cd tolerance and Cd accumulation. Moreover, HcZIP2 was identified to be involved in Cd uptake and transport in kenaf. Our findings provide a deeper understanding of the molecular pathways underlying Cd accumulation and detoxification mechanisms in kenaf.

Understanding the response in Pugionium cornutum (L.) Gaertn. seedling leaves under drought stress using transcriptome and proteome integrated analysis

Background

Drought is one of the crucial constraints limiting horticultural plant’s production and development around the world. Pugionium cornutum is an annual or biennial xerophyte with strong environmental adaptability and drought resistance; however, the mechanisms with respect to response to drought stress remain largely unclear.

Methods

After seedling emergence, the gravimetric method was used to control soil relative water content (SRWC). Drought stress was applied to the six-leaf stage P. cornutum seedlings. The soil water content of different drought stress levels (L) was controlled by gravimetric method as follows: control (L1): 70–75% SRWC; moderate drought level (L2): 40–45% SRWC; severe drought level (L3): 30–35% SRWC, and the water was added to different drought stress levels at about 18:00 p.m. every day. The experiment ended when the leaves of P. cornutum showed severe wilting (10-leaf stage). Samples were harvested and stored at −80 °C for physiological determination, and transcriptomic and proteomic sequencing.

Results

Compared with L1, the leaves of P. cornutum seedlings were increasingly wilted after drought treatment; the SRWC of the drought-stress leaves decreased notably while the leaf water potential was rose; the proline, malondialdehyde (MDA) content increased with the continuous drought treatment but peroxidase (POD) activity decreased. Besides, 3,027 differential genes (DGs) and 196 differential proteins (DPs), along with 1,943 DGs and 489 DPs were identified in L2-L1 and L3-L1, respectively. The transcriptome and proteome integrated analysis manifested that only 30 and 70 were commonly regulated both in L2-L1 and L3-L1, respectively. Of which, 24 and 61 DGs or DPs showed the same trend including sHSPs, APX2, GSTU4, CML42, and POD, etc. However, most of DGs or DPs were regulated only at the transcriptome or proteome level mainly including genes encoding signal pathway (PYR1, PYLs, SnRK2J, PLC2, CDPK9/16/29, CML9, MAPKs), transcription factors (WRKYs, DREB2A, NAC055, NAC072, MYB and, HB7) and ion channel transporters (ALMT4, NHX1, NHX2 and TPK2). These genes or proteins were involved in multiple signaling pathways and some important metabolism processes, which offers valuable information on drought-responsive genes and proteins for further study in P. cornutum.

Responses of transcriptome and metabolome in the roots of Pugionium cornutum (L.) Gaertn to exogenously applied phthalic acid

BACKGROUND

The yield and quality of Pugionium cornutum (L.) Gaertn., a healthy, green vegetable with low sugar and high protein contents and high medicinal value, is severely affected by autotoxicity, which is a leading factor in the formation of plant disease. To help characterize the autotoxicity mechanism of P. cornutum (L.) Gaertn., we performed transcriptomic and metabolic analysis of the roots of P. cornutum (L.) Gaertn. response to phthalic acid, an autotoxin from P. cornutum (L.) Gaertn.

RESULTS

In this study, high-throughput sequencing of nine RNA-seq libraries generated from the roots.of P. cornutum (L.) Gaertn. under different phthalic acid treatments yielded 37,737 unigenes. In total, 1085 (703 upregulated and 382 downregulated) and 5998 (4385 upregulated and 1613 downregulated) DEGs were identified under 0.1 and 10 mmol·L^- 1 phthalic acid treatment, respectively, compared with the control treatment. Glutathione metabolism was among the top five important enriched pathways. In total, 457 and 435 differentially accumulated metabolites were detected under 0.1 and 10 mmol·L^- 1 phthalic acid treatment compared with the control, respectively, of which 223 and 253, respectively, increased in abundance. With the increase in phthalic acid concentration, the accumulation of ten metabolites increased significantly, while that of four metabolites decreased significantly, and phthalic acid, dambonitol, 4-hydroxy-butyric acid, homocitrulline, and ethyl β-D-glucopyranoside were 100 times more abundant under the 10 mmol·L^- 1 phthalic acid treatment than under the control. Seventeen differentially expressed genes significantly associated with phthalic acid content were identified. In addition, the L-histidinol content was highest under 0.1 mmol·L^- 1 phthalic acid, and a total of eleven differentially expressed genes were significantly positively correlated with the L-histidinol content, all of which were annotated to heat shock proteins, aquaporins and cysteine proteases.

CONCLUSIONS

Accumulation of autotoxins altered the metabolic balance in P. cornutum (L.) Gaertn. and influenced water absorption and carbon and nitrogen metabolism. These important results provide insights into the formation mechanisms of autotoxicity and for the subsequent development of new control measures to improve the production and quality of replanted plants.

Lactobacillus acidophilus LA14 Alleviates Liver Injury

Although the probiotic Lactobacillus acidophilus LA14 is used worldwide, its effect on liver diseases remains unelucidated. Here, 32 rats were divided into four groups, gavaged with L. acidophilus LA14 (3 × 10⁹ CFU) or phosphate-buffered saline for 7 days, and then intraperitoneally injected with d-galactosamine or saline. After 24 h, blood, liver, ileum, and feces samples were collected for liver injury, inflammation, intestinal barrier, gut microbiota, metabolome, and transcriptome analyses. Pretreatment with L. acidophilus LA14 alleviated the d-galactosamine-induced elevation of serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), and bile acids; mitigated the histological injury to the liver and gut; and suppressed the inflammatory cytokines macrophage inflammatory protein 1α (MIP-1α), MIP-3α, and MCP-1. L. acidophilus LA14 also ameliorated the d-galactosamine-induced dysbiosis of the gut microbiota and metabolism, such as the enrichment of Bacteroides sp. strain dnLKV3 and the depletion of Streptococcus, butanoic acid, and N-acetyl-d-glucosamine. The underlying mechanism of L. acidophilus LA14 included prevention of not only the d-galactosamine-induced upregulation of infection- and tumor-related pathways but also the d-galactosamine-induced downregulation of antioxidation-related pathways during this process, as reflected by the liver transcriptome and proteome analyses. Furthermore, the administration of L. acidophilus LA14 to healthy rats did not alter the tested liver indicators but significantly enriched the beneficial Lactobacillus and Bifidobacterium species, promoted metabolism and regulated pathways to improve immunity. The ability of L. acidophilus LA14 to alleviate liver injury was further confirmed with an acetaminophen-induced mouse model. These results might provide a reference for future studies on the application of L. acidophilus LA14 for the prevention of liver injury.

IMPORTANCE The probiotic Lactobacillus acidophilus LA14 is widely used, but its effect on liver diseases has not been elucidated. We explored the protective effect of L. acidophilus LA14 on the liver using rats with d-galactosamine-induced liver injury. Pretreatment with L. acidophilus LA14 alleviated the d-galactosamine-induced elevation of serum ALT, AST, ALP, and bile acids, mitigated the histological injury to the liver and gut, and suppressed the inflammatory cytokines MIP-1α, MIP-3α, and MCP-1. These effects were correlated with the modulations of the gut microbiome, metabolome, and hepatic gene expression induced by L. acidophilus LA14. Moreover, the ability of L. acidophilus LA14 to alleviate liver injury was further confirmed with an acetaminophen-induced mouse model. These results might provide a reference for future studies on the application of L. acidophilus LA14 for the prevention of liver injury.

Chloride is beneficial for growth of the xerophyte Pugionium cornutum by enhancing osmotic adjustment capacity under salt and drought stresses

Chloride (Cl-) is pervasive in saline soils, and research on its influence on plants has mainly focused on its role as an essential nutrient and its toxicity when excessive accumulation occurs. However, the possible functions of Cl- in plants adapting to abiotic stresses have not been well documented. Previous studies have shown that the salt tolerance of the xerophytic species Pugionium cornutum might be related to high Cl- accumulation. In this study, we investigated the Cl--tolerant characteristics and possible physiological functions of Cl- in the salt tolerance and drought resistance of P. cornutum. We found that P. cornutum can accumulate a large amount of Cl- in its shoots, facilitating osmotic adjustment and turgor generation under saline conditions. Application of DIDS (4,4´-diisothiocyanostilbene-2,2´-disulfonic acid), a blocker of anion channels, significantly inhibited Cl- uptake, and decreased both the Cl- content and its contribution to leaf osmotic adjustment, resulting in the exacerbation of growth inhibition in response to NaCl. Unlike glycophytes, P. cornutum was able to maintain NO3- homeostasis in its shoots when large amounts of Cl- were absorbed and accumulated. The addition of NaCl mitigated the deleterious effects of osmotic stress on P. cornutum because Cl- accumulation elicited a strong osmotic adjustment capacity. These findings suggest that P. cornutum is a Cl--tolerant species that can absorb and accumulate Cl- to improve growth under salt and drought stresses.

Characterization and expression analysis of immune-related genes in the red swamp crayfish, Procambarus clarkii in response to lipopolysaccharide challenge

To learn more about red swamp crayfish related genes in response to bacterial infections, we investigated immune-related genes induced by lipopolysaccharide (LPS) in the hepatopancreas using high-throughput sequencing method. In present the study, a total of 55,107 unigenes were identified, with an average length of 678 bp. A total of 2215 differentially expressed genes (DEGs) were found, including 669 up-regulated genes and 1546 down-regulated genes. The result of Gene ontology (GO) analysis revealed that 3017 DEGs were enriched in 19 biological process subcategories, 17 cellular component subcategories and 15 molecular function subcategories. The top 20 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that "ribosome" was the most abundant group, which had 34 DEGs. KEGG enrichment analysis identified several immune response pathways. Real-time quantitative reverse transcription-PCR (qRT-PCR) results exhibited that several immune responsive genes were greatly up-regulated following LPS stimulation as observed in the results of high-throughput sequencing. Overall, this study provides new insight into the immune defense mechanisms of P. clarkii against LPS infection.

De novo transcriptome assembly and co-expression network analysis of Cynanchum thesioides: Identification of genes involved in resistance to drought stress

Cynanchum thesioides are upright, xerophytic shrubs that are widely distributed in arid and semi-arid areas of China, North Korea, Mongolia and Siberia. To date, little is known about the molecular mechanisms of drought resistance in C. thesioides. To better understand drought resistance, we used transcriptome analysis and Illumina sequencing technology on C. thesioides, to identify drought-responsive genes. Using de novo assembly 55,268 unigenes were identified from 207.58 Gb of clean data. Amongst these, 36,265 were annotated with gene descriptions, conserved domains, gene ontology terms and metabolic pathways. The sequencing results showed that genes that were differentially expressed (DEGs) under drought stress were enriched in pathways such as carbon metabolism, starch and sucrose metabolism, amino acid biosynthesis, phenylpropanoid biosynthesis and plant hormone signal transduction. Moreover, many functional genes were up-regulated under severe drought stress to enhance tolerance. Weighted gene co-expression network analysis showed that there were key hub genes related to drought stress. Hundreds of candidate genes were identified under severe drought stress, including transcriptional factors such as MYB, G2-like, ERF, C2H2, NAC, NF-X1, GRF, HD-ZIP, HB-other, HSF, C3H, GRAS, WRKY, bHLH and Trihelix. These data are a valuable resource for further investigation into the molecular mechanism for drought stress in C. thesioides and will facilitate exploration of drought resistance genes.

Key Maize Drought-Responsive Genes and Pathways Revealed by Comparative Transcriptome and Physiological Analyses of Contrasting Inbred Lines

To unravel the molecular mechanisms underpinning maize (Zea mays L.) drought stress tolerance, we conducted comprehensive comparative transcriptome and physiological analyses of drought-tolerant YE8112 and drought-sensitive MO17 inbred line seedlings that had been exposed to drought treatment for seven days. Resultantly, YE8112 seedlings maintained comparatively higher leaf relative water and proline contents, greatly increased peroxidase activity, but decreased malondialdehyde content, than MO17 seedlings. Using an RNA sequencing (RNA-seq)-based approach, we identified a total of 10,612 differentially expressed genes (DEGs). From these, we mined out four critical sets of drought responsive DEGs, including 80 specific to YE8112, 5140 shared between the two lines after drought treatment (SD_TD), five DEGs of YE8112 also regulated in SD_TD, and four overlapping DEGs between the two lines. Drought-stressed YE8112 DEGs were primarily associated with nitrogen metabolism and amino-acid biosynthesis pathways, whereas MO17 DEGs were enriched in the ribosome pathway. Additionally, our physiological analyses results were consistent with the predicted RNA-seq-based findings. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) analysis and the RNA-seq results of twenty representative DEGs were highly correlated (R² = 98.86%). Crucially, tolerant line YE8112 drought-responsive genes were predominantly implicated in stress signal transduction; cellular redox homeostasis maintenance; MYB, NAC, WRKY, and PLATZ transcriptional factor modulated; carbohydrate synthesis and cell-wall remodeling; amino acid biosynthesis; and protein ubiquitination processes. Our findings offer insights into the molecular networks mediating maize drought stress tolerance.