Complete genome assembly provides a high-quality skeleton for pan-NLRome construction in melon.

Melon (Cucumis melo L.), being under intensive domestication and selective breeding, displays an abundant phenotypic diversity. Wild germplasm with tolerance to stress represents an untapped genetic resource for discovery of disease-resistance genes. To comprehensively characterize resistance genes in melon, we generate a telomere-to-telomere (T2T) and gap-free genome of wild melon accession PI511890 (C. melo var. chito) with a total length of 375.0 Mb and a contig N50 of 31.24 Mb. The complete genome allows us to dissect genome architecture and identify resistance gene analogs. We construct a pan-NLRome using seven melon genomes, which include 208 variable and 18 core nucleotide-binding leucine-rich repeat receptors (NLRs). Multiple disease-related transcriptome analyses indicate that most up-regulated NLRs induced by pathogens are shell or cloud NLRs. The T2T gap-free assembly and the pan-NLRome not only serve as essential resources for genomic studies and molecular breeding of melon but also provide insights into the genome architecture and NLR diversity.

Integrated full-length transcriptome and metabolome analysis reveals the defence response of melon to gummy stem blight.

Gummy stem blight (GSB), a widespread disease causing great loss to cucurbit production, has become a major threat to melon cultivation. However, the melon-GSB interaction remains largely unknown. Here, full-length transcriptome and widely targeted metabolome were used to investigate the defence responses of resistant (PI511089) and susceptible (Payzawat) melon accessions to GSB pathogen infection at 24 h. The biosynthesis of secondary metabolites and MAPK signalling pathway were specifically enriched for differentially expressed genes in PI511890, while carbohydrate metabolism and amino acid metabolism were specifically enriched in Payzawat. More than 1000 novel genes were identified and MAPK signalling pathway was specifically enriched for them in PI511890. There were 11 793 alternative splicing events involving in the defence response to GSB. Totally, 910 metabolites were identified in Payzawat and PI511890, and flavonoids were the dominant metabolites. Integrated full-length transcriptome and metabolome analysis showed eriodictyol and oxalic acid were the potential marker metabolites for GSB resistance in melon. Moreover, posttranscription regulation was widely involved in the defence response of melon to GSB pathogen infection. These results not only improve our understanding on the interaction between melon and GSB, but also facilitate the genetic improvement of melon with GSB resistance.

Telomere-to-telomere genome assembly of melon (Cucumis melo L. var. inodorus) provides a high-quality reference for meta-QTL analysis of important traits.

Melon is an important horticultural crop with extensive diversity in many horticultural groups. To explore its genomic diversity, it is necessary to assemble more high-quality complete genomes from different melon accessions. Meanwhile, a large number of QTLs have been mapped in several studies. Integration of the published QTLs onto a complete genome can provide more accurate information for candidate gene cloning. To address these problems, a telomere-to-telomere (T2T) genome of the elite melon landrace Kuizilikjiz (Cucumis melo L. var. inodorus) was de novo assembled and all the published QTLs were projected onto it in this study. The results showed that a high-quality Kuizilikjiz genome with the size of 379.2 Mb and N50 of 31.7 Mb was de novo assembled using the combination of short reads, PacBio high-fidelity long reads, Hi-C data, and a high-density genetic map. Each chromosome contained the centromere and telomeres at both ends. A large number of structural variations were observed between Kuizilikjiz and the other published genomes. A total of 1294 QTLs published in 67 studies were collected and projected onto the T2T genome. Several clustered, co-localized, and overlapped QTLs were determined. Furthermore, 20 stable meta-QTLs were identified, which significantly reduced the mapping intervals of the initial QTLs and greatly facilitated identification of the candidate genes. Collectively, the T2T genome assembly together with the numerous projected QTLs will not only broaden the high-quality genome resources but also provide valuable and abundant QTL information for cloning the genes controlling important traits in melon.

Fine mapping of a novel QTL DM9.1 conferring downy mildew resistance in melon.

Downy mildew (DM) is a major foliar disease globally causing great economic loss in melon production. Utilizing disease-resistant cultivars is the most efficient approach for disease control, while discovery of disease-resistant genes is crucial for the success of DM-resistant breeding. To address this problem, two F2 populations were constructed using the DM-resistant accession PI 442177 in this study, and QTLs conferring DM resistance were mapped using linkage map and QTL-seq analysis, respectively. A high-density genetic map with the length of 1096.7 cM and density of 0.7 cM was generated by using the genotyping-by-sequencing data of a F2 population. A major QTL DM9.1 with the phenotypic variance explained proportion of 24.3-37.7% was consistently detected at the early, middle, and late growth stages using the genetic map. QTL-seq analyses on the two F2 populations also validated the presence of DM9.1. Kompetitive Allele-Specific PCR (KASP) assay was further carried out to fine map DM9.1 into 1.0 Mb interval. A KASP marker co-segregating with DM9.1 was successfully developed. These results not only provided valuable information for DM-resistant gene cloning, but also offered useful markers for melon DM-resistant breeding programs.

Comprehensive physio-biochemical and transcriptomic characterization to decipher the network of key genes under waterlogging stress and its recuperation in Prunus persica.

Waterlogging is a major abiotic stress that plants encounter as a result of climate change impacts. Peach is very sensitive to hypoxia during waterlogging, which causes poor tree vigor and huge economic losses. The molecular mechanism underlying the peach response to waterlogging and reoxygenation remains unclear. Here, the physiological and molecular responses of 3-week-old peach seedlings under waterlogged and recovery conditions were comprehensively analyzed. As a result, waterlogging significantly reduced plant height and biomass with inhibition of root growth when compared with control and reoxygenation. Similar results were observed for photosynthetic activities and gaseous exchange parameters. Waterlogging increased lipid peroxidation, hydrogen peroxide, proline, glutamic acid and glutathione contents, while superoxide dismutase, peroxidases and catalase activities were decreased. The glucose and fructose contents were accumulated, contrary to sucrose which was reduced remarkably throughout the stress periods. The level of endogenous indole acetic acid (IAA) was increased in waterlogging but decreased after reoxygenation. However, the change trends of jasmonic acid (JA), cytokinins and abscisic acid (ABA) levels were opposite to IAA. In transcriptomic analysis, there were 13,343 differentially expressed genes (DEGs) with higher and 16,112 genes with lower expression. These DEGs were greatly enriched in carbohydrate metabolism, anaerobic fermentation, glutathione metabolism and IAA hormone biosynthesis under waterlogging, while they were significantly enriched in photosynthesis, reactive oxygen species scavenging, ABA and JA hormones biosynthesis in reoxygenation. Moreover, several genes related to stress response, carbohydrate metabolism and hormones biosynthesis were significantly changed in waterlogging and reoxygenation, which indicated unbalanced amino acid, carbon and fatty acid pools in peach roots. Taken together, these results suggest that glutathione, primary sugars and hormone biosynthesis and signaling might play key roles in plant response to waterlogging. Our work provides a comprehensive understanding of gene regulatory networks and metabolites in waterlogging stress and its recuperation, which will facilitate peach waterlogging control.

Chromosome-level and graphic genomes provide insights into metabolism of bioactive metabolites and cold-adaption of Pueraria lobata var. montana.

Pueraria lobata var. montana (P. montana) belongs to the genus Pueraria and originated in Asia. Compared with its sister P. thomsonii, P. montana has stronger growth vigour and cold-adaption but contains less bioactive metabolites such as puerarin. To promote the investigation of metabolic regulation and genetic improvement of Pueraria, the present study reports a chromosome-level genome of P. montana with length of 978.59 Mb and scaffold N50 of 80.18 Mb. Comparative genomics analysis showed that P. montana possesses smaller genome size than that of P. thomsonii owing to less repeat sequences and duplicated genes. A total of 6,548 and 4,675 variety-specific gene families were identified in P. montana and P. thomsonii, respectively. The identified variety-specific and expanded/contracted gene families related to biosynthesis of bioactive metabolites and microtubules are likely the causes for the different characteristics of metabolism and cold-adaption of P. montana and P. thomsonii. Moreover, a graphic genome was constructed based on 11 P. montana accessions. Total 92 structural variants were identified and most of which are related to stimulus-response. In conclusion, the chromosome-level and graphic genomes of P. montana will not only facilitate the studies of evolution and metabolic regulation, but also promote the breeding of Pueraria.

Characterization of Steel Slag Filler and Its Effect on Aging Resistance of Asphalt Mastic with Various Aging Methods.

Steel slag is the by-product of the steelmaking industry, the negative influences of which prompt more investigation into the recycling methods of steel slag. The purpose of this study is to characterize steel slag filler and study its feasibility of replacing limestone filler in asphalt concrete by evaluating the resistance of asphalt mastic under various aging methods. Firstly, steel slag filler, limestone filler, virgin asphalt, steel slag filler asphalt mastic and limestone filler asphalt mastic were prepared. Subsequently, particle size distribution, surface characterization and pore characterization of the fillers were evaluated. Finally, rheological property, self-healing property and chemical functional groups of the asphalt mastics with various aging methods were tested via dynamic shear rheometer and Fourier transform infrared spectrometer. The results show that there are similar particle size distributions, however, different surface characterization and pore characterization in the fillers. The analysis to asphalt mastics demonstrates how the addition of steel slag filler contributes to the resistance of asphalt mastic under the environment of acid and alkaline but is harmful under UV radiation especially. In addition, the pore structure in steel slag filler should be a potential explanation for the changing resistance of the asphalt mastics. In conclusion, steel slag filler is suggested to replace limestone filler under the environment of acid and alkaline, and environmental factor should be taken into consideration when steel slag filler is applied to replace natural fillers in asphalt mastic.

Environmental Impact on VOCs Emission of a Recycled Asphalt Mixture with a High Percentage of RAP.

Recycling of reclaimed asphalt pavement (RAP) has gradually emerged as a hot topic in the current research of building materials. Manufacturing the recycled asphalt mixture with a high RAP content still remains a major challenge due to the problem of inferior water damage resistance and fatigue cracking resistance. The aim of this study is to evaluate the servicing performance of recycled asphalt mixture with high percentage of RAP and assess its environmental impact on volatile organic compounds (VOCs) emission. To further explore the intrinsic factor on the performance of a recycled asphalt mixture, the mixed asphalt binder with a different content of extracted RAP binder was firstly investigated. The results show that the larger the content of RAP binder, the lower the mechanical indexes and VOCs emission. There exists an internal relationship between the chemical composition and VOCs release behavior with the variation of the recycled asphalt binder content. Based on the results of mixed recycled asphalt binder, the road servicing performance of a rather high utilization of RAP (i.e., 50%, 60%, and 70%) was assessed. It was found that the reuse of RAP aggregates has little influence on the volume performance of recycled asphalt mixture, and servicing performances still meet the construction requirements in spite of a descending trend. Moreover, a significant reduction effect on VOCs emission was found in the mixing stage of recycled asphalt mixture, indicating that the VOCs emission can be decreased by 94.82% when the content of RAP aggregates increases to 70%. The recycling of RAP with a high content contributes to the sustainable development of road engineering and the construction of green pavements.

Resibufogenin suppresses tumor growth and inhibits glycolysis in ovarian cancer by modulating PIM1.

Ovarian cancer is a common human malignancy of the female reproductive system. However, chemotherapy has been proven to have limited effectiveness in a majority of patients. Resibufogenin (RB) is a major active ingredient in cinobufacini, which has been used in the treatment of human malignancies as adjunct agents. This study was designed to examine the anti-cancer effect of RB and the underlying mechanisms in ovarian cancer. Our results showed that RB treatment resulted in cell death, cell cycle arrest, and apoptosis in ovarian cancer cells. The anti-growth and pro-apoptotic effects of RB were also validated in xenograft mice models. Proteomics analysis indicated that RB was able to alter the expressions of several genes, which were involved in the regulation of glycolysis. The suppression effect of RB in the glycolysis pathway of ovarian cancer cells was validated by decreased glucose consumption, lactate production, and extracellular acidification rate (ECAR). We proposed that PIM1 functioned as the key target that mediated the anti-cancer effect of RB against ovarian cancer cells. Our results have revealed that RB downregulated PIM1 in ovarian cancer cells and its downstream genes involved in glycolysis. Moreover, our results indicated that the anti-growth activities and suppressing effect of RB on glycolysis were enhanced significantly by PIM1 knockdown but was attenuated by ectopic PIM1 expression. This provided evidence to support the role of PIM1 in the anti-cancer activities of RB.