A chromosome‐level genome assembly reveals the genetic basis of cold tolerance in a notorious rice insect pest,Chilo suppressalis

The rice stem borer, Chilo suppressalis, is one of the most damaging insect pests to rice production worldwide. Although C. suppressalis has been the focus of numerous studies examining cold tolerance and diapause, plant–insect interactions, pesticide targets and resistance, and the development of RNAi‐mediated pest management, the absence of a high‐quality genome has limited deeper insights. To address this limitation, we generated a draft C. suppressalis genome constructed from both Illumina and PacBio sequences. The assembled genome size was 824.35 Mb with a contig N₅₀ of 307 kb and a scaffold N₅₀ of 1.75 Mb. Hi‐C scaffolding assigned 99.2% of the bases to one of 29 chromosomes. Based on universal single‐copy orthologues (BUSCO), the draft genome assembly was estimated to be 97% complete and is predicted to encompass 15,653 protein‐coding genes. Cold tolerance is an extreme survival strategy found in animals. However, little is known regarding the genetic basis of the winter ecology of C. suppressalis. Here, we focused our orthologous analysis on those gene families associated with animal cold tolerance. Our finding provided the first genomic evidence revealing specific cold‐tolerant strategies in C. suppressalis, including those involved in glucose‐originated glycerol biosynthesis, triacylglycerol‐originated glycerol biosynthesis, fatty acid synthesis and trehalose transport‐intermediate cold tolerance. The high‐quality C. suppressalis genome provides a valuable resource for research into a broad range of areas in molecular ecology, and subsequently benefits developing modern pest control strategies.     

Glycine metabolomic changes induced by anticancer agents in A549 cells

Amino Acids - Glycine plays a key role in rapidly proliferating cancer cells such as A549 cells. Targeting glycine metabolism is considered as a potential means for cancer treatment. However, the...     

Systematic profiling of staralog response to acquired drug resistant kinase gatekeeper mutations in targeted cancer therapy

Amino Acids - Kinase-targeted therapy has been widely used as a lifesaving strategy for cancer patients. However, many patients treated with targeted cancer drugs are clinically observed to rapidly...     

The Chimonanthus salicifolius genome provides insight into magnoliid evolution and flavonoid biosynthesis

Chimonanthus salicifolius, a member of the Calycanthaceae of magnoliids, is one of the most famous medicinal plants in Eastern China. Here, we report a chromosome‐level genome assembly of C. salicifolius, comprising 820.1 Mb of genomic sequence with a contig N50 of 2.3 Mb and containing 36 651 annotated protein‐coding genes. Phylogenetic analyses revealed that magnoliids were sister to the eudicots. Two rounds of ancient whole‐genome duplication were inferred in the C. salicifolious genome. One is shared by Calycanthaceae after its divergence with Lauraceae, and the other is in the ancestry of Magnoliales and Laurales. Notably, long genes with > 20 kb in length were much more prevalent in the magnoliid genomes compared with other angiosperms, which could be caused by the length expansion of introns inserted by transposon elements. Homologous genes within the flavonoid pathway for C. salicifolius were identified, and correlation of the gene expression and the contents of flavonoid metabolites revealed potential critical genes involved in flavonoids biosynthesis. This study not only provides an additional whole‐genome sequence from the magnoliids, but also opens the door to functional genomic research and molecular breeding of C. salicifolius.     

Mass loss and nutrient release during the decomposition of sixteen types of plant litter with contrasting quality under three precipitation regimes

Mass loss and nutrient release during litter decomposition drive biogeochemical cycling in terrestrial ecosystems. However, the relationship between the litter decomposition process and the decomposition stage, precipitation, and litter quality has rarely been addressed, precluding our understanding of how litter decomposition regulates nutrient cycling in various ecosystems and their responses to climate change. In this study, we measured mass loss as well as carbon and nutrient releases during the decomposition of 16 types of leaf litter under three precipitation treatments over 12 months in a common garden experiment (i.e., using standardized soil and climatic conditions). Sixteen types of leaves were divided into three functional groups (evergreen, deciduous, and herbaceous). The objectives were to understand the effects of decomposition stages and precipitation regimes on litter decomposition and to examine the relationship between this effect and chemical properties. The mass loss and release of nitrogen and potassium were significantly higher in the 6‐ to 12‐month stage of decomposition (high temperature and humidity) than in the 0‐ to 6‐month stage. Phosphorus was relatively enriched in evergreen leaves after 6 months of decomposition. The rates of mass loss and nutrient release were significantly greater in herbaceous than in deciduous and evergreen leaves. Increasing precipitation from 400 to 800 mm accelerated mass loss and potassium release but decreased phosphorus release in the 0‐ to 6‐month stage of decomposition. These results highlighted the contribution to and complexity of litter chemical properties in litter decomposition.     

The correlation of microRNA-499 rs3746444 T>C locus with the susceptibility of gastric cancer: from a case–control study to a meta-analysis

The relationship between rs3746444 T>C single-nucleotide polymorphism (SNP) in microRNA (mir)-499 and risk of gastric cancer (GC) has been widely investigated. However, the association was still unconfirmed. Here, we first recruited 490 GC patients and 1476 controls, and conducted a case-control study. And we did not find any association between rs3746444 T>C SNP polymorphism and risk of GC. Subsequently, we conducted a meta-analysis to explore the association of mir-499 rs3746444 polymorphism with GC development. Two authors searched the PubMed and EMBASE databases up to October 15, 2019 independently. Finally, nine literatures involving 12 independent studies were included. In total, 3954 GC cases and 9745 controls were recruited for meta-analysis. The results suggested that allele model, homozygote model and recessive model could increase the risk of overall GC (P = 0.002, 0.009 and 0.013, respectively). When we excluded the studies violated HWE, this association was also found in allele model (P = 0.020) and dominant model (P= 0.044). In subgroup analyses, we identified that rs3746444 SNP in mir-499 increased the risk of GC in Asians and gastric cardiac adenocarcinoma (GCA) subgroups. No significant bias of selection was found (all P>0.1). Test of sensitivity analysis indicated that our findings were stable. Additionally, we found that the power value was 0.891 in the allele model, suggesting the reliability of our findings. In summary, our analysis confirmed the association between rs3746444 and the risk of GC, especially in Asians and in patients with GCA.     

Variation in rare earth element (REE), aluminium (Al) and silicon (Si) accumulation among populations of the hyperaccumulator Dicranopteris linearis in southern China

Plant and Soil - Dicranopteris linearis is a rare earth element (REE), aluminium (Al) and silicon (Si) hyperaccumulator plant which occurs in southern China. To date, there have been no studies on...     

Development and characterization of 33 polymorphic microsatellite markers in Trachurus japonicus by SLAF-seq technology

Trachurus japonicus is an economically important fish in the northwestern Pacific Ocean. However, its resources have declined seriously and there is an urgent need for a wide-range of investigations of the existing genetic resources. This requires a large number of diverse molecular markers with high discriminating power. In this study, we identified 43,264 perfect SSRs in T. japonicus genome using SLAF-seq technology. Of these, we randomly selected 106 SSRs (tri-nucleotide to hexa-nucleotide) to test for polymorphism. Eventually, we successfully developed a total of 33 loci including 8 tri-nucleotide and 25 long repeat motifs (tetra-nucleotide to hexa-nucleotide). The number of alleles (Na) of these loci ranged from 4 to 24 (mean 12.6). The observed heterozygosity (Ho) and expected heterozygosity (He) varied from 0.258 to 0.969 (mean 0.723) and from 0.452 to 0.962 (mean 0.827), respectively. All loci except TJ6-7 were highly informative (PIC > 0.5). These results showed that the shortlisted 33 loci exhibited moderate to relatively high genetic diversity, of which 18 were regarded as highly polymorphic and well-resolved. In summary, these diverse and potential microsatellites detected in our study provide substantial genetic basis for the screening of polymorphic SSR markers of T. japonicus and also provide a powerful tool to perform further studies on the genetic resource assessment and conservation of T. japonicus.