[Effects of nitrogen reduction combined with organic materials on crop yield, photosynthetic characteristics, and product quality of corn-cabbage rotation system]. / å‡æ°®é æ–½æœ‰æœºç‰©æ–™å¯¹çŽ‰ç±³-ç™½èœè½®ä½œç³»ç»Ÿä½œç‰©äº§é‡ã€å ‰åˆç‰¹æ€§å’Œäº§å“å“è´¨çš„å½±å“.

Nitrogen reduction combined with organic materials is an important measure to achieve or even increase crop yield retention at the background of fertilizer reduction. We conducted a pot experiment to explore the effects of nitrogen reduction combined with organic materials on yield, photosynthetic characteristics, and product quality of agricultural products of maize-cabbage rotation system in yellow soil area of Guizhou. There were five treatments, including no fertilizer (CK), conventional fertilizer (CF), nitrogen reduction (20%, the same below) combined with biochar (RF+B), nitrogen reduction combined with rapeseed cake (RF+O), and nitrogen reduction combined with both biochar and rapeseed cake (RF+BO). Leaf photosynthetic characteristics were measured in maize (seedling stage, jointing stage, heading stage, and mature stage) and cabbage (seedling stage, growing stage and harvest stage). The biological characters, yield and quality indices were investigated in the harvest period. Compared with CF, RF+BO significantly enhanced the yield of corn and cabbage by 9.7% and 39.2%, respectively, while RF+O had no effect, and RF+B did not affet maize yield. RF+BO improved the biological properties of maize and cabbage, including the 100-kernel weight of maize, and plant height, maximum leaf length and total biomass of cabbage. Furthermore, the green holding period and high photosynthetic duration of maize and cabbage were prolonged, among which, maize leaf SPAD was increased respectively by 42.7%, 11.0%, 12.8%, and 30.3% at seedling, jointing, heading, and mature stages, the cabbage leaf SPAD was increased by 13.5%, 9.2%, and 30.3% in seedling, growing and harvest stages, respectively. The net photosynthetic rate (Pn) of maize was increased by 11.1%, 10.9%, and 119.8% in seedling, jointing, and mature stages, while that of cabbage was increased by 12.7% and 14.6% in growing and harvest stages, respectively. The stomatal conductance (gs) of maize was increased by 58.3% and 41.7% in jointing and harvest stages, while that of cabbage was increased by 10%, 64.7%, and 19.2% in seedling, growing, and harvest stages, respectively. The transpiration rate (Tr) of maize was increased by 55.0%, 10.6%, 14.0%, and 143.9% in seedling, jointing, heading, and mature stages, respectively, while that of cabbage was increased by 26.1% in growing stage. The nutritional quality of maize and cabbage was significantly improved. The contents of reducing sugar, starch, and crude protein in maize were increased by 16.2%, 3.5% and 20.3%. The contents of Vc, amino acid, and reducing sugar in cabbage were increased by 26.3%, 21.0% and 27.8%, separately. In conclusion, 20% nitrogen reduction combined with biochar and rapeseed cake had positive effects on crop growth, yield increase, green retention period, high photosynthetic duration, and agricultural product quality improvement in Guizhou yellow soil maize-cabbage rotation system, the overall effect of which was the best. Nitrogen reduction combined with single organic material overally did not affect crop yield, photosynthetic characteristics, and quality.

Long Read Single-Molecule Real-Time Sequencing Elucidates Transcriptome-Wide Heterogeneity and Complexity in Esophageal Squamous Cells.

Esophageal squamous cell carcinoma is a leading cause of cancer death. Mapping the transcriptional landscapes such as isoforms, fusion transcripts, as well as long noncoding RNAs have played a central role to understand the regulating mechanism during malignant processes. However, canonical methods such as short-read RNA-seq are difficult to define the entire polyadenylated RNA molecules. Here, we combined single-molecule real-time sequencing with RNA-seq to generate high-quality long reads and to survey the transcriptional program in esophageal squamous cells. Compared with the recent annotations of human transcriptome (Ensembl 38 release 91), single-molecule real-time data identified many unannotated transcripts, novel isoforms of known genes and an expanding repository of long intergenic noncoding RNAs (lincRNAs). By integrating with annotation of lincRNA catalog, 1,521 esophageal-cancer-specific lincRNAs were defined from single-molecule real-time reads. Kyoto Encyclopedia of Genes and Genomes enrichment analysis indicated that these lincRNAs and their target genes are involved in a variety of cancer signaling pathways. Isoform usage analysis revealed the shifted alternative splicing patterns, which can be recaptured from clinical samples or supported by previous studies. Utilizing vigorous searching criteria, we also detected multiple transcript fusions, which are not documented in current gene fusion database or readily identified from RNA-seq reads. Two novel fusion transcripts were verified based on real-time PCR and Sanger sequencing. Overall, our long-read single-molecule sequencing largely expands current understanding of full-length transcriptome in esophageal cells and provides novel insights on the transcriptional diversity during oncogenic transformation.

Genome Sequences Provide Insights into the Reticulate Origin and Unique Traits of Woody Bamboos.

Polyploidization is a major driver of speciation and its importance to plant evolution has been well recognized. Bamboos comprise one diploid herbaceous and three polyploid woody lineages, and are members of the only major subfamily in grasses that diversified in forests, with the woody members having a tree-like lignified culm. In this study, we generated four draft genome assemblies of major bamboo lineages with three different ploidy levels (diploid, tetraploid, and hexaploid). We also constructed a high-density genetic linkage map for a hexaploid species of bamboo, and used a linkage-map-based strategy for genome assembly and identification of subgenomes in polyploids. Further phylogenomic analyses using a large dataset of syntenic genes with expected copies based on ploidy levels revealed that woody bamboos originated subsequent to the divergence of the herbaceous bamboo lineage, and experienced complex reticulate evolution through three independent allopolyploid events involving four extinct diploid ancestors. A shared but distinct subgenome was identified in all polyploid forms, and the progenitor of this subgenome could have been critical in ancient polyploidizations and the origin of woody bamboos. Important genetic clues to the unique flowering behavior and woody trait in bamboos were also found. Taken together, our study provides significant insights into ancient reticulate evolution at the subgenome level in the absence of extant donor species, and offers a potential model scenario for broad-scale study of angiosperm origination by allopolyploidization.

Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants.

BACKGROUND: The double digest restriction-site associated DNA sequencing technology (ddRAD-seq) is a reduced representation sequencing technology by sampling genome-wide enzyme loci developed on the basis of next-generation sequencing. ddRAD-seq has been widely applied to SNP marker development and genotyping on animals, especially on marine animals as the original ddRAD protocol is mainly built and trained based on animal data. However, wide application of ddRAD-seq technology in plant species has not been achieved so far. Here, we aim to develop an optimized ddRAD library preparation protocol be accessible to most angiosperm plant species without much startup pre-experiment and costs. RESULTS: We first tested several combinations of enzymes by in silico analysis of 23 plant species covering 17 families of angiosperm and 1 family of bryophyta and found AvaII + MspI enzyme pair produced consistently higher number of fragments in a broad range of plant species. Then we removed two purifying and one quantifying steps of the original protocol, replaced expensive consumables and apparatuses by conventional experimental apparatuses. Besides, we shortened P1 adapter from 37 to 25 bp and designed a new barcode-adapter system containing 20 pairs of barcodes of varying length. This is an optimized ddRAD strategy for angiosperm plants that is economical, time-saving and requires little technical expertise or investment in laboratory equipment. We refer to this simplified protocol as MiddRAD and we demonstrated the utility and flexibility of our approach by resolving phylogenetic relationships of two genera of woody bamboos (Dendrocalamus and Phyllostachys). Overall our results provide empirical evidence for using this method on different model and non-model plants to produce consistent data. CONCLUSIONS: As MiddRAD adopts an enzyme pair that works for a broad range of angiosperm plants, simplifies library constructing procedure and requires less DNA input, it will greatly facilitate designing a ddRAD project. Our optimization of this method may make ddRAD be widely used in fields of plant population genetics, phylogenetics, phylogeography and molecular breeding.

Vitreoscilla hemoglobin promotes Salecan production by Agrobacterium sp. ZX09.

Salecan is a novel exopolysaccharide produced by the strain Agrobacterium sp. ZX09, and it is composed of only glucose monomers. The unique chemical composition and excellent physicochemical properties make Salecan a promising material for applications in coagulation, lubrication, protection against acute liver injury, and alleviating constipation. In this study, we cloned the Vitreoscilla hemoglobin gene into a broad-host-range plasmid pCM158. Without antibiotic selection, there was negligible loss of the plasmid in the host Agrobacterium sp. ZX09 after one passage of cultivation. The expression of Vitreoscilla hemoglobin was demonstrated by carbon monoxide (CO) difference spectrum. The engineered strain Agrobacterium sp. ZX09 increased Salecan yield by 30%. The other physiological changes included its elevated respiration rate and cellular invertase activity.