A chorismate mutase from Radopholus similis plays an essential role in pathogenicity

In the process of infecting plants, plant parasitic nematodes release a series of proteins that play an essential role in the successful infection and pathogenesis of plant cells and tissues through stylets or body walls. In this study,based on transcriptome data, a chorismate mutase gene of Radopholus similis(RsCM) was identified and cloned,which is a single copy gene specifically expressed in the oesophageal gland and highly expressed in juveniles and females. Transient expression of RsCM in tobacco leaves showed that it was localised in the cytoplasm and nucleus of tobacco leaf cells, which inhibited the pattern-triggered immunity(PTI) induced by flg22, including callose deposition and defence gene expression, and cell death induced by immune elicitors BAX, but could not inhibit cell death induced by immune elicitors Gpa2/RBP-1. The RNA interference(RNAi) transgenic tomato of RsCM obviously inhibited the infection, pathogenicity, and reproduction of R. similis. However, the resistance of the overexpression transgenic tomato of RsCM to R. similis infection was significantly reduced, and the expression levels of two salicylic acid(SA) pathway genes(PR1 and PR5) in roots infected by the nematode were significantly down-regulated,which indicated that RsCM might be involved in the inhibition of SA pathway. The results of this study demonstrate that RsCM suppresses the host immune system and might be a new target for the control of R. similis, which also provides new data for the function and mechanism of CM genes of migratory parasitic plant nematodes.

The Physalis floridana genome provides insights into the biochemical and morphological evolution of Physalis fruits

The fruits of Physalis(Solanaceae)have a unique structure,a lantern-like fruiting calyx known as inflated calyx syndrome(ICS)or the Chinese lantern,and are rich in steroid-related compounds.However,the genetic variations underlying the origin of these characteristic traits and diversity in Physalis remain largely unknown.Here,we present a high-quality chromosome-level reference genome assembly of Physalis floridana(~1.40Gb in size)with a contig N50 of~4.87Mb.Through evolutionary genomics and experimental approaches,we found that the loss of the SEP-like MADS-box gene MBP21 subclade is likely a key mutation that,together with the previously revealed mutation affecting floral MPF2 expression,might have contributed to the origination of ICS in Physaleae,suggesting that the origination of a morphological novelty may have resulted from an evolutionary scenario in which one mutation compensated for another deleterious mutation.Moreover,the significant expansion of squalene epoxidase genes is potentially associated with the natural variation of steroid-related compounds in Physalis fruits.The results reveal the importance of gene gains(duplication)and/or subsequent losses as genetic bases of the evolution of distinct fruit traits,and the data serve as a valuable resource for the evolutionary genetics and breeding of solanaceous crops.

An in-situ biochar-enhanced anaerobic membrane bioreactor for swine wastewater treatment under various organic loading rates

A biochar-assisted anaerobic membrane bioreactor(BC-AnMBR)was conducted to evaluate the performance in treating swine wastewater with different organic loading rates(OLR)ranging from 0.38 to 1.13 kg-COD/(m3.d).Results indicated that adding spent coffee grounds biochar(SCG-BC)improved the organic removal efficiency compared to the conventional AnMBR,with an overall COD removal rate of>95.01%.Meanwhile,methane production of up to 0.22 LCH4/gCOD with an improvement of 45.45%was achieved under a high OLR of 1.13 kg-COD/(m3.d).Furthermore,the transmembrane pressure(TMP)in the BC-AnMBR system was stable at 4.5 kPa,and no irreversible membrane fouling occurred within 125 days.Microbial community analysis revealed that the addition of SCG-BC increased the relative abundance of autotrophic methanogenic archaea,particularly Methanosarcina(from 0.11%to 11.16%)and Methanothrix(from 16.34%to 24.05%).More importantly,Desulfobacterota and Firmicutes phylum with direct interspecific electron transfer(DIET)capabilities were also enriched with autotrophic methanogens.Analysis of the electron transfer pathway showed that the concentration of c-type cytochromes increased by 38.60%in the presence of SCGBC,and thus facilitated the establishment of DIET and maintained high activity of the elec-tron transfer system even at high OLR.In short,the BC-AnMBR system performs well under various OLR conditions and is stable in the recovery energy system for swine wastewater.

Genome-wide identification, expression analysis of auxin-responsive GH_3 family genes in maize(Zea mays L.) under abiotic stresses

Auxin is involved in different aspects of plant growth and development by regulating the expression of auxin-responsive family genes. As one of the three major auxin-responsive families, GH3 (Gretchen Hagen3) genes participate in auxin homeostasis by catalyzing auxin conjugation and bounding free indole-3-acetic acid (IAA) to amino acids. However, how GH3 genes function in responses to abiotic stresses and various hormones in maize is largely unknown. Here, the latest updated maize (Zea mays L.) reference genome sequence was used to characterize and analyze the ZmGH3 family genes from maize. The results showed that 13 ZmGH3 genes were mapped on five maize chromosomes (total 10 chromosomes). Highly diversified gene structures and tissue-specific expression patterns suggested the possibility of function diversification for these genes in response to environmental stresses and hormone stimuli. The expression patterns of ZmGH3 genes are responsive to several abiotic stresses (salt, drought and cadmium) and major stress-related hormones (abscisic acid, salicylic acid and jasmonic acid). Various environmental factors suppress auxin free IAA contents in maize roots suggesting that these abiotic stresses and hormones might alter GH3-mediated auxin levels. The respon-siveness of ZmGH3 genes to a wide range of abiotic stresses and stress-related hormones suggested that ZmGH3s are involved in maize tolerance to environmental stresses.

The linkage maps of Dendrobium species based on RAPD and SRAP markers

Dendrobium plants are used commonly as tonic herbs and health food in many Asian countries, especially in China. Here we report the genetic map construction of two Dendrobium species with a double pseudo-testcross strategy using random amplified polymorphic DNA （RAPD） and sequence-related amplified polymorphism （SRAP） markers. A F1 mapping population of 90 individuals was developed from a cross between D. officinale and D. hercoglossum. A total of 307 markers, including 209 RAPD and 98 SRAP, were identified and used for genetic linkage group （LG） analysis. The D. officinale linkage map consisted of 11 major linkage groups and 3 doublets, which covered 629.4 cM by a total of 62 markers with an average locus distance of 11.2 cM between two adjacent markers. The D. hercoglos- sum linkage map contained 112 markers mapped on 15 major and 4 minor linkage groups, spanning a total length of 1,304.6 cM with an average distance of I 1.6 cM between two adjacent markers. The maps constructed in this study covered 92.7% and 82.7% of the D. hercoglossum and D. officinale genomes respectively, providing an important basis for the mapping of horticultural and medicinal traits and for the application of marker-assisted selection in Dendrobium breeding program.

Microbial community structure and dynamics of starch-fed and glucose-fed chemostats during two years of continuous operation

The microbial community structures of two mesophilic anaerobic chemostats, one fed with glucose, the other with starch as sole carbon sources, were studied at various dilution rates （0.05-0.25 d-1 for glucose and 0.025-0.1 d-1 for starch） during two years continuous operation. In the glucose-fed chemostat, the aceticlastic methanogen Methanosaeta spp. and hydrogenotrophic methanogen Methanoculleus spp. predominated at low dilution rates, whereas Methanosaeta spp. and the hydrogenotrophic Methanobacterium spp. predominated together when dilution rates were greater than 0.1 d 1. Bacteria affiliated with the phyla Bacteroidetes, Spiro- chaetes, and Actinobacteria predominated at dilution rates of 0.05, 0.1, and 0.15 d-l, respectively, while Firmicutes predominated at higher dilution rates （0.2 and 0.25 d-l）. In the starch-fed chemostat, the aceticlastic and hydrogeno- trophic methanogens coexisted at all dilution rates. Although bacteria belonging to only two phyla were mainly responsible for starch degradation （Spirochaetes at the dilution rate of 0.08 d-1 and Firmicutes at other dilution rates）, different bacterial genera were identified at different dilution rates. With the exception of Archaea in the glucose-fed chemostat, the band patterns revealed by denaturing gradient gel electrophoresis （DGGE） of the microbial communities in the two chemostats displayed marked changes during long-term operation at a constant dilution rate. The bacterial community changed with changes in the dilution rate, and was erratic during long- term operation in both glucose-fed and starch-fed chemo- stats.

Mass spectrometry imaging and single-cell transcriptional profiling reveal the tissue-specific regulation of bioactive ingredient biosynthesis in Taxus leaves

Taxus leaves provide the raw industrial materials for taxol,a natural antineoplastic drug widely used in the treatment of various cancers.However,the precise distribution,biosynthesis,and transcriptional regulation of taxoids and other active components in Taxus leaves remain unknown.Matrix-assisted laser desorption/ionization–mass spectrometry imaging analysis was used to visualize various secondary metabolites in leaf sections of Taxus mairei,confirming the tissue-specific accumulation of different active metabolites.Single-cell sequencing was used to produce expression profiles of 8846 cells,with a median of 2352 genes per cell.Based on a series of cluster-specific markers,cells were grouped into 15 clusters,suggesting a high degree of cell heterogeneity in T.mairei leaves.Our data were used to create the first Taxus leaf metabolic single-cell atlas and to reveal spatial and temporal expression patterns of several secondary metabolic pathways.According to the cell-type annotation,most taxol biosynthesis genes are expressed mainly in leaf mesophyll cells;phenolic acid and flavonoid biosynthesis genes are highly expressed in leaf epidermal cells(including the stomatal complex and guard cells);and terpenoid and steroid biosynthesis genes are expressed specifically in leaf mesophyll cells.A number of novel and cell-specific transcription factors involved in secondary metabolite biosynthesis were identified,including MYB17,WRKY12,WRKY31,ERF13,GT_2,and bHLH46.Our research establishes the transcriptional landscape of major cell types in T.mairei leaves at a single-cell resolution and provides valuable resources for studying the basic principles of cell-type-specific regulation of secondary metabolism.