Improved genome annotation of Brassica oleracea highlights the importance of alternative splicing

Brassica oleracea has been developed into many important crops,including cabbage,kale,cauliflower,broccoli and so on.The genome and gene annotation of cabbage(cultivar JZS),a representative morphotype of B.oleracea,has been widely used as a common reference in biological research.Although its genome assembly has been updated twice,the current gene annotation still lacks information on untranslated regions(UTRs)and alternative splicing(AS).Here,we constructed a high-quality gene annotation(JZSv3)using a full-length transcriptome acquired by nanopore sequencing,yielding a total of 59452 genes and 75684 transcripts.Additionally,we re-analyzed the previously reported transcriptome data related to the development of different tissues and cold response using JZSv3 as a reference,and found that 3843 out of 11908 differentially expressed genes(DEGs)underwent AS during the development of different tissues and 309 out of 903 cold-related genes underwent AS in response to cold stress.Meanwhile,we also identified many AS genes,including BolLHCB5 and BolHSP70,that displayed distinct expression patterns within variant transcripts of the same gene,highlighting the importance of JZSv3 as a pivotal reference for AS analysis.Overall,JZSv3 provides a valuable resource for exploring gene function,especially for obtaining a deeper understanding of AS regulation mechanisms.

崇左和防城港两地的台风韦帕(201907)降雨雨滴谱对比分析

利用崇左国家气象观测站、防城国家基准气候站的雨滴谱观测数据,结合观测站雨量数据及雷达观测资料,分析2019年8月2~3日台风“韦帕”影响期间内陆背风侧(LSI)、近海岸迎风侧(WSC)不同降水阶段的雨滴谱结构特征及其差异。结果显示,台风“韦帕”降雨以中、小雨滴贡献为主,尤其中雨滴贡献率稳定在70%以上。LSI处以层状云降水为主,雨强相对平缓,WSC处表现为积层混合云降水,雨强较大且波动剧烈。因强烈的对流上升运动导致WSC的雨滴数浓度、雨滴直径明显大于LSI。LSI处在台风登陆后雨势增强的最主要因素是雨滴直径增大,WSC处由台风眼墙转变为强对流螺旋雨带影响后其雨势增强则主要是由于雨滴数浓度增加。台风“韦帕”对流降水的质量加权平均直径均值为1.85 mm,对数标准化数浓度均值为3.95 mm^(-1)m^(-3);LSI处对流降水位于海洋性对流区域内,而WSC处则介于海洋性和大陆性对流之间。

Schlafen家族蛋白在肿瘤和病毒感染中的研究进展

Schlafen(SLFN)家族基因是在人类与小鼠中首先被发现的具有调控细胞生长及T细胞分化等诸多生物学功能的重要基因。该家族基因在小鼠、马和人等各个物种中广泛存在并具有较高的同源性。研究表明,SLFN蛋白在抑制细胞增殖、驱动减数分裂、调控造血细胞、下调血小板数量及调节免疫应答等方面均起到重要的作用,同时还可抑制HIV-1和流感等病毒复制。此外,SLFN蛋白还被发现与肿瘤的治疗密切相关,可以作为预测肿瘤发展进程和化疗敏感性的分子标记。本文介绍了SLFN家族蛋白的分类、结构和主要特征、定位与功能,重点综述了其在肿瘤和病毒感染等相关领域的研究进展,以期为SLFN蛋白新功能的探究提供新思路,对蛋白发挥作用的可能机制给予提示,并为各相关领域的研究提供参考。

Northward Shift in Landfall Locations of Tropical Cyclones over the Western North Pacific during the Last Four Decades

This study analyzes landfall locations of tropical cyclones(TCs)over the western North Pacific during 1979–2018.Results demonstrate that the landfall locations of TCs over this region have shifted northward during the last four decades,primarily due to the shift of landfalling TC tracks,with the decreasing/increasing proportion of westward/northward TC tracks.In particular,the northward shift of the landfalling TCs was not related to their formation locations,which have not markedly changed,whereas"no-landed"TCs have significantly shifted northward.TC movement was significantly and positively correlated to the zonal component of the steering flow,while the correlation between TC movement and the meridional component of the steering flow was relatively unobvious.The westward steering flow in the tropical central Pacific that occurred around the formation and early development of the westward TCs was significantly weakened,which was unfavorable for their westward movement,thereby,causing the higher proportions of northward moving tracks.This weakened westward flow was related to the northward shift of the subtropical high ridge,which was caused by significant weakening of the southern part of the subtropical high.The vertical wind shear,sea surface temperature,and convective available potential energy also showed that the northern region of the western North Pacific became more favorable for TC development,whereas the upper divergence,low-layer relative vorticity,and accumulated water vapor content were not obviously related to the northward shift of TCs.

Atmospheric Response to Mesoscale Ocean Eddies over the South China Sea

The South China Sea（SCS） is an eddy-active area. Composite analyses based on 438 mesoscale ocean eddies during 2000–2012 revealed the status of the atmospheric boundary layer is influenced remarkably by such eddies. The results showed cold-core cyclonic（warm-core anticyclonic） eddies tend to cool（warm） the overlying atmosphere and cause surface winds to decelerate（accelerate）. More than 5% of the total variance of turbulent heat fluxes, surface wind speed and evaporation rate are induced by mesoscale eddies. Furthermore, mesoscale eddies locally affect the columnar water vapor, cloud liquid water, and rain rate. Dynamical analyses indicated that both variations of atmospheric boundary layer stability and sea level pressure are responsible for atmospheric anomalies over mesoscale eddies. To reveal further details about the mechanisms of atmospheric responses to mesoscale eddies, atmospheric manifestations over a pair of cold and warm eddies in the southwestern SCS were simulated. Eddy-induced heat flux anomalies lead to changes in atmospheric stability. Thus, anomalous turbulence kinetic energy and friction velocity arise over the eddy dipole, which reduce（enhance） the vertical momentum transport over the cold（warm） eddy, resulting in the decrease（increase） of sea surface wind. Diagnoses of the model＇s momentum balance suggested that wind speed anomalies directly over the eddy dipole are dominated by vertical mixing terms within the atmospheric boundary layer, while wind anomalies on the edges of eddies are produced by atmospheric pressure gradient forces and atmospheric horizontal advection terms.

Morphological Characteristics of Precipitation Areas over the Tibetan Plateau Measured by TRMM PR

The multidimensional morphological characteristics(including scale, horizontal shape and 3 D morphology) of precipitation areas over the Tibetan Plateau in summer were studied using 15 years(1998–2012) of observational data from the precipitation radar onboard the Tropical Rainfall Measuring Mission satellite. As the scale of the precipitation area increased from 20 to 150 km, the near-surface rain rate(RRav) of the precipitation area increased by up to 78%(from ~1.12 to ~2 mm h~(-1)). Linear precipitation areas had the lowest median RRav(~1 mm h~(-1) over the eastern Tibetan Plateau),whereas square-shaped precipitation areas had the highest median RRav(~1.58 mm h~(-1) over the eastern Tibetan Plateau).The 3D morphology was defined as the ratio of the average vertical scale to the average horizontal scale, where a large value corresponds to thin and tall, and a small value corresponds to plump and short. Thin-and-tall precipitation areas and plump-and-short precipitation areas had a greater median RRav, whereas the precipitation areas with a moderate 3D morphology had the lowest median RRav. The vertical structure of the precipitation-area reflectivity was sensitive to both size and 3D morphology, but was not sensitive to the horizontal shape. The relationship between RRav and the morphological characteristics was most significant over the southern slopes of the Tanggula Mountains and the Tibetan Plateau east of 100°E. The morphological characteristics of precipitation areas are therefore closely related to the intensity of precipitation and could potentially be used to forecast precipitation and verify numerical models.

Variations in High-frequency Oscillations of Tropical Cyclones over the Western North Pacific

Variations in the high-frequency oscillations of tropical cyclones （TCs） over the western North Pacific （WNP） are studied in numerical model simulations. Power spectrum analysis of maximum wind speeds at 10 m （MWS10） from an ensemble of 15 simulated TCs shows that oscillations are significant for all TCs. The magnitudes of oscillations in MWS10 are similar in the WNP and South China Sea （SCS）; however, the mean of the averaged significant periods in the SCS （1.93 h） is shorter than that in the open water of the WNP （2.83 h）. The shorter period in the SCS is examined through an ensemble of simulations, and a case simulation as well as a sensitivity experiment in which the continent is replaced by ocean for Typhoon Hagupit （2008）. The analysis of the convergence efficiency within the boundary layer suggests that the shorter periods in the SCS are possibly due to the stronger terrain effect, which intensifies convergence through greater friction. The enhanced convergence strengthens the disturbance of the gradient and thermal wind balances, and then contributes to the shorter oscillation periods in the SCS.

Satellite Observations of Reflectivity Maxima above the Freezing Level Induced by Terrain

Previous studies have recognized reflectivity maxima above the freezing level(RMAF) within stratiform precipitation over mountain slopes, however, quantitative studies are limited due to the lack of adequate identification criteria. Here, we establish an identification method for RMAF precipitation and apply it to the Tropical Rainfall Measuring Mission(TRMM) Precipitation Radar(PR) observations. Using the TRMM 2A25 product from 1998 to 2013, we show that the RMAF structure in reflectivity profiles can be effectively identified. RMAF exists not only in stratiform precipitation but also in convective precipitation. RMAF frequency is positively correlated with elevation, which is thought to be caused by enhanced updrafts in the middle layers of stratiform precipitation, or in the low to middle layers of convective precipitation over mountains. The average RMAF heights in stratiform and convective precipitation were 1.35 and 2.01 km above the freezing level, respectively, which is lower than previous results. In addition, our results indicate that the RMAF structure increased the echo top height and enhanced precipitation processes above the RMAF height, but it suppressed the downward propagation of ice particles and the near-surface rain rate. Future studies of orographic precipitation should take into account the impact of the RMAF structure and its relevant dynamic triggers.

OcBSA:An NGS-based bulk segregant analysis tool for outcross populations

Constructing inbred lines for self-incompatible species and species with long generation times is challenging,making the use of F1 outcross/segregating populations the main strategy for genetic studies of such species.However,there is a lack of dedicated algorithms/tools for rapid quantitative trait locus(QTL)mapping using the F1 populations.To this end,we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 populations.OcBSA transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 population.Testing of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and accuracy.In addition,the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple,pear,peach,citrus,grape,tea,and rice.We also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this study.The OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene,which regulates potato flower color.Taken together,these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing species.For ease of use,we have developed both Windows and Linux versions of OcBSA,which are freely available at:https://gitee.com/Bioinformaticslab/OcBSA.

Improved outcomes in E2A::HLF positive B-cell acute lymphoblastic leukemia by chimeric antigen receptor T cell therapy and BCL-2 inhibitor

To the Editor:The fusion gene E2A::HLF(TCF3::HLF)is formed by t(17;19)(q21-22;p13),which presents in<1%of B-cell acute lymphoblastic leukemia(B-ALL)and mainly occurs in older children and adolescents.[1]Such patients were often accompanied by drug resistance and early relapse,which confer an extremely poor prognosis,and even intensive chemotherapy and hematopoietic stem cell transplantation(HSCT)cannot improve their survival.[2]A few studies suggested that chimeric antigen receptor T(CAR-T)cell therapy or BCL-2 inhibitors might benefit such patients.

The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceaepolyploidizationandits distinct traits

Orychophragmus violaceus,referred to as‘‘eryuelan’’(February orchid)in China,is an early-flowering ornamental plant.The high oil content and abundance of unsaturated fatty acids in O.violaceus seeds make it a potential high-quality oilseed crop.Here,we generated a whole-genome assembly for O.violaceus using Nanopore and Hi-C sequencing technologies.The assembled genome of O.violaceus was~1.3 Gb in size,with 12 pairs of chromosomes.Through investigation of ancestral genome evolution,we determined that the genome of O.violaceus experienced a tetraploidization event from a diploid progenitor with the translocated proto-Calepineae karyotype.Comparisons between the reconstructed subgenomes of O.violaceus identified indicators of subgenome dominance,indicating that subgenomes likely originated via allotetraploidy.O.violaceus was phylogenetically close to the Brassica genus,and tetraploidy in O.violaceus occurred approximately 8.57 million years ago,close in time to the whole-genome triplication of Brassica that likely arose via an intermediate tetraploid lineage.However,the tetraploidization in Orychophragmus was independent of the hexaploidization in Brassica,as evidenced by the results from detailed phylogenetic analyses and comparisons of the break and fusion points of ancestral genomic blocks.Moreover,identification of multi-copy genes regulating the production of high-quality oil highlighted the contributions of both tetraploidization and tandem duplication to functional innovation in O.violaceus.These findings provide novel insights into the polyploidization evolution of plant species and will promote both functional genomic studies and domestication/breeding efforts in O.violaceus.

Unstable Allotetraploid Tobacco Genome due to Frequent Homeologous Recombination, -. Segmental Deletion, and Chromosome Loss

The types of mutations and their corresponding frequencies are difficult to measure in complex genomes. In this study, a high-throughput method was developed to identify spontaneous loss-of-function alleles for the resistance gene N and the transgenic avirulence gene P50 in allotetraploid tobacco. A total of 2134 loss- of-function alleles of the N gene were identified after screening 14 million F1 hybrids. Analysis of these mutants revealed striking evolutionary patterns for genes in polyploids. Only 14 of the loss-of-function mutations were caused by spontaneous point mutations or indels, while the others were caused by home- ologous recombination （with a frequency of 1/12 000） or chromosome loss （1/15 000）. Loss of the chromosome with the PS0 insertion occurred at a similar frequency （1/13 000）, and the frequency of spon- taneous segmental deletion in this chromosome was 1/16 000. Both homeologous recombination and chromosome loss considerably decreased the viability of the mutants. Our data suggest that the high mutation rate in polyploids is probably due to the occurrence of homeologous recombination and the toler- ance of large mutations such as chromosome loss in polyploid genomes. Frequent mutations tend to drive polyploids to extinction unless a novel mutation helps the polyploid to effectively compete with diploids or find a new ecological niche.

Pathogen Spectrum of Hand,Foot,and Mouth Disease Based on Laboratory Surveillance—China,2018

What is already known about this topic?Enterovirus 71(EV-A71)is the main causative pathogen for severe and fatal patients with Hand,Foot,and Mouth Disease(HFMD)in China's Mainland from 2008 to 2017.Non-EV-A71 and non-CV-A16(other enterovirus)serotypes were the major causativeserotypes for mild HFMD in years of 2013,2015,and 2017.What is added by this report?In 2018,other enterovirus serotypes replaced EV-A71 for the first time as the major cause of severe HFMD with a proportion of 70.7%.However,at the national level,only a small proportion of the other enterovirus serotypes were further identified as CV-A6 and CVA10.What are the limitations for public health practice?Further identification of other enterovirus serotypes is highly recommended for provincial CDCs,especially for severe HFMD.Studies contributing to a multivalent vaccine for HFMD should be prioritized.

Pepper variome reveals the history and key loci associated with fruit domestication and diversification

Pepper(Capsicum spp.)is an important vegetable crop that provides a unique pungent sensation when eaten.Through construction of a pepper variome map,we examined the main groups that emerged during domestication and breeding of C.annuum,their relationships and temporal succession,and the molecular events underlying the main transitions.The results showed that the initial differentiation in fruit shape and pungency,increase in fruit weight,and transition from erect to pendent fruits,as well as the recent appearance of large,blocky,sweet fruits(bell peppers),were accompanied by strong selection/fixation of key alleles and introgressions in two large genomic regions.Furthermore,we identified Up,which encodes a BIG GRAIN protein involved in auxin transport,as a key domestication gene that controls erect vs pendent fruit orientation.The up mutation gained increased expression especially in the fruit pedicel through a 579-bp sequence deletion in its 5′upstream region,resulting in the phenotype of pendent fruit.The function of Up was confirmed by virus-induced gene silencing.Taken together,these findings constitute a cornerstone for understanding the domestication and differentiation of a key horticultural crop.

The CREB Regulated Transcription Coactivator 2 Suppresses HIV-1 Transcription by Preventing RNA PolⅡfrom Binding to HIV-1 LTR

The CREB-regulated transcriptional co-activators(CRTCs),including CRTC1,CRTC2 and CRTC3,enhance transcription of CREB-targeted genes.In addition to regulating host gene expression in response to cAMP,CRTCs also increase the infection of several viruses.While human immunodeficiency virus type 1(HIV-1)long terminal repeat(LTR)promoter harbors a cAMP response element and activation of the cAMP pathway promotes HIV-1 transcription,it remains unknown whether CRTCs have any effect on HIV-1 transcription and HIV-1 infection.Here,we reported that CRTC2 expression was induced by HIV-1 infection,but CRTC2 suppressed HIV-1 infection and diminished viral RNA expression.Mechanistic studies revealed that CRTC2 inhibited transcription from HIV-1 LTR and diminished RNA PolⅡoccupancy at the LTR independent of its association with CREB.Importantly,CRTC2 inhibits the activation of latent HIV-1.Together,these data suggest that in response to HIV-1 infection,cells increase the expression of CRTC2 which inhibits HIV-1 gene expression and may play a role in driving HIV-1 into latency.

Construction of a high-density mutant population of Chinese cabbage facilitates the genetic dissection of agronomic traits

Chinese cabbage(Brassica rapa ssp.pekinensis)is an economically important vegetable crop throughout the world,especially in Asia.High-quality genome sequences are available for Chinese cabbage,but gene functional studies remain challenging.To promote functional genomic studies of Chinese cabbage,we generated an ethyl methane sulfonate(EMS)mutant population of~8000 M_(2) plants using the double haploid inbred line A03 as the parent.The genome of A03 was sequenced and used as a reference for high-throughput functional characterization of gene mutations at the whole-genome level.A total of 300 M_(2) to M_(5) EMS mutants were phenotypically screened and then sequenced,revealing 750629 SNPs and 46272 InDel mutations that cover 98.27%of all predicted genes in the A03 genome.A forward-genetics approach was successfully used to identify two genes with chloroplast-related functions that are responsible for the yellow leaf mutant trait.A reverse-genetics approach was also used to identify associations between mutations in five genes of the glucosinolate biosynthetic pathway and variations in glucosinolate content of the mutant plants.In addition,we built the Chinese cabbage EMS mutation database(CCEMD,www.bioinformaticslab.cn/EMSmutation/home)to increase the usability of this mutant population resource.In summary,we performed large-scale screening of a heading Chinese cabbage EMS mutant collection at the phenotypic and genotypic levels,which will facilitate gene mining of Chinese cabbage and might also be useful for the study of other Brassica crops.

Genome Assembly and Population Resequencing Reveal the Geographical Divergence of Shanmei(Rubus corchorifolius)

Rubus corchorifolius(Shanmei or mountain berry,2n=14)is widely distributed in China,and its fruits possess high nutritional and medicinal values.Here,we reported a highquality chromosome-scale genome assembly of Shanmei,with contig size of 215.69 Mb and 26,696 genes.Genome comparison among Rosaceae species showed that Shanmei and Fupenzi(Rubus chingii Hu)were most closely related,followed by blackberry(Rubus occidentalis),and that environmental adaptation-related genes were expanded in the Shanmei genome.Further resequencing of 101 samples of Shanmei collected from four regions in the provinces of Yunnan,Hunan,Jiangxi,and Sichuan in China revealed that among these samples,the Hunan population of Shanmei possessed the highest diversity and represented the more ancestral population.Moreover,the Yunnan population underwent strong selection based on the nucleotide diversity,linkage disequilibrium,and historical effective population size analyses.Furthermore,genes from candidate genomic regions that showed strong divergence were significantly enriched in the flavonoid biosynthesis and plant hormone signal transduction pathways,indicating the genetic basis of adaptation of Shanmei to the local environment.The high-quality assembled genome and the variome dataset of Shanmei provide valuable resources for breeding applications and for elucidating the genome evolution and ecological adaptation of Rubus species.