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| 1 | Segmental Translocation Contributed to the Origin of the Brassica S-locus显示文摘Self-incompatibility(SI),which has recurred during the evolution of plants,is one of the most important cross-pollination mating systems.Three S-loci have been reported in Brassicaceae,namely,Arabidopsis lyrata(Al),Brassica(Br),and Leavenworthia alabamica(La)S-loci.Here,through multi-genomic comparative analysis of 20 species,we revealed that the most ancient S-locus was formed prior to the divergence of Brassicaceae lineage I and II.Itwas retained and inherited by Arabidopsis,as the Al S-locus in Brassicaceae lineage I.Furthermore,we found that the Br S-locus,which has been widely used in the breeding of Brassica crops to generate hybrid seeds,was formed through segmental translocation(ST)in the hexaploid ancestor of Brassica in Brassicaceae lineage II.The Br S-locus was evolved through a ST from one of the triplicated ancestral S-locus paralogs in the Brassica hexaploidy ancestor,while the other two S-locus paralogs were lost.Together with the previous discovery that the La S-locus was formed through a secondary origin in Brassicaceae lineage I,we conclude the monophyletic origin of Al and Br S-loci and clarify the evolutionary route of S-loci in the Brassicaceae family.Our findings will contribute to evolutionary studies and breeding applications of the S-locus in Brassicaceae. | Yinan Cui Mu Zhuang Jian Wu Jisheng Liu Yiyue Zhang Lingkui Zhang Yile Huang Xu Cai Jianli Liang Kang Zhang Xiaowu Wang Feng Cheng | 2020 | Horticultural Plant Journal2020，6，3： | 2 |
| 2 | The gap-free potato genome assembly reveals large tandem gene clusters of agronomical importance in highly repeated genomic regions显示文摘Dear Editor,Potato is a vital food security crop and is ranked as the world’s third most important food crop after rice and wheat.In 2011,the first genome assembly of a doubled monoploid potato DM1-3516 R44(DM)was released(Potato Genome Sequencing Consortium,2011),which has been widely used as one of the most popular reference genomes in the last decade and served as a valuable resource in plant genomics and potato genetics community(Leisner et al.,2018;Yang et al.,2020;Zheng et al.,2020). | Xiaohui Yang Lingkui Zhang Xiao Guo Jianfei Xu Kang Zhang Yinqing Yang Yu Yang Yinqiao Jian Daofeng Dong Sanwen Huang Feng Cheng Guangcun Li | 2023 | Molecular Plant2023，16，2： | 2 |
| 3 | The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceaepolyploidizationandits distinct traits显示文摘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. | Kang Zhang Yinqing Yang Xin Zhang Lingkui Zhang Yu Fu Zhongwei Guo Shumin Chen Jian Wu James C.Schnable Keke Yi Xiaowu Wang Feng Cheng | 2023 | Plant Communications2023，4，2： | 0 |
| 4 | Dehydrative Glycosylation Enabled by a Comproportionation Reaction of 2-Aryl-1,3-dithiane 1-Oxide显示文摘Summaryof main observation and conclusion A new dehydrativeglycosylation reaction has been established by capitalizing on the compropor-tionation reaction of 2-aryl-1,3-dithiane 1-oxides promoted by triflic anhydride(Tf2O).By wedding the high potency of thiophilic promoter system with the step efficiency of dehydrative glycosylation,this reagentunderwent facile intermolecular oxothio acetalization with C1-hemiacetal donor to install a temporary leaving group,rendering a transient electrophilic center at the remote site to the anomeric position.The sulfenyltriflate tethered at the ter-minus concomitantly activated the sulfide intramolecularly to afford the oxocarbenium ion,thereby facilitating the title glycosylation.Aside from accom-modating broad range functional groups and inactive hemiacetal substrates,the present activation protocol also proved expedient for 1,3-diol protection.Most importantly,this method further provided a fresh perspective for the application of sulfur chemistry to carbohydrate chemistry. | Lei Cai Jing Zeng Ting Li Ying Xiao Xiang Ma Xiong Xiao Qin Zhang Lingkui Meng Qian Wan | 2020 | Chinese Journal of Chemistry2020，38，1： | 0 |
| 5 | Forecasting NDVI in multiple complex areas using neural network techniques combined feature engineering显示文摘NDVI(Normalized difference vegetation index)is a critical variable for monitoring climate change,studying ecological balance,and exploring the pattern of regional phenology.Traditional neural network models only consider image features in time series prediction,while historical data and its changes play an important role in time series forecasting.For this study,we proposed convolutional neural networks(CNN)combined feature engineering forecasting model(SF-CNN),which integrated both the advantages of image characteristics learned from CNN and statistic characteristics calculated by historical data related to the forecast period to improve the accuracy of NDVI predictions in the next 3 months with 30-day interval at multiple complex areas.To intuitively show the performance of SF-CNN,it was compared with CNN using the same parameters.Results mainly showed that(1)in terms of visual analysis,the texture,pattern,and structure of predicted NDVI using SF-CNN are similar to the observed NDVI,and SF-CNN exhibits strong generalization ability;(2)in terms of quantitative assessment,SF-CNN generally outperforms CNN,and it can improve the reliability and robustness for predicting NDVI through simple statistical characteristics while reducing the uncertainties;(3)SF-CNN can learn seasonal and sudden changes in four different and complex study areas with considerable accuracy and without extra data. | Changlu Cui Wen Zhang ZhiMing Hong LingKui Meng | 2020 | International Journal of Digital Earth2020，13，12： | 0 |
| 6 | Genome Assembly and Population Resequencing Reveal the Geographical Divergence of Shanmei(Rubus corchorifolius)显示文摘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. | Yinqing Yang Kang Zhang Ya Xiao Lingkui Zhang Yile Huang Xing Li Shumin Chen Yansong Peng Shuhua Yang Yongbo Liu Feng Cheng | 2022 | Genomics, Proteomics & Bioinformatics2022，20，6： | 0 |
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