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| 1 | Plant Polyploidy: Origin, Evolution, and Its Influence on Crop Domestication显示文摘The prevalence and recurrence of polyploidization in plant species make it one of the most important evolutionary events in plants, and as a result, polyploidization is an extensively investigated research field. Due to the rapid development of sequencing technologies, there is increased evidence to support that polyploidization plays an important role in the diversification of plant species, evolution of genes, and the domestication of crops. Here, we reviewed the influence of polyploidization on various aspects of plant evolution, mainly focused on polyploid origin, characteristics, subsequent genome divergence, and its impact on gene function innovation and crop domestication. The occurrence of many independent polyploidization events in plants was found to be tightly associated with the timing of extreme climate events or natural disasters on earth, leading to mass extinction while possibly facilitating increased polyploidization. Following allo-polyploidization, a distinct phenomenon known as sub-genome dominance occurred during sub-genome evolution, which was found to be associated with the methylation of transposons. Extensive gene fractionations(lost) following polyploidization were reported in almost all paleo-polyploids, and the evolutionary fates of multi-copy genes, such as sub-/neo-functionalization, were further proposed to illustrate their underlying mechanisms. Moreover,polyploidization was found to significantly impact species diversification, with subsequent effects on crop domestication and the development of traits with agronomic importance. Based on the progress of plant polyploidization studies, we discussed several main topics that might further improve our understanding of polyploid evolution and that are likely contribute to the application of polyploidization in crop breeding in the near future. | Kang Zhang Xiaowu Wang Feng Cheng | 2019 | Horticultural Plant Journal2019，5，6： | 12 |
| 2 | Genome triplication drove the diversification of Brassica plants显示文摘The genus Brassica belongs to the plant family Brassicaceae,which includes many important crop species that are used as oilseed,condiments,or vegetables throughout the world.Brassica plants comprise many diverse species,and each species contains rich morphotypes showing extreme traits.Brassica species experienced an extra whole genome triplication(WGT)event compared with the model plant Arabidopsis thaliana.Whole genome sequencing of the Brassica species Brassica rapa,Brassica oleracea and others demonstrated that WGT plays an important role in the speciation and morphotype diversification of Brassica plants.Comparative genomic analysis based on the genome sequences of B.rapa and A.thaliana clearly identified the WGT event and further demonstrated that the translocated Proto-Calepine Karyotype(tPCK,n57)was the diploid ancestor of the three subgenomes in B.rapa.Following WGT,subsequent extensive genome fractionation,block reshuffling and chromosome reduction accompanied by paleocentromere descent from the three tPCK subgenomes during the rediploidization process produced stable diploid species.Genomic rearrangement of the diploid species and their hybridization then contributed to Brassica speciation.The subgenome dominance effect and biased gene retention,such as the over-retention of auxin-related genes after WGT,promoted functional gene evolution and thus propelled the expansion of rich morphotypes in the Brassica species.In conclusion,the WGT event initiated subsequent genomic and gene-level evolution,which further drove Brassica speciation and created rich morphotypes in each species. | Feng Cheng Jian Wu Xiaowu Wang | 2014 | Horticulture Research2014，1，1： | 11 |
| 3 | Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies显示文摘Brassica rapa comprises several important cultivated vegetables and oil crops.Current reference genome assemblies of Brassica rapa are quite fragmented and not highly contiguous,thereby limiting extensive genetic and genomic analyses.Here,we report an improved assembly of the B.rapa genome(v3.0)using single-molecule sequencing,optical mapping,and chromosome conformation capture technologies(Hi-C).Relative to the previous reference genomes,our assembly features a contig N50 size of 1.45 Mb,representing a~30-fold improvement.We also identified a new event that occurred in the B.rapa genome~1.2 million years ago,when a long terminal repeat retrotransposon(LTR-RT)expanded.Further analysis refined the relationship of genome blocks and accurately located the centromeres in the B.rapa genome.The B.rapa genome v3.0 will serve as an important community resource for future genetic and genomic studies in B.rapa.This resource will facilitate breeding efforts in B.rapa,as well as comparative genomic analysis with other Brassica species. | Lei Zhang Xu Cai Jian Wu Min Liu Stefan Grob Feng Cheng Jianli Liang Chengcheng Cai Zhiyuan Liu Bo Liu Fan Wang Song Li Fuyan Liu Xuming Li Lin Cheng Wencai Yang Mai-he Li Ueli Grossniklaus Hongkun Zheng Xiaowu Wang | 2018 | Horticulture Research2018，5，1： | 10 |
| 4 | A de novo Genome of a Chinese Radish Cultivar显示文摘Here, we report a high-quality draft genome of a Chinese radish(Raphanus sativus) cultivar. This draft contains 387.73 Mb of assembled scaffolds, 83.93% of the scaffolds were anchored onto nine pseudochromosomes and 95.09% of 43 240 protein-coding genes were functionally annotated. 184.75 Mb(47.65%) of repeat sequences was identified in the assembled genome. By comparative analyses of the radish genome against 10 other plant genomes, 2 275 genes in 780 gene families were found unique to R. sativus. This genome is a good reference for genomic study and of great value for genetic improvement of radish. | ZHANG Xiaohui YUE Zhen MEI Shiyong QIU Yang YANG Xinhua CHEN Xiaohua CHENG Feng WU Zhangyan SUN Yuyan JING Yi LIU Bo SHEN Di WANG Haiping CUI Na DUAN Yundan WU Jian WANG Jinglei GAN Caixia WANG Jun WANG Xiaowu LI Xixiang | 2015 | Horticultural Plant Journal2015，1，3： | 10 |
| 5 | Brassica rapa Genome 2.0: A Reference Upgrade through Sequence Re-assembly and Gene Re-annotation显示文摘 | Chengcheng Cai Xiaobo Wang Bo Liu Jian Wu Jianli Liang Yinan Cui Feng Cheng Xiaowu Wang | 2017 | Molecular Plant2017，10，4： | 6 |
| 6 | A naturally occurring variation in the BrMAM-3 gene is associated with aliphatic glucosinolate accumulation in Brassica rapa leaves显示文摘Glucosinolate profiles significantly vary among Brassica rapa genotypes.However,the molecular basis of these variations is largely unknown.In this study,we investigated a major quantitative trait locus(QTL)controlling aliphatic glucosinolate accumulation in B.rapa leaves.The QTL,which encompasses three tandem MAM genes and two MYB genes,was detected in two BC2DH populations.Among the five-candidate genes,only the expression level of BrMAM-3(Bra013007)was significantly correlated with the accumulation of aliphatic glucosinolates in B.rapa leaves.We identified a naturally occurring insertion within exon 1 of BrMAM-3,which is predicted to be a loss-of-function mutation,as confirmed by qRT-PCR.We determined that the loss of function was associated with the low glucosinolate content in B.rapa accessions.Furthermore,overexpressing the BrMAM-3 gene resulted in an increase in total aliphatic glucosinolates in Arabidopsis transgenic lines.Our study provides insights into the molecular mechanism underlying the accumulation of aliphatic glucosinolates in B.rapa leaves,thereby facilitating in the manipulation of total aliphatic glucosinolate content in Brassica crops. | Jifang Zhang Hui Wang Zhiyuan Liu Jianli Liang Jian Wu Feng Cheng Shiyong Mei Xiaowu Wang | 2018 | Horticulture Research2018，5，1： | 5 |
| 7 | Hotspots of Independent and Multiple Rounds of LTR-retrotransposon Bursts in Brassica Species显示文摘Long terminal repeat retrotransposons(LTR-RTs) are a predominant group of plant transposable elements(TEs) that are an important component of plant genomes. A large number of LTR-RTs have been annotated in the genomes of the agronomically important oil and vegetable crops of the genus Brassica. Herein, full-length LTR-RTs in the genomes of Brassica and other closely related species were systematically analyzed. The full-length LTR-RT content varied greatly(from 0.43% to 23.4%) between different species, with Gypsy-like LTR-RTs constituting a primary group across these genomes. More importantly, many annotated LTR-RTs(from 10.03% to 33.25% of all detected LTR-RTs) were found to be enriched in localized hotspot regions. Furthermore, all of the analyzed species showed evidence of having experienced at least one round of a LTR-RT burst, with Raphanus sativus experiencing three or more. Moreover, these relatively ancient LTR-RT amplifications exhibited a clear expansion at specific time points. To gain a further understanding of this timing, Brassica rapa, B. oleracea, and R. sativus were examined for the presence of syntenic regions, but none were present. These findings indicate that these LTR-RT burst events were not inherited from a common ancestor,but instead were species-specific bursts that occurred after the divergence of Brassica species. This study further exemplifies the complexities of TE amplifications during the evolution of plant genomes and suggests that these LTR-RT bursts play an important role in genome expansion and divergence in Brassica species. | CAI Xu CUI Yinan ZHANG Lei WU Jian LIANG Jianli CHENG Lin WANG Xiaowu CHENG Feng | 2018 | Horticultural Plant Journal2018，4，4： | 3 |
| 8 | A High Density Linkage Map Facilitates QTL Mapping of Flowering Time in Brassica rapa显示文摘Flowering is a major developmental transition in the life-history of plants. Flowering time is under complex genetic control. In this study, 172 doubled haploid(DH) lines derived from a cross between two Chinese cabbage(Brassica rapa ssp. pekinensis) DH lines, Y177 and Y195, were used for a high density linkage map construction and quantitative trait locus(QTL) mapping for flowering time in B. rapa. Parents and DH lines were resequenced at depth of 5× and 0.5× coverage, respectively. In total, 22 747 SNPs were called from the resequencing data and combined into 1 708 bins to construct the genetic linkage map. The map length was 958.6 c M, containing 887 bins and the average interval between binmarkers was 1.08 c M. A total of six QTLs controlling flowering time were detected under four different conditions. Potential candidate flowering homologues located near QTLs were identified with the aid of B. rapa genome annotation. | LIU Jing LIU Bo CHENG Feng LIANG Jianli WANG Xiaowu WU Jian | 2016 | Horticultural Plant Journal2016，2，4： | 3 |
| 9 | Residual stress variation in SiC_(f)/SiC composite during heat treatment and its effects on mechanical behavior显示文摘Residual stress originated from thermal expansion mismatch determines the mechanical properties of ceramic matrix composites(CMCs).Here,continuous SiC fiber reinforced SiC matrix(SiC_(f)/SiC)composites were fabricated by nano-infiltration and transient eutectic-phase(NITE)method,and the residual stress of the composites was investigated using high-temperature Raman spectrometer.With temperature increasing from room temperature to 1400℃,the residual stresses of the matrix and the fiber decrease from 1.29 to 0.62 GPa and from 0.84 to 0.55 GPa in compression respectively,while that of the interphase decreases from 0.16 to 0.10 GPa in tension.The variation of residual stress shows little effect on the tensile strength of the composites,while causes a slight decrease in the tensile strain.The suppression of fiber/matrix debonding and fiber pulling-out caused by the residual stress reduction in the interphase is responsible for the decreasing tensile strain.This work can open up new alternatives for residual stress analysis in CMCs. | Xiaowu CHEN Guofeng CHENG Junmin ZHANG Feiyu GUO Haijun ZHOU Chunjin LIAO Hongda WANG Xiangyu ZHANG Shaoming DONG | 2020 | Journal of Advanced Ceramics2020，9，5： | 3 |
| 10 | 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 |
| 11 | Author Correction:Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies显示文摘Since the publication of this article,the authors have noticed that the total gene models(45,985),tandem arrays(2077),tandem genes(4963),redundancy removed(43,099),syntenic genes(39,858),nonsyntenic genes(3241),genes on chromosomes(45,411),genes on scaffolds(574)of B.rapa reference genome v3.0 were mistaken in the article. | Lei Zhang Xu Cai Jian Wu Min Liu Stefan Grob Feng Cheng Jianli Liang Chengcheng Cai Zhiyuan Liu Bo Liu Fan Wang Song Li Fuyan Liu Xuming Li Lin Cheng Wencai Yang Mai-he Li Ueli Grossniklaus Hongkun Zheng Xiaowu Wang | 2019 | Horticulture Research2019，6，1： | 2 |
| 12 | Development of InDel markers for Brassica rapa based on whole-genome re-sequencing显示文摘 | Bo Liu Yan Wang Wen Zhai Jie Deng Hui Wang Yang Cui Feng Cheng Xiaowu Wang Jian Wu | 2013 | Theoretical and Applied Genetics2013，，1： | 1 |
| 13 | Development of InDel markers for Brassica rapa based on whole-genome re-sequencing显示文摘 | Bo Liu Yan Wang Wen Zhai Jie Deng Hui Wang Yang Cui Feng Cheng Xiaowu Wang Jian Wu | 2013 | Theoretical and Applied Genetics2013，，1： | 1 |
| 14 | Formation cross section of 10Be measured by accelerator mass spectrometry technique显示文摘 | Liu Lianfan Cheng Xiaowu Zhou Weinan | 1994 | High Energy Physics and Nuclear Physics1994，19，09： | 1 |
| 15 | Structural changes of a bacteriophage upon DNA packaging and maturation显示文摘Dear Editor,Tailed,double-stranded DNA(dsDNA)bacteriophages,which belong to the order of Caudovirales,have a tail attached to a pentameric vertex of the icosahedral capsid shell(head)through a 12-fold portal(Johnson and Chiu,2007).The phages package genomic dsDNA into a round procapsid using the portal in complex with an ATP-dependent terminase complex as the motor.During packaging,the procapsid shell expands to a more angular intermediate to match the size of the viral genome(Guo et al.,2014).When the phage head is full,the portal detects internal pressure and conveys a signal from the inner capsid to the exterior,which triggers a sequence of events-the terminase complex cleaving mature DNA genome from a multi-genome concatemer,the release of the terminase complex from the portal,and the attachment of the tail complex-in the completion of phage assembly(Lander et al.,2006;Johnson and Chiu,2007).At the beginning of phage infection,the tail is responsible for receptor recognition,and the portal and tail act as a tunnel for DNA delivery into the host cytoplasm(Johnson and Chiu,2007).These mechanisms of DNA packaging and ejection may also be conserved in many other DNA viruses,including herpesvirus(Wang et al.,2020;Yang et al.,2020). | Wenyuan Chen Hao Xiao Xurong Wang Shuanglin Song Zhen Han Xiaowu Li Fan Yang Li Wang Jingdong Song Hongrong Liu Lingpeng Cheng | 2020 | Protein & Cell2020，11，5： | 1 |
| 16 | High Serum Hyaluronic Acid and HBV Viral Load are Main Prognostic Factors of Local Recurrence after Complete Radiofrequency Ablation of Hepatitis B-Related Small Hepatocellular Carcinoma显示文摘 | Feng Xia MD PhD Eric C. H. Lai MBChB FRACS Wan-Yee Lau MD FRCS FACS FRACS(Hon) Kuansheng Ma MD PhD Xiaowu Li MD PhD Ping Bie MD PhD Cheng Qian MD PhD | 2012 | Annals of Surgical Oncology2012，，4： | 1 |
| 17 | Glucosinolate biosynthetic genes in Brassica rapa显示文摘 | Hui Wang Jian Wu Silong Sun Bo Liu Feng Cheng Rifei Sun Xiaowu Wang | 2011 | Gene2011，，2： | 1 |
| 18 | High Serum Hyaluronic Acid and HBV Viral Load are Main Prognostic Factors of Local Recurrence after Complete Radiofrequency Ablation of Hepatitis B-Related Small Hepatocellular Carcinoma显示文摘 | Feng Xia MD PhD Eric C. H. Lai MBChB FRACS Wan-Yee Lau MD FRCS FACS FRACS(Hon) Kuansheng Ma MD PhD Xiaowu Li MD PhD Ping Bie MD PhD Cheng Qian MD PhD | 2012 | Annals of Surgical Oncology2012，，4： | 1 |
| 19 | High Serum Hyaluronic Acid and HBV Viral Load are Main Prognostic Factors of Local Recurrence after Complete Radiofrequency Ablation of Hepatitis B-Related Small Hepatocellular Carcinoma显示文摘 | Feng Xia Eric Lai Wan-Yee Lau Kuansheng Ma Xiaowu Li Ping Bie Cheng Qian | 2012 | Annals of Surgical Oncology2012，，4： | 1 |
| 20 | Symmetry-mismatch reconstruction of genomes and associated proteins within icosahedral viruses using cryo-EM显示文摘 | Xiaowu Li Hongrong Liu Lingpeng Cheng | 2016 | Biophysics Reports2016，2，1： | 1 |
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