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| 1 | Antimicrobial resistance in Acinetobacter baumannii : From bench to bedside显示文摘Acinetobacter baumannii(A. baumannii) is undoubtedly one of the most successful pathogens in the modern healthcare system. With invasive procedures, antibiotic use and immunocompromised hosts increasing in recent years, A. baumannii has become endemic in hospitals due to its versatile genetic machinery, which allows it to quickly evolve resistance factors, and to its remarkable ability to tolerate harsh environments. Infections and outbreaks caused by multidrugresistant A. baumannii(MDRAB) are prevalent and have been reported worldwide over the past twenty or more years. To address this problem effectively, knowledge of species identification, typing methods, clinical manifestations, risk factors, and virulence factors is essential. The global epidemiology of MDRAB is monitored by persistent surveillance programs. Because few effective antibiotics are available, clinicians often face serious challenges when treating patients with MDRAB. Therefore, a deep understanding of the resistance mechanisms used by MDRAB can shed light on two possible strategies to combat the dissemination of antimicrobial resistance: stringent infection control and antibiotic treatments, of which colistin-based combination therapy is the mainstream strategy. However, due to the current unsatisfying therapeutic outcomes, there is a great need to develop and evaluate the efficacy of new antibiotics and to understand the role of other potential alternatives, such as antimicrobial peptides, in the treatment of MDRAB infections. | Ming-Feng Lin Chung-Yu Lan | 2014 | World Journal of Clinical Cases2014，2，12： | 55 |
| 2 | Next-generation sequencing technology:A technology review and future perspective显示文摘As one of the most powerful tools in biomedical research,DNA sequencing not only has been improving its productivity at an exponential growth rate but has also been evolving into a new layout of technological territories toward engineering and physical disciplines over the past three decades.In this technical review,we look into technical characteristics of the next-generation sequencers and provide insights into their future development and applications.We envisage that some of the emerging platforms are capable of supporting the USD1000 genome and USD100 genome goals if given a few years for technical maturation.We also suggest that scientists from China should play an active role in this campaign that will have a profound impact on both scientific research and societal healthcare systems. | ZHOU XiaoGuang1,REN LuFeng1,LI YunTao2,ZHANG Meng1,YU YuDe2 & YU Jun1 1 Key Laboratory of Genome Sciences and Information,Beijing Institute of Genomics,Chinese Academy of Sciences,Beijing 100029,China 2 Institute of Semiconductors,Chinese Academy of Sciences,Beijing 100083,China | 2010 | Science China(Life Sciences)2010，53，1： | 27 |
| 3 | Rapeseed research and production in China显示文摘Rapeseed(Brassica napus L.) is the largest oilseed crop in China and accounts for about 20% of world production.For the last 10 years,the production,planting area,and yield of rapeseed have been stable,with improvement of seed quality and especially seed oil content.China is among the leading countries in rapeseed genomic research internationally,having jointly with other countries accomplished the whole genome sequencing of rapeseed and its two parental species,Brassica oleracea and Brassica rapa.Progress on functional genomics including the identification of QTL governing important agronomic traits such as yield,seed oil content,fertility regulation,disease and insect resistance,abiotic stress,nutrition use efficiency,and pod shattering resistance has been achieved.As a consequence,molecular markers have been developed and used in breeding programs.During 2005–2014,215 rapeseed varieties were registered nationally,including 210 winter-and 5 spring-type varieties.Mechanization across the whole process of rapeseed production was investigated and operating instructions for all relevant techniques were published.Modern techniques for rapeseed field management such as high-density planting,controlled-release fertilizer,and biocontrol of disease and pests combined with precision tools such as drones have been developed and are being adopted in China.With the application of advanced breeding and production technologies,in the near future,the oil yield and quality of rapeseed varieties will be greatly increased,and more varieties with desirable traits,especially early maturation,high yield,high resistance to biotic and abiotic stress,and suitability for mechanized harvesting will be developed.Application of modern technologies on the mechanized management of rapeseed will greatly increase grower profit. | Qiong Hu Wei Hua Yan Yin Xuekun Zhang Lijiang Liu Jiaqin Shi Yongguo Zhao Lu Qin Chang Chen Hanzhong Wang | 2017 | The Crop Journal2017，5，2： | 25 |
| 4 | Genome analysis of Taraxacum kok-saghyz Rodin provides new insights into rubber biosynthesis显示文摘The Russian dandelion Taraxacum kok-saghyz Rodin(TKS), a member of the Composite family and a potential alternative source of natural rubber(NR) and inulin, is an ideal model system for studying rubber biosynthesis. Here we present the draft genome of TKS, the first assembled NR-producing weed plant. The draft TKS genome assembly has a length of 1.29 Gb, containing 46 731 predicted protein-coding genes and68.56% repeats, in which the LTR-RT elements predominantly contribute to the genome enlargement. We analyzed the heterozygous regions/genes, suggesting its possible involvement in inbreeding depression.Through comparative studies between rubber-producing and non-rubber-producing plants, we found that enzymes of the mevalonate(MVA) pathway and rubber elongation might be critical for rubber biosynthesis, and several key isoforms have been isolated and shown to be predominantly expressed in the latex, indicating their crucial functions in rubber biosynthesis. Moreover, for two important families in rubber elongation, the CPT/CPTL and REF/SRPP families, diverse evolutionary tracks have been revealed. These results provide valuable resources and new insights into the mechanism of NR biosynthesis,and facilitate the development of alternative NR-producing crops. | Tao Lin Xia Xu Jue Ruan Shizhong Liu Shigang Wu Xiujuan Shao Xiaobo Wang Lin Gan Bi Qin Yushuang Yang Zhukuan Cheng Suhua Yang Zhonghua Zhang Guosheng Xiong Sanwen Huang Hong Yu Jiayang Li | 2018 | National Science Review2018，5，1： | 22 |
| 5 | Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement显示文摘Cultivated peanut (Arachis hypogaea) is an allotetraploid crop planted in Asia, Africa, and America for edible oil and protein. To explore the origins and consequences of tetraploidy, we sequenced the allotetraploid A. hypogaea genome and compared it with the related diploid Arachis duranensis and Arachis ipaensis genomes. We annotated 39 888 A-subgenome genes and 41 526 B-subgenome genes in allotetraploid peanut. The A. hypogaea subgenomes have evolved asymmetrically, with the B subgenome resembling the ancestral state and the A subgenome undergoing more gene disruption, loss, conversion, and transposable element proliferation, and having reduced gene expression during seed development despite lacking genome-wide expression dominance. Genomic and transcriptomic analyses identified more than 2 500 oil metabolism-related genes and revealed that most of them show altered expression early in seed development while their expression ceases during desiccation, presenting a comprehensive map of peanut lipid biosynthesis. The availability of these genomic resources will facilitate a better understanding of the complex genome architecture, agronomically and economically important genes, and genetic improvement of peanut. | Xiaoping Chen Qing Lu Hao Liu Jianan Zhang Yanbin Hong Haofa Lan Haifen Li Jinpeng Wang Haiyan Liu Shaoxiong Li Manish K.Pandey Zhikang Zhang Guiyuan Zhou Jigao Yu Guoqiang Zhang Jiaqing Yuan Xingyu Li Shijie Wen Fanbo Meng Shanlin Yu Xiyin Wang Kadambot H.M.Siddique Zhong-Jian Liu Andrew H.Paterson Rajeev K.Varshney Xuanqiang Liang | 2019 | Molecular Plant2019，12，7： | 23 |
| 6 | A Chromosome-Scale Genome Assembly of Paper Mulberry(Bmussonetia papyrifera)Provides New Insights into Its Forage and Papermaking Usage显示文摘Paper mulberry(Broussonetia papyrifera)is a well-known woody tree historically used for Cai Lun papermaking,one of the four great inventions of ancient China.More recently,Paper mulberry has also been used as forage to address the shortage of feedstuff because of its digestible crude fiber and high protein contents.In this study,we obtained a chromosome-scale genome assembly for Paper mulberry using integrated approaches,including Illumina and PacBio sequencing platform as well as Hi-C,optical,and genetic maps.The assembled Paper mulberry genome consists of 386.83 Mb,which is close to the estimated size,and 99.25%(383.93 Mb)of the assembly was assigned to 13 pseudochromosomes.Comparative genomic analysis revealed the expansion and contraction in the flavonoid and lignin biosynthetic gene families,respectively,accounting for the enhanced flavonoid and decreased lignin biosynthesis in Paper mulberry.Moreover,the increased ratio of syringyl-lignin to guaiacyl-lignin in Paper mulberry underscores its suitability for use in medicine,forage,papermaking,and barkcloth making.We also identified the rootassociated microbiota of Paper mulberry and found that Pseudomonas and Rhizobia were enriched in its roots and may provide the source of nitrogen for its stems and leaves via symbiotic nitrogen fixation.Collectively,these results suggest that Paper mulberry might have undergone adaptive evolution and recruited nitrogen-fixing microbes to promote growth by enhancing flavonoid production and altering lignin monomer composition.Our study provides significant insights into genetic basis of the usefulness of Paper mulberry in papermaking and barkcloth making,and as forage.These insights will facilitate further domestication and selection as well as industrial utilization of Paper mulberry worldwide. | Xianjun Peng Hui Liu Peilin Chen Feng Tang Yanmin Hu Fenfen Wang Zhi Pi Meiling Zhao Naizhi Chen Hui Chen Xiaokang Zhang Xueqing Yan Min Liu Xiaojun Fu Guofeng Zhao Pu Yao Lili Wang He Dai Xuming Li Wei Xiong Wencai Xu Hongkun Zheng Haiyan Yu Shihua Shen | 2019 | Molecular Plant2019，12，5： | 18 |
| 7 | Recent Progress on Functional Genomics Research of Enterovirus 71显示文摘Enterovirus 71(EV71) is one of the main pathogens that causes hand-foot-and-mouth disease(HFMD). HFMD caused by EV71 infection is mostly self-limited; however, some infections can cause severe neurological diseases, such as aseptic meningitis, brain stem encephalitis, and even death. There are still no effective clinical drugs used for the prevention and treatment of HFMD. Studying EV71 protein function is essential for elucidating the EV71 replication process and developing anti-EV71 drugs and vaccines. In this review, we summarized the recent progress in the studies of EV71 noncoding regions(50 UTR and 30 UTR) and all structural and nonstructural proteins, especially the key motifs involving in viral infection, replication, and immune regulation. This review will promote our understanding of EV71 virus replication and pathogenesis, and will facilitate the development of novel drugs or vaccines to treat EV71. | Huiqiang Wang Yuhuan Li | 2019 | Virologica Sinica2019，34，1： | 14 |
| 8 | Genome Sequences Provide Insights into the Reticulate Origin and Unique Traits of Woody Bamboos显示文摘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. | Zhen-Hua Guo Peng-Fei Ma Guo-Qian Yang Jin-Yong Hu Yun-Long Liu En-Hua Xia Mi-Cai Zhong Lei Zhao Gui-Ling Sun Yu-Xing Xu You-Jie Zhao Yi-Chi Zhang Yu-Xiao Zhang Xue-Mei Zhang Meng-Yuan Zhou Ying Guo Cen Guo Jing-Xia Liu Xia-Ying Ye Yun-Mei Chen Yang Yang Bin Han Choun-Sea Lin Ying Lu De-Zhu Li | 2019 | Molecular Plant2019，12，10： | 13 |
| 9 | Global Pharmacopoeia Genome Database is an integrated and mineable genomic database for traditional medicines derived from eight international pharmacopoeias显示文摘Genomic data have demonstrated considerable traction in accelerating contemporary studies in traditional medicine. However,the lack of a uniform format and dispersed storage limits the full potential of herb genomic data. In this study, we developed a Global Pharmacopoeia Genome Database(GPGD). The database contains 34,346 records for 903 herb species from eight global pharmacopoeias(Brazilian, Egyptian, European, Indian, Japanese, Korean, the Pharmacopoeia of the People’s Republic of China, and U.S. Pharmacopoeia’s Herbal Medicines Compendium). In particular, the GPGD contains 21,872 DNA barcodes from 867 species, 2,203 organelle genomes from 674 species, 55 whole genomes from 49 species, 534 genomic sequencing datasets from 366 species, and 9,682 transcriptome datasets from 350 species. Among the organelle genomes, 534 genomes from 366 species were newly generated in this study. Whole genomes, organelle genomes, genomic fragments, transcriptomes, and DNA barcodes were uniformly formatted and arranged by species. The GPGD is publicly accessible at http://gffzzf938e9d610ce4c4ah90n9vbnwu5ww6o0k.ffgz.tsg.suse.edu.cn and serves as an essential resource for species identification, decomposition of biosynthetic pathways, and molecular-assisted breeding analysis. Thus, the database is an invaluable resource for future studies on herbal medicine safety, drug discovery, and the protection and rational use of herbal resources. | Baosheng Liao Haoyu Hu Shuiming Xiao Guanru Zhou Wei Sun Yang Chu Xiangxiao Meng Jianhe Wei Han Zhang Jiang Xu Shilin Chen | 2022 | Science China(Life Sciences)2022，65，4： | 11 |
| 10 | The Coix Genome Provides Insights into Panicoideae Evolution and Papery Hull Domestication显示文摘Coix is a grass crop domesticated as early as the Neolithic era.It is still widely cultivated for both highly nutritional food and medicinal use.However,the genetic study and breeding of this crop are hindered by the lack of a sequenced genome.Here,we report de novo sequencing and assembly of the 1619-Mb genome of Coix,and annotation of 75.39%repeats and 39629 protein-coding genes.Comparative genomics analysis showed that Coix is more closely related to sorghum than maize,but intriguingly only Coix and maize had a recent genome duplication event,which was not detected in sorghum.We further constructed a genetic map and mapped several important traits,especially the strength of hull.Selection of papery hull(thin:easy dehulling)from the stony hull(thick:difficult dehulling)in wild progenitors was a key step in Coix domestication.The papery hull makes seed easier to process and germinate.Anatomic and global transcriptome analysis revealed that the papery hull is a result of inhibition of cell division and wall biogenesis.We also successfully demonstrated that seed hull pressure resistance is controlled by two major quantitative trait loci(QTLs),which are associated with hull thickness and color,respectively.The two QTLs were further fine mapped within intervals of 250 kb and 146 kb,respectively.These resources provide a platform for evolutionary studies and will facilitate molecular breeding of this important crop. | Chao Guo Yanan Wang Aiguo Yang Jun He Chaowen Xiao Shanhua Lv Fengming Han Yibing Yuan Yuan Yuan Xiaolong Dong Juan Guo YawenYang-Hailan Liu Ningzhi Zuo Yaxi Hu Kangxu Zhao Zhengbo Jiang Xing Wang Tingting Jiang Yaou Sherf Moju Cao Yuan Wang Zhaobo Long Tingzhao Rong Luqi Huang Shufeng Zhou | 2020 | Molecular Plant2020，13，2： | 11 |
| 11 | Genome-wide identification and characterization of HSP gene superfamily in whitefly (Bemisia tabacl)and expression profiling analysis under temperature stress显示文摘Heat shock proteins (HSP)are essential molecular chaperones that play important roles in the stress stimulation of insects.Bemisia tabaci,a phloem feeder and invasive species,can cause extensive crop damage through direct feeding and transmission of plant viruses.Here we employed comprehensive genomics approaches to identity HSP superfamily members in the Middle East Asia Minor 1 whitefly genome.In total,we identified 26 Hsp genes,including three Hsp90,17 Hsp70,one Hsp60 and five sHSP (small heat shock protein)genes.The HSP gene superfamily of whitefly is expanded compared with the other five insects surveyed here.The gene structures among the same families are relatively conserved.Meanwhile,the motif compositions and secondary structures of BtHsp proteins were predicted.In addition,quantitative polymerase chain reaction analysis showed that the expression patterns of BtHsp gene superfamily were diverse across different tissues of whiteflies.Most Hsp genes were induced or repressed by thermal stress (40℃)and cold treatment (4℃)in whitefly.Silencing the expression of BtHsp70-6 significantly decreased the survival rate of whitefly under 45℃.All the results showed the Hsps conferred thermo-tolerance or cold-tolerance to whiteflies that protect them from being affected by detrimental temperature conditions.Our observations highlighted the molecular evolutionary properties and the response mechanism to temperature assaults of Hsp genes in whitefly. | Xin-Ru Wang Chao Wang Fei-Xue Ban Dan-Tong Zhu Shu-Sheng Liu Xiao-Wei Wang | 2019 | Insect Science2019，26，1： | 11 |
| 12 | Molecularly targeted therapy for advanced hepatocellular carcinoma-a drug development crisis?显示文摘Hepatocellular carcinoma is the fastest growing cause of cancer related death globally. Sorafenib,a multitargeted kinase inhibitor,is the only drug proven to improve outcomes in patients with advanced disease offering modest survival benefit. Although comprehensive genomic mapping has improved understanding of the genetic aberrations in hepatocellular cancer(HCC),this knowledge has not yet impacted clinical care. The last few years have seen the failure of several first and second line phase Ⅲ clinical trials of novel molecularly targeted therapies,warranting a change in the way new therapies are investigated in HCC. Potential reasons for these failures include clinical and molecular heterogeneity,trial design and a lack of biomarkers. This review discusses the current crisis in HCC drug development and how we should learn from recent trial failures to develop a more effective personalised treatment paradigm for patients with HCC. | Kiruthikah Thillai Paul Ross Debashis Sarker | 2016 | World Journal of Gastrointestinal Oncology2016，8，2： | 9 |
| 13 | Wheat genomic study for genetic improvement of traits in China显示文摘Bread wheat(Triticum aestivum L.)is a major crop that feeds 40%of the world’s population.Over the past several decades,advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat,and the genetic basis of agronomically important traits,which promote the breeding of elite varieties.In this review,we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield,end-use traits,flowering regulation,nutrient use efficiency,and biotic and abiotic stress responses,and various breeding strategies that contributed mainly by Chinese scientists.Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools,highthroughput phenotyping platforms,sequencing-based cloning strategies,high-efficiency genetic transformation systems,and speed-breeding facilities.These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process,ultimately contributing to more sustainable agriculture in China and throughout the world. | Jun Xiao Bao Liu Yingyin Yao Zifeng Guo Haiyan Jia Lingrang Kong Aimin Zhang Wujun Ma Zhongfu Ni Shengbao Xu Fei Lu Yuannian Jiao Wuyun Yang Xuelei Lin Silong Sun Zefu Lu Lifeng Gao Guangyao Zhao Shuanghe Cao Qian Chen Kunpu Zhang Mengcheng Wang Meng Wang Zhaorong Hu Weilong Guo Guoqiang Li Xin Ma Junming Li Fangpu Han Xiangdong Fu Zhengqiang Ma Daowen Wang Xueyong Zhang Hong-Qing Ling Guangmin Xia Yiping Tong Zhiyong Liu Zhonghu He Jizeng Jia Kang Chong | 2022 | Science China(Life Sciences)2022，65，9： | 9 |
| 14 | The Genome of Cucurbita argyrosperma (Silver- Seed Gourd) Reveals Faster Rates of Protein- Coding Gene and Long Noncoding RNA Turnover and Neofunctionalization within Cucurbita显示文摘Whole-genome duplications are an important source of evolutionary novelties that change the mode and tempo at which genetic elements evolve within a genome. The Cucurbita genus experienced a wholegenome duplication around 30 million years ago, although the evolutionary dynamics of the coding and noncoding genes in this genus have not yet been scrutinized. Here, we analyzed the genomes of four Cucurbita species, in eluding a newly assembled genome of Cucurbita argyrosperma, and compared the gene con tents of these species with those of five other members of the Cucurbitaceae family to assess the evolutionary dynamics of protein-coding and long intergenic noncoding RNA (lincRNA) genes after the genome duplication. We report that Cucurbita genomes have a higher protein-coding gene birth-death rate compared with the genomes of the other members of the Cucurbitaceae family. C. argyrosperma gene families associated with pollination and transmembrane transport had significantly faster evolutionary rates. lincRNA families showed high levels of gene turnover throughout the phylogeny, and 67.7% of the lincRNA families in Cucurbita showed evidence of birth from the neofunctionalization of previously existing protein-coding genes. Collectively, our results suggest that the whole-genome duplication in Cucurbita resulted in faster rates of gene family evolution through the neofunctionalization of duplicated genes. | Josue Barrera-Red on do Enrique Ibarra-Laclette Alejandra Vazquez-Lobo Yocelyn T. Gutierrez-Guerrero Guillermo Sanchez de la Vega Daniel Pinero Salvador Montes-Hernandez Rafael Lira-Saade Luis E. Eguiarte | 2019 | Molecular Plant2019，12，4： | 9 |
| 15 | Early detection of diabetic kidney disease: Present limitations and future perspectives显示文摘Diabetic kidney disease(DKD) is one of the most common diabetic complications, as well as the leading cause of chronic kidney disease and end-stage renal disease around the world. To prevent the dreadful consequence, development of new assays for diagnostic of DKD has always been the priority in the research field of diabetic complications. At present, urinary albumin-to-creatinine ratio and estimated glomerular filtration rate(eG FR) are the standard methods for assessing glomerular damage and renal function changes in clinical practice. However, due to diverse tissue involvement in different individuals, the so-called 'non-albuminuric renal impairment' is not uncommon, especially in patients with type 2 diabetes. On the other hand, the precision of creatinine-based GFR estimates is limited in hyperfiltration status. These facts make albuminuria and eG FR less reliable indicators for early-stage DKD. In recent years, considerable progress has been made in the understanding of the pathogenesis of DKD, along with the elucidation of its genetic profiles and phenotypic expression of different molecules. With the help of ever-evolving technologies, it has gradually become plausible to apply the thriving information in clinical practice. The strength and weakness of several novel biomarkers, genomic, proteomic and metabolomic signatures in assisting the early diagnosis of DKD will be discussed in this article. | Chih-Hung Lin Yi-Cheng Chang Lee-Ming Chuang | 2016 | World Journal of Diabetes2016，7，14： | 9 |
| 16 | Population Genomic Analysis and De Novo Assembly Reveal the Origin of Weedy Rice as an Evolutionary Game显示文摘Crop weediness,especially that of weedy rice(Oryza sativa f.spontanea),remains mysterious.Weedy rice possesses robust ecological adaptability;however,how this strain originated and gradually formed proprietary genetic features remains unclear?Here,we demonstrate that weedy rice at Asian high latitudes(WRAH)is phylogenetically well defined and possesses unselected genomic characteristics in many divergence regions between weedy and cultivated rice.We also identified novel quantitative trait loci underlying weedy-specific traits,and revealed that a genome block on the end of chromosome 1 is associated with rice weediness.To identify the genomic modifications underlying weedy rice evolution,we generated the first de novo assembly of a high-quality weedy rice genome(WR04-6),and conducted a comparative genomics study between WR04-6 with other rice reference genomes.Multiple lines of evidence,including the results of demographic scenario comparisons,suggest that differentiation between weedy rice and cultivated rice was initiated by genetic improvement of cultivated rice and that the essence of weediness arose through semi-domestication.A plant height model further implied that the origin of WRAH can be modeled as an evolutionary game and indicated that strategy-based selection driven by fitness shaped its genomic diversity. | Jian Sun Dianrong Ma Liang Tang Minghui Zhao Guangchen Zhangh Wenjia Wang Jiayu Song Xiang Li Zimeng Liu Wenxing Zhang Quan Xu Yuncheng Zhou Jianzhong Wu Toshio Yamamoto Fei Dai Yan Lei Song Li Gang Zhou Hongkun Zheng Zhengjin Xu Wenfu Chen | 2019 | Molecular Plant2019，12，5： | 9 |
| 17 | Core Metabolic Features and Hot Origin of Bathyarchaeota显示文摘The archaeal phylum Bathyarchaeota comprises highly diversified subgroups and is considered to be one of the most abundant microorganisms on earth. The metabolic features and evolution of this phylum still remain largely unknown. In this article, a comparative metabolic analysis of 15 newly reconstructed and 36 published metagenomic assembled genomes (MAGs) spanning 10 subgroups was performed, revealing the core metabolic features of Bathyarchaeota—namely, protein, lipid, and benzoate degradation;glycolysis;and the Wood–Ljungdahl (WL) pathway, indicating an acetyl-CoA-centralized metabolism within this phylum. Furthermore, a partial tricarboxylic acid (TCA) cycle, acetogenesis, and sulfur-related metabolic pathways were found in specific subgroups, suggesting versatile metabolic capabilities and ecological functions of different subgroups. Intriguingly, most of the MAGs from the Bathy-21 and -22 subgroups, which are placed at the phylogenetic root of all bathyarchaeotal lineages and likely represent the ancient Bathyarchaeota types, were found in hydrothermal environments and encoded reverse gyrase, suggesting a hyperthermophilic feature. This work reveals the core metabolic features of Bathyarchaeota, and indicates a hot origin of this archaeal phylum. | Xiaoyuan Feng Yinzhao Wang Rahul Zubin Fengping Wang | 2019 | Engineering2019，5，3： | 7 |
| 18 | Genomics-based plant germplasm research(GPGR)显示文摘Plant germplasm underpins much of crop genetic improvement.Millions of germplasm accessions have been collected and conserved ex situ and/or in situ,and the major challenge is now how to exploit and utilize this abundant resource.Genomics-based plant germplasm research(GPGR) or 'Genoplasmics' is a novel cross-disciplinary research field that seeks to apply the principles and techniques of genomics to germplasm research.We describe in this paper the concept,strategy,and approach behind GPGR,and summarize current progress in the areas of the definition and construction of core collections,enhancement of germplasm with core collections,and gene discovery from core collections.GPGR is opening a new era in germplasm research.The contribution,progress and achievements of GPGR in the future are predicted. | Jizeng Jia Hongjie Li Xueyong Zhang Zichao Li Lijuan Qiu | 2017 | The Crop Journal2017，5，2： | 7 |
| 19 | Recent progress in alfalfa(Medicago sativa L.)genomics and genomic selection显示文摘Alfalfa(M. sativa L.) is a highly valuable forage crop, providing >58 Mt of hay, silage, and pasture each year in the United States. As alfalfa is an outcrossing autotetraploid crop,however, breeding for enhanced agronomic traits is challenging and progress has historically not been rapid. Methods that make use of genotypic information and statistical models to generate a genomic estimated breeding value(GEBV) for each plant at a young age hold a great deal of promise to accelerate breeding gains. An emerging genomic breeding pipeline employs SNP chips or genotyping-by-sequencing(GBS) to identify SNP markers in a training population, followed by the use of a statistical model to find associations between the discovered SNPs and traits of interest, followed by genomic selection(GS), a breeding program utilizing the trained model to predict breeding values and making selections based on the estimated breeding value(EBV). Much work has been done in recent years in all of these areas, to generate marker sets and discover SNPs associated with desirable traits, and the application of these technologies in alfalfa breeding programs is under way. However, GBS/GWAS/GS is still a new breeding paradigm,and work is ongoing to evaluate different models, software, and methods for use in such programs. In this review, we look at the progress of alfalfa genomics over the past halfdecade, and review work comparing models and methods relevant to this new type of breeding strategy. | Charles Hawkins Long-Xi Yu | 2018 | The Crop Journal2018，6，6： | 6 |
| 20 | Microarray analysis of gene expression profiles in the bovine mammary gland during lactation显示文摘Mammary glands undergo functional and metabolic changes during virgin,lactation and dry periods.A total of 122 genes were identified as differentially expressed,including 79 up-regulated and 43 down-regulated genes during lactation compared with virgin and dry periods.Gene ontology analysis showed the functional classification of the up-regulated genes in lactation,including transport,biosynthetic process,signal transduction,catalytic activity,immune system process,cell death,and positive regulation of the developmental process.Microarray data clarified molecular events in bovine mammary gland lactation. | HOU XiaoMing,LI QingZhang & HUANG TianYing Key Laboratory of Dairy Science of Education Ministry,Northeast Agricultural University,Harbin 150030,China | 2010 | Science China(Life Sciences)2010，53，2： | 6 |
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