|
|
|
题名
|
作者
|
年代
|
出处
|
被引量
|
| 1 | WGDI:A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes显示文摘Evidence of whole-genome duplications(WGDs)and subsequent karyotype changes has been detected in most major lineages of living organisms on Earth.To clarify the complex resulting multi-layered patterns of gene collinearity in genome analyses,there is a need for convenient and accurate toolkits.To meet this need,we developed WGDI(Whole-Genome Duplication Integrated analysis),a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidization events and cross-species genome alignments.WGDI supports three main workflows(polyploid inference,hierarchical inference of genomic homology,and ancestral chromosome karyotyping)that can improve the detection of WGD and characterization of WGD-related events based on high-quality chromosome-level genomes.Significantly,it can extract complete synteny blocks and facilitate reconstruction of detailed karyotype evolution.This toolkit is freely available at GitHub(https://github.com/SunPengChuan/wgdi).As an example of its application,WGDI convincingly clarified karyotype evolution in Aquilegia coerulea and Vitis vinifera following WGDs and rejected the hypothesis that Aquilegia contributed as a parental lineage to the allopolyploid origin of core dicots. | Pengchuan Sun Beibei Jiao Yongzhi Yang Lanxing Shan Ting Li Xiaonan Li Zhenxiang Xi Xiyin Wang Jianquan Liu | 2022 | Molecular Plant2022，15，12： | 5 |
| 2 | Coriander Genomics Database:a genomic,transcriptomic,and metabolic database for coriander显示文摘Coriander(Coriandrum sativum L.),also known as cilantro,is a globally important vegetable and spice crop.Its genome and that of carrot are models for studying the evolution of the Apiaceae family.Here,we developed the Coriander Genomics Database(CGDB,http://cgdb.bio2db.com/)to collect,store,and integrate the genomic,transcriptomic,metabolic,functional annotation,and repeat sequence data of coriander and carrot to serve as a central online platform for Apiaceae and other related plants.Using these data sets in the CGDB,we intriguingly found that seven transcription factor(TF)families showed significantly greater numbers of members in the coriander genome than in the carrot genome.The highest ratio of the numbers of MADS TFs between coriander and carrot reached 3.15,followed by those for tubby protein(TUB)and heat shock factors.As a demonstration of CGDB applications,we identified 17 TUB family genes and conducted systematic comparative and evolutionary analyses.RNA-seq data deposited in the CGDB also suggest dose compensation effects of gene expression in coriander.CGDB allows bulk downloading,significance searches,genome browser analyses,and BLAST searches for comparisons between coriander and other plants regarding genomics,gene families,gene collinearity,gene expression,and the metabolome.A detailed user manual and contact information are also available to provide support to the scientific research community and address scientific questions.CGDB will be continuously updated,and new data will be integrated for comparative and functional genomic analysis in Apiaceae and other related plants. | Xiaoming Song Fulei Nie Wei Chen Xiao Ma Ke Gong Qihang Yang Jinpeng Wang Nan Li Pengchuan Sun Qiaoying Pei Tong Yu Jingjing Hu Xinyu Li Tong Wu Shuyan Feng Xiu-Qing Li Xiyin Wang | 2020 | Horticulture Research2020，7，1： | 4 |
| 3 | Detrital Zircon U–Pb Geochronology and Provenance of Bayan Obo Group, Northern Margin of North China Craton: New Implications for the Position of NCC in Rodinia显示文摘The paleoposition of North China Craton in Rodinia has long been in controversial. This paper mainly focuses on the U-Pb geochronological studies of detrital zircons obtained from Bayan Obo Group exposed in the Shangdu area, Inner Mongolia, aiming to provide more information for interprating this problem. Based on the acquired data, this paper comes to the following conclusions. Firstly, the depositional age of Bayan Obo Group might be from Meso- to Neoproterozoic according to the zircons U-Pb dating results. The lower succession of this group, namely Dulahala and Jianshan formations deposited between 1800 and 1650 Ma. The Halahuogete and Bilute formations deposited between 1500 and 1350 Ma. For Baiyinbaolage and Hujiertu formations, their depositional age was 1250-900 Ma. Secondly, for the provenance of Bayan Obo Group, this paper believes detrital zircons with age of 2.51-2.71 Ga and 2.00-2.48 Ga were from Guyang, Xi Ulanbulang and Zhuozi area;the Khondalite Belt provided detrital zircons with age of 1.95-1.80 Ga;zircons with age of 1.60-1.75 Ga might come from granitic rocks in Miyun Area. The magmatism after 1.60 Ga was rarely recorded in the NCC, therefore those zircons with ages younger than 1.60 Ga might come from outside of NCC. The magmatism with the same age existed in Baltic, Amazonia and Laurentia. Based on previous paleomagnetic researches, this paper proposes that NCC might receive detritus from Baltic during 1560-1350 Ma and had affinity with Laurentia and Amazonia at ~0.9 Ga in Rodinia. Baltic, Amazonia and Laurentia might be potential provenances for non-NCC detritus in Bayan Obo Group. | LI Changhai LIU Zhenghong XU Zhongyuan DONG Xiaojie LI Pengchuan SHI Qiang WANG Shijie | 2019 | Acta Geologica Sinica(English Edition)2019，93，5： | 4 |
| 4 | New Discovery of ~2.65 Ga Tonalitic Gneiss in the Southern Jilin Province, China显示文摘Objective The North China Craton(NCC)is almost continuously widespread TTGs of 3.8–2.5 Ga,and the intrusive peak appears at^2.53 Ga,indicating that the Neoarchean is the most important period of continental growth in the NCC(Wan Yusheng et al.,2017).Recently studies reveal that the TTGs were formed during^2.7 Ga and 2.6–2.5 Ga in southern Jilin Province,NE of the NCC(Wang Chaoyang et al.,2017;Guo et al.,2017),whereas 2.7–2.6 | LI Pengchuan LIU Zhenghong XU Zhongyuan DONG Xiaojie LI Shichao | 2018 | Acta Geologica Sinica(English Edition)2018，92，5： | 2 |
| 5 | The Corylus mandshurica genome provides insights into the evolution of Betulaceae genomes and hazelnut breeding显示文摘Hazelnut is popular for its flavor,and it has also been suggested that hazelnut is beneficial to cardiovascular health because it is rich in oleic acid.Here,we report the first high-quality chromosome-scale genome for the hazelnut species Corylus mandshurica(2n=22),which has a high concentration of oleic acid in its nuts.The assembled genome is 367.67Mb in length,and the contig N50 is 14.85 Mb.All contigs were assembled into 11 chromosomes,and 28,409 protein-coding genes were annotated.We reconstructed the evolutionary trajectories of the genomes of Betulaceae species and revealed that the 11 chromosomes of the hazelnut genus were derived from the most ancestral karyotype in Betula pendula,which has 14 protochromosomes,by inferring homology among five Betulaceae genomes.We identified 96 candidate genes involved in oleic acid biosynthesis,and 10 showed rapid evolution or positive selection.These findings will help us to understand the mechanisms of lipid synthesis and storage in hazelnuts.Several gene families related to salicylic acid metabolism and stress responses experienced rapid expansion in this hazelnut species,which may have increased its stress tolerance.The reference genome presented here constitutes a valuable resource for molecular breeding and genetic improvement of the important agronomic properties of hazelnut. | Ying Li Pengchuan Sun Zhiqiang Lu Jinyuan Chen Zhenyue Wang Xin Du Zeyu Zheng Ying Wu Hongyin Hu Jiao Yang Jianxiang Ma Jianquan Liu Yongzhi Yang | 2021 | Horticulture Research2021，8，1： | 1 |
| 6 | Different therapeutic proportion of patients undergone coronary angiography in the era of development in MSCT显示文摘Objective To study the different therapeutic proportion of the patient populations undergone coronary angiography (CAG) in the era of development in multislice spiral computed tomography(MSCT). Methods Two hundred and fifty four consecutive patients(mean age 59.24±10.65) , who underwent CAG at Daxing Hospital from February 2007 through October 2007, were enrolled, 160 patients were male and 94 were female. By evaluating from the coronary angiogram, the patients were not diagnosed to have coronary heart disease(CHD) with less than 50% diameter stenosis of coronary artery; the patients to have CHD with more than or equal to 50% stenosis of coronary artery; the patients were performed the procedure of percutaneous coronary intervention(PCI) with more than or equal to 70% stenosis; the patients were proposed to have coronary aortic bypass graft(CABG) surgery with left main coronary artery lesions or diffuse triple coronary artery lesions. Results In the 254 consecutive patients, 59 patients(23.2%) had not been diagnosed to have CHD; 195(76.8%)to have CHD, of these patients with CHD, 49 patients(19.3%)were not indicated for PCI (including the patients receiving follow-up coronary angiography after stenting), 81(31.9%)had been performed the procedure of stent implantation, 57(22.4%)proposed to have CABG, 8(3.1%)the procedure of PCI had not been successful, or had not been performed because of patients opposing to this therapy. Conclusion Multislice spiral computed tomography can be applied as a non-invasive screening tool to exclude the presence of CHD, to increase the positive proportion of the populations with CHD in all patients receiving coronary angiograhpy, to avoid the use of CAG in a subset of | Juan Deng Wenbin Wang Shuoqing Hu Yue Xiao Feng Liang Xuewei Guo Haiying Wang Pengchuan Zhang Dayi Hu Tianchang Li Chuzhong Tang Jiyun Wang Changlin Lu | 2008 | Journal of Geriatric Cardiology2008，5，2： | 0 |
| 7 | Discovery of a ~1.37 Ga Granite in the Eastern Part of the Northern Margin of the North China Craton and its Geological Significance显示文摘Diabase sills with baddeleyite/zircon U-Pb ages of-1.32 Ga have been found in many areas of the North China Craton(NCC)(Peng,2015).Some researchers have proposed that this magmatic event should be related to the breakup of the Columbia supercontinent.A few studies have reported this period of granitoids only to be present in the Shangdu,Huade.and Sonid Zuoqi areas(Zhang et al.,2012;Sun I.ixin et al..2018).This study concerns the first discovery of a-1.37 Ga granite in the southern Jilin Province,in the eastern part of the northern margin of the NCC.It has great significance for the study of the breakup of the Colombia supercontinent,the magmatism of the NCC,and the relationship between the supercontinent and other continents during this period. | WEN Kai SUN Guosheng LIU Zhenghong XU Zhongyuan LI Pengchuan | 2020 | Acta Geologica Sinica(English Edition)2020，94，2： | 0 |
| 8 | An ancient whole-genome duplication event and its contribution to flavor compounds in the tea plant (Camellia sinensis)显示文摘Tea,coffee,and cocoa are the three most popular nonalcoholic beverages in the world and have extremely high economic and cultural value.The genomes of four tea plant varieties have recently been sequenced,but there is some debate regarding the characterization of a whole-genome duplication(WGD)event in tea plants.Whether the WGD in the tea plant is shared with other plants in order Ericales and how it contributed to tea plant evolution remained unanswered.Here we re-analyzed the tea plant genome and provided evidence that tea experienced only WGD event after the core-eudicot whole-genome triplication(WGT)event.This WGD was shared by the Polemonioids-Primuloids-Core Ericales(PPC)sections,encompassing at least 17 families in the order Ericales.In addition,our study identified eight pairs of duplicated genes in the catechins biosynthesis pathway,four pairs of duplicated genes in the theanine biosynthesis pathway,and one pair of genes in the caffeine biosynthesis pathway,which were expanded and retained following this WGD.Nearly all these gene pairs were expressed in tea plants,implying the contribution of the WGD.This study shows that in addition to the role of the recent tandem gene duplication in the accumulation of tea flavor-related genes,the WGD may have been another main factor driving the evolution of tea flavor. | Ya Wang Fei Chen Yuanchun Ma Taikui Zhang Pengchuan Sun Meifang Lan Fang Li Wanping Fang | 2021 | Horticulture Research2021，8，1： | 0 |
| 9 | Zircon U-Pb geochronology,geochemistry and tectonic implication of volcanic rocks from Manketouebo Formation in Keyihe area of northern Great Xing'an Range显示文摘Zircon U-Pb isotope dating and whole-rock geochemical analyses were undertaken for the rhyolite,rhyolitic lithic crystal tuff and dacitic tuff from the Manketouebo Formation in the Keyihe area,in order to constrain their genesis and tectonic significance.Zircon LA-ICP-MS U-Pb data indicate that the rhyolite and rhyolitic lithic crystal tuff were formed during 137±5 Ma and 143±1 Ma,respectively.These volcanic rocks have high SiO2(70.03%–76.46%)and K2O+Na2O(8.10%–9.52%)contents,but low CaO(0.03%–0.95%)and MgO(0.07%–0.67%)contents,which belong to the peraluminous and high-K calc-alkaline rocks.They are enriched in light rare earth elements(REEs),and exhibit fractionation of light over heavy REEs,withδEu values of 0.37–0.83.The volcanic rocks are enriched in LILEs(e.g.,Rb,U and K)and depleted in HFSEs(e.g.,Nb,Ti,P and Ta).The chemical composition suggests that these volcanic rocks formed by partial melting of crust material.Combined with previous regional research results,the authors consider that the volcanic rocks of the Manketouebo Formation in the Keyihe area were formed under an extensional environment related to the closure of the Mongolia–Okhotsk Ocean. | JIA Jinfeng WANG Yang LI Pengchuan | 2023 | Global Geology2023，26，3： | 0 |
| 10 | Paleo-polyploidization in Lycophytes显示文摘Lycophytes and seed plants constitute the typical vascular plants.Lycophytes have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed plants.Here,genomic analyses including the homologous gene dot plot analysis detected multiple paleo-polyploidization events,with one occurring approximately 13–15 million years ago(MYA)and another about 125–142 MYA,during the evolution of the genome of Selaginella moellendorffii,a model lycophyte.In addition,comparative analysis of reconstructed ancestral genomes of lycophytes and angiosperms suggested that lycophytes were affected by more paleopolyploidization events than seed plants.Results from the present genomic analyses indicate that paleo-polyploidization has contributed to the successful establishment of both lineages—lycophytes and seed plants—of vascular plants. | Jinpeng Wang Jigao Yu Pengchuan Sun Chao Li Xiaoming Song Tianyu Lei Yuxian Li Jiaqing Yuan Sangrong Sun Hongling Ding Xueqian Duan Shaoqi Shen Yanshuang Shen Jing Li Fanbo Meng Yangqin Xie Jianyu Wang Yue Hou Jin Zhang Xianchun Zhang Xiu-Qing Li Andrew HPaterson Xiyin Wang | 2020 | Genomics, Proteomics & Bioinformatics2020，18，3： | 0 |
您所在的机构暂未开通此部分的功能，请联系管理员