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phylogenomic tracing of asymptomatic transmission in a COVID-19 outbreak

The Innovation 2021年第2期2卷 150-156页

作者： Ju Zhang Nan Ding Yangzi Song Rui Song Yang Pan Linghang Wang Shuo Yan Qi Wang Shanfang Ma Lirong Wei Fengting Yu Lianhe Lu Fujie Zhang Chen Chen Hui Zeng Beijing Ditan Hospital Capital Medical UniversityBeijing 100015China Beijing Key Laboratory of Emerging Infectious Diseases Beijing 100015China Institute for Infectious Disease and Endemic Disease Control Beijing Center for Disease Prevention and ControlBeijing 100013China These authors contributed equally

SARS-CoV-2 has caused over 100 million deaths and continues to spread rapidly around the world.Asymptomatic transmission of SARS-CoV-2 is the Achilles’heel of COVID-19 public health control measures.phylogenomic data on SARS-CoV-2 could provide more direct information about asymptomatic transmission.In this study,using a novel MINERVA sequencing technology,we traced asymptomatic transmission of COVID-19 patients in Beijing,China.One hundred and seventy-eight close contacts were quarantined,and 14 COVID-19 patients were laboratory confirmed by RT-PCR.We provide direct phylogenomic evidence of asymptomatic transmission by constructing the median joining network in the cluster.These data could help us to determine whether the current symptom-based screening should cover asymptomatic persons.

关键词： SARS-CoV-2 COVID-19 asymptomatic transmission outbreak phylogenomic

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Plastome sequencing of Myripnois dioica and comparison within Asteraceae

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Plant Diversity 2019年第5期41卷 315-322页

作者： Nan Lin Xu Zhang Tao Deng Jianwen Zhang Aiping Meng Hengchang Wang Hang Sun Yanxia Sun CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical GardenChinese Academy of SciencesWuhanHubei430074China University of Chinese Academy of Sciences Beijing100049China CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan650201China

Myripnois is a monotypic shrub genus in the daisy family constricted to northern China.Although wild populations of Myripnois dioica are relatively rare,this plant may potentially be cultured as a fine ornamental.In the present study,we sequenced the complete plastome of M.dioica,generating the first plastome sequences of the subfamily Pertyoideae.The plastome of M.dioica has a typical quadripartite circular structure.A large^20-kb and a small^3-kb inversion were detected in the large single copy(LSC)region and shared by other Asteraceae species.Plastome phylogenomic analyses based on 78 Asteraceae species and three outgroups revealed four groups,corresponding to four Asteraceae subfamilies:Asteroideae,Cichorioideae,Pertyoideae and Carduoideae.Among these four subfamilies,Pertyoideae is sister to Asteroideae+Cichorioideae;Carduoideae is the most basal clade.In addition,we characterized 13 simple sequence repeats(SSRs)that may be useful in future studies on population genetics.

关键词： Myripnois Asteraceae Plastomes Large inversion phylogenomic analyses

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Genetic Contribution of Paleopolyploidy to Adaptive Evolution in Angiosperms

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Molecular Plant 2020年第1期13卷 59-71页

作者： Shengdan Wu Baocai Han Yuannian Jiao State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China

Ancient whole-genome duplications (WGDs or polyploidy) are prevalent in plants, and some WGDs occurred during the timing of severe global environmental changes. It has been suggested that WGDs may have contributed to plant adaptation. However, this still lacks empirical evidence at the genetic level to support the hypothesis. Here, we investigated the survivors of gene duplicates from multiple ancient WGD events on the major branches of angiosperm phylogeny, and aimed to explore genetic evidence supporting the significance of polyploidy. Duplicated genes co-retained from three waves of independent WGDs (～120 million years ago [Ma], ～66, and <20 Ma) were investigated in 25 selected species. Gene families functioning in low temperature and darkness were commonly retained gene duplicates after the eight independently occurring WGDs in many lineages around the Cretaceous-Paleocene boundary, when the global cooling and darkness were the two main stresses. Moreover, the commonly retained duplicates could be key factors which may have contributed to the robustness of the critical stress-related pathways. In addition, genome-wide transcription factors (TFs) functioning in stresses tend to retain duplicates after waves of WGDs, and the coselected gene duplicates in many lineages may play critical roles during severe environmental stresses. Collectively, these results shed new light on the significant contribution of paleopolyploidy to plant adaptation during global environmental changes in the evolutionary history of angiosperms.

关键词： whole-genome duplication paleopolyploidy adaptive evolution phylogenomic Cretaceous-Paleocene boundary gene regulatory network

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A Transcriptional Network Promotes Anthocyanin Biosynthesis in Tomato Flesh

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Molecular Plant 2020年第1期13卷 42-58页

作者： Chuanlong Sun Lei Deng Minmin Du Jiuhai Zhao Qian Chen Tingting Huang Hongling Jiang Chang-Bao Li Chuanyou Li State Key Laboratory of Plant Genomics National Centre for Plant Gene Research(Beijing)Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(North China) Ministry of AgricultureBeijing Vegetable Research CenterBeijing Academy of Agriculture and Forestry SciencesBeijing 100097China State Key Laboratory of Crop Biology College of AgronomyShandong Agricultural UniversityTai'anShandong Province 271018China lnstitute of Vegetable Qingdao Academy of Agricultural SciencesQingdaoShandong Province 266100China

Dietary anthocyanins are important health-promoting antioxidants that make a major contribution to the quality of fruits. It is intriguing that most tomato cultivars do not produce anthocyanins in fruit. However, the purple tomato variety Indigo Rose, which has the dominant Aft locus combined with the recessive atv locus from wild tomato species, exhibits light-dependent anthocyanin accumulation in the fruit skin. Here, we report that Aft encodes a functional anthocyanin activator named SlAN2-like, while atv encodes a nonfunctional version of the anthocyanin repressor SlMYBATV. The expression of SlAN2-like is responsive to light, and the functional SlAN2-like can activate the expression of both anthocyanin biosynthetic genes and their regulatory genes, suggesting that SlAN2-like acts as a master regulator in the activation of anthocyanin biosynthesis. We further showed that cultivated tomatoes contain nonfunctional alleles of SlAN2-like and therefore fail to produce anthocyanins. Consistently, expression of a functional SlAN2-like gene driven by the fruit-specific promoter in a tomato cultivar led to the activation of the entire anthocyanin biosynthesis pathway and high-level accumulation of anthocyanins in both the peel and flesh. Taken together, our study exemplifies that efficient engineering of complex metabolic pathways could be achieved through tissue-specific expression of master transcriptional regulators.

关键词： whole-genome duplication paleopolyploidy adaptive evolution phylogenomic Cretaceous-Paleocene boundary gene regulatory network

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The Introgression and Gene Family Contraction Driven the Evolution,Lifestyle and Host Shift of Hypocrealean Fungi

The Introgression and Gene Family Contraction Driven the Evo...

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中国菌物学会2016年学术年会

作者： Weiwei Zhang Xiaoli Cheng Yiling Lai Kuan Li Xiaoling Zhang Chengshu Wang Lei Cai Wenying Zhuang Meichun Xiang Xingzhong Liu

Hypocrealean fungi（Ascomycota） are well-known for their diverse lifestyles and have vital influences on agriculture and ecosystem,including important phytopathogenic fungi,entomopathogenic fungi,mycoparasites,and grass endophytes.Although such diverse lifestyles that shift frequently during the evolutionary process have been analyzed by multigene analysis,the phylogeny and mechanisms from phylogenomics remain unknown.Using whole genomes from 45 species with diverse lifestyles,we constructed the phytopathogen-basal phylogeny and dated the divergence of each lineage.A new evolutionary process of hypocrealean fungi was proposed:Nectriaceae as plant pathogens is the primitive group,and animal pathogens of Cordycipitaceae,Ophiocordycipitaceae,and Clavicipitaceae were parallel diverged;Hypocreaceae as mycoparasites diverged after Cordycipitaceae;and plant endophytes of Clavicipitaceae were differentiated after the Gramineae originated was evolved.Significant introgression was detected in certain lineages of hypocrealean fungi and the main genetic resources for the fungi adapting to new lifestyles are shared from the ancestral species through introgression.In the meanwhile,the contraction of gene families is closely related with the transition of lifestyles and main evolutionary tendency.The introgression and gene family contraction are the main factors that drive the evolution,diverse lifestyles,and host shift of hypocrealean fungi.

关键词： phylogenomic evolutionary process introgression lifestyle

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