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学者姓名：赵茜
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Abstract ：
Following the milestone success of the Human Genome Project, the 'Encyclopedia of DNA Elements (ENCODE)' initiative was launched in 2003 to unearth information about the numerous functional elements within the genome. This endeavor coincided with the emergence of numerous novel technologies, accompanied by the provision of vast amounts of whole-genome sequences, high-throughput data such as ChIP-Seq and RNA-Seq. Extracting biologically meaningful information from this massive dataset has become a critical aspect of many recent studies, particularly in annotating and predicting the functions of unknown genes. The core idea behind genome annotation is to identify genes and various functional elements within the genome sequence and infer their biological functions. Traditional wet-lab experimental methods still rely on extensive efforts for functional verification. However, early bioinformatics algorithms and software primarily employed shallow learning techniques; thus, the ability to characterize data and features learning was limited. With the widespread adoption of RNA-Seq technology, scientists from the biological community began to harness the potential of machine learning and deep learning approaches for gene structure prediction and functional annotation. In this context, we reviewed both conventional methods and contemporary deep learning frameworks, and highlighted novel perspectives on the challenges arising during annotation underscoring the dynamic nature of this evolving scientific landscape.
Keyword ：
bioinformatic bioinformatic deep learning deep learning genome annotation genome annotation genome sequence genome sequence RNA-Seq technology RNA-Seq technology
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| GB/T 7714 | Chen, Zhaojia , ul Ain, Noor , Zhao, Qian et al. From tradition to innovation: conventional and deep learning frameworks in genome annotation [J]. | BRIEFINGS IN BIOINFORMATICS , 2024 , 25 (3) . |
| MLA | Chen, Zhaojia et al. "From tradition to innovation: conventional and deep learning frameworks in genome annotation" . | BRIEFINGS IN BIOINFORMATICS 25 . 3 (2024) . |
| APA | Chen, Zhaojia , ul Ain, Noor , Zhao, Qian , Zhang, Xingtan . From tradition to innovation: conventional and deep learning frameworks in genome annotation . | BRIEFINGS IN BIOINFORMATICS , 2024 , 25 (3) . |
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In male competition, large and costly ejaculates are advantageous. Prior research on male accessory gland secretions in Plutella xylostella left open questions about how males modulate their mating behaviors and ejaculate composition allocation in response to varying levels of competition. The current study aimed to delve deeper into these unexplored facets. A totally of 928 ejaculate proteins were identified across males exposed to different competition conditions. Notably, males courting under non-, low-, and high-competition scenarios exhibited 867, 635, and 858 ejaculate proteins, respectively. Approximately 10% of these ejaculate proteins displayed variations that aligned with changes in competition intensity. Subsequent analyses focused on the proteins transferred to females, revealing that 44% of ejaculate proteins were transferred, with 37 proteins exhibiting differential expression. Functional analyses uncovered their crucial roles in sperm maturation, motility, and capacitation. Our findings reveal adaptive adjustments in ejaculate protein abundance and transmission in P. xylostella as a response to varying competition levels. Moreover, fluorescent sperm labeling indicated higher sperm transfer during low competition correlated with shorter sperm length. Furthermore, evidence suggests that males shorten their courtship duration and extend their mating duration when faced with competition. These results illustrate how competition drives ejaculate investment and behavioral plasticity, offering valuable insights for advancements in assisted reproductive technologies and pest management strategies.
Keyword ：
Competition Competition Ejaculate proteome Ejaculate proteome Mating behavior Mating behavior
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| GB/T 7714 | Zheng, Yahong , Shi, Lingping , Jing, Zhang et al. Plasticity in moth mating behavior and ejaculate proteomic diversity induced by male competition [J]. | JOURNAL OF INSECT PHYSIOLOGY , 2024 , 156 . |
| MLA | Zheng, Yahong et al. "Plasticity in moth mating behavior and ejaculate proteomic diversity induced by male competition" . | JOURNAL OF INSECT PHYSIOLOGY 156 (2024) . |
| APA | Zheng, Yahong , Shi, Lingping , Jing, Zhang , Li, Huixia , Wu, Lingli , Qian, Zhao . Plasticity in moth mating behavior and ejaculate proteomic diversity induced by male competition . | JOURNAL OF INSECT PHYSIOLOGY , 2024 , 156 . |
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Plutella xylostella exhibits exceptional reproduction ability, yet the genetic basis underlying the high reproductive capacity remains unknown. Here, we demonstrate that an orphan gene, lushu, which encodes a sperm protein, plays a crucial role in male reproductive success. Lushu is located on the Z chromosome and is prevalent across different P. xylostella populations worldwide. We subsequently generated lushu mutants using transgenic CRISPR/Cas9 system. Knockout of Lushu results in reduced male mating efficiency and accelerated death in adult males. Furthermore, our findings highlight that the deficiency of lushu reduced the transfer of sperms from males to females, potentially resulting in hindered sperm competition. Additionally, the knockout of Lushu results in disrupted gene expression in energy-related pathways and elevated insulin levels in adult males. Our findings reveal that male reproductive performance has evolved through the birth of a newly evolved, lineage-specific gene with enormous potentiality in fecundity success. These insights hold valuable implications for identifying the target for genetic control, particularly in relation to species-specific traits that are pivotal in determining high levels of fecundity. Graphical abstract
Keyword ：
insulin insulin male reproductive fitness male reproductive fitness orphan gene orphan gene sperm competition sperm competition sperm protein sperm protein
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| GB/T 7714 | Zhao, Qian , Zheng, Yahong , Li, Yiying et al. An Orphan Gene Enhances Male Reproductive Success in Plutella xylostella [J]. | MOLECULAR BIOLOGY AND EVOLUTION , 2024 , 41 (7) . |
| MLA | Zhao, Qian et al. "An Orphan Gene Enhances Male Reproductive Success in Plutella xylostella" . | MOLECULAR BIOLOGY AND EVOLUTION 41 . 7 (2024) . |
| APA | Zhao, Qian , Zheng, Yahong , Li, Yiying , Shi, Lingping , Zhang, Jing , Ma, Dongna et al. An Orphan Gene Enhances Male Reproductive Success in Plutella xylostella . | MOLECULAR BIOLOGY AND EVOLUTION , 2024 , 41 (7) . |
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Chemosensory proteins (CSPs) can bind and transport odorant molecules, which are believed to be involved in insect chemoreception. Here, we investigated three CSPs in perception of volatiles in Empoasca onukii. Expression profiles showed that although EonuCSP4, EonuCSP 6-1 and EonuCSP6-2 were ubiquitously expressed in heads, legs, thoraxes and abdomen, they were all highly expressed in the antennae of E. onukii. Further, fluorescence competitive binding assays revealed that EonuCSP4 and 6-1 had binding affinities for three plant volatiles, suggesting their possible involvement in the chemosensory process. Among them, EonuCSP6-1 showed relatively high binding affinities for benzaldehyde. Behavioral assays revealed that the adults of E. onukii showed a significant preference for two compounds including benzaldehyde. The predicted three-dimensional (3D) structures of these 3 CSP have the typical six alpha-helices, which form the hydrophobic ligand-binding pocket. We therefore suggest that Eoun6-1 might be involved in the chemoreception of the host-related volatiles for E. onukii. Our data may provide a chance of finding a suitable antagonist of alternative control strategies which block the perception of chemosensory signals in pest, preventing the food- orientation behaviors.
Keyword ：
benzaldehyde benzaldehyde chemosensory proteins chemosensory proteins Empoasca onukii Empoasca onukii insect chemoreception insect chemoreception plant volatiles plant volatiles
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| GB/T 7714 | Zhang, Liwen , Zhao, Mingxian , Aikeremu, Feiruoran et al. Involvement of three chemosensory proteins in perception of host plant volatiles in the tea green leafhopper, Empoasca onukii [J]. | FRONTIERS IN PHYSIOLOGY , 2023 , 13 . |
| MLA | Zhang, Liwen et al. "Involvement of three chemosensory proteins in perception of host plant volatiles in the tea green leafhopper, Empoasca onukii" . | FRONTIERS IN PHYSIOLOGY 13 (2023) . |
| APA | Zhang, Liwen , Zhao, Mingxian , Aikeremu, Feiruoran , Huang, Huoshui , You, Minsheng , Zhao, Qian . Involvement of three chemosensory proteins in perception of host plant volatiles in the tea green leafhopper, Empoasca onukii . | FRONTIERS IN PHYSIOLOGY , 2023 , 13 . |
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Tea green leafhopper (TGL), Empoasca onukii, is of biological and economic interest. Despite numerous studies, the mechanisms underlying its adaptation and evolution remain enig-matic. Here, we use previously untapped genome and population genetics approaches to examine how the pest adapted to different environmental variables and thus has expanded geographically. We complete a chromosome-level assembly and annotation of the E. onukii genome, showing nota-ble expansions of gene families associated with adaptation to chemoreception and detoxification. Genomic signals indicating balancing selection highlight metabolic pathways involved in adaptation to a wide range of tea varieties grown across ecologically diverse regions. Patterns of genetic vari-ations among 54 E. onukii samples unveil the population structure and evolutionary history across different tea-growing regions in China. Our results demonstrate that the genomic changes in key pathways, including those linked to metabolism, circadian rhythms, and immune system functions, may underlie the successful spread and adaptation of E. onukii. This work highlights the genetic and molecular basis underlying the evolutionary success of a species with broad economic impacts, and provides insights into insect adaptation to host plants, which will ultimately facilitate more sustain-able pest management.
Keyword ：
Evolutionary history Evolutionary history Genomic variation Genomic variation Local adaptation Local adaptation Population genetics Population genetics Tea green leafhopper Tea green leafhopper
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| GB/T 7714 | Zhao, Qian , Shi, Longqing , He, Weiyi et al. Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution [J]. | GENOMICS PROTEOMICS & BIOINFORMATICS , 2023 , 20 (6) : 1092-1105 . |
| MLA | Zhao, Qian et al. "Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution" . | GENOMICS PROTEOMICS & BIOINFORMATICS 20 . 6 (2023) : 1092-1105 . |
| APA | Zhao, Qian , Shi, Longqing , He, Weiyi , Li, Jinyu , You, Shijun , Chen, Shuai et al. Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution . | GENOMICS PROTEOMICS & BIOINFORMATICS , 2023 , 20 (6) , 1092-1105 . |
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BACKGROUND The tea green leafhopper, Empoasca onukii Matsuda, is the most destructive insect pest of tea plantations in East Asia. Despite its economic importance and previous studies on this species, it remains unclear as to how this small-sized pest can have such wide range. RESULTS By sequencing three mitochondrial genes and 17 microsatellite loci, we revealed the regional structure and demographic expansion of 59 E. onukii populations in China. Bayesian analysis of population genetic structure (BAPS) on microsatellites identified four genetic groups with spatial discontinuities, while analysis on mitochondrial genes inferred five nested and differentiated clusters. Both the Mantel test and the generalized linear model indicated a significant pattern of isolation by geographic distance in E. onukii populations. Based on the approximate Bayesian computation approach, E. onukii was found to have originated from southwestern China and expanded northward and eastward. While MIGRATE-N and Bayesian stochastic search variable selection (BSSVS) procedure in BEAST confirmed the possible eastward and northward dispersal from Yunnan, they also detected more gene flow from the derived populations in central and southeastern China. CONCLUSION Our results suggest that the current distribution and structure of E. onukii is complicatedly influenced by human activities of cultivation, wide dissemination of tea in ancient China as well as recent transportation of tea seedlings for establishing new tea plantations. Insights into genetic differentiation and demographic expansion patterns from this study provide an important basis for the development of area-wide management of the E. onukii populations. (c) 2022 Society of Chemical Industry.
Keyword ：
demographic expansion demographic expansion gene flow gene flow genetic structure genetic structure management management tea green leafhopper tea green leafhopper
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| GB/T 7714 | Li, Jinyu , Shi, Longqing , Vasseur, Liette et al. Genetic analyses reveal regional structure and demographic expansion of the predominant tea pest Empoasca onukii (Hemiptera: Cicadellidae) in China [J]. | PEST MANAGEMENT SCIENCE , 2022 , 78 (7) : 2838-2850 . |
| MLA | Li, Jinyu et al. "Genetic analyses reveal regional structure and demographic expansion of the predominant tea pest Empoasca onukii (Hemiptera: Cicadellidae) in China" . | PEST MANAGEMENT SCIENCE 78 . 7 (2022) : 2838-2850 . |
| APA | Li, Jinyu , Shi, Longqing , Vasseur, Liette , Zhao, Qian , Chen, Jie , You, Minsheng et al. Genetic analyses reveal regional structure and demographic expansion of the predominant tea pest Empoasca onukii (Hemiptera: Cicadellidae) in China . | PEST MANAGEMENT SCIENCE , 2022 , 78 (7) , 2838-2850 . |
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Abstract ：
Tea green leafhopper(TGL),Empoasca onukii,is of biological and economic interest.Despite numerous studies,the mechanisms underlying its adaptation and evolution remain enig-matic.Here,we use previously untapped genome and population genetics approaches to examine how the pest adapted to different environmental variables and thus has expanded geographically.We complete a chromosome-level assembly and annotation of the E.onukii genome,showing nota-ble expansions of gene families associated with adaptation to chemoreception and detoxification.Genomic signals indicating balancing selection highlight metabolic pathways involved in adaptation to a wide range of tea varieties grown across ecologically diverse regions.Patterns of genetic vari-ations among 54 E.onukii samples unveil the population structure and evolutionary history across different tea-growing regions in China.Our results demonstrate that the genomic changes in key pathways,including those linked to metabolism,circadian rhythms,and immune system functions,may underlie the successful spread and adaptation of E.onukii.This work highlights the genetic and molecular basis underlying the evolutionary success of a species with broad economic impacts,and provides insights into insect adaptation to host plants,which will ultimately facilitate more sustain-able pest management.
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| GB/T 7714 | Qian Zhao , Longqing Shi , Weiyi He et al. Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution [J]. | 基因组蛋白质组与生物信息学报（英文版） , 2022 , (6) : 1092-1105 . |
| MLA | Qian Zhao et al. "Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution" . | 基因组蛋白质组与生物信息学报（英文版） 6 (2022) : 1092-1105 . |
| APA | Qian Zhao , Longqing Shi , Weiyi He , Jinyu Li , Shijun You , Shuai Chen et al. Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution . | 基因组蛋白质组与生物信息学报（英文版） , 2022 , (6) , 1092-1105 . |
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【目的】microRNA(miRNA)在昆虫生长发育中发挥重要功能，本研究拟通过鉴定小菜蛾不同发育阶段的miRNA，挖掘幼虫偏好表达的miRNA及其潜在功能。【方法】对小菜蛾卵、3龄幼虫、蛹和成虫的miRNA开展高通量测序，结合生物信息学分析方法，筛选在幼虫期偏好表达的miRNA;借助实时荧光定量PCR技术，验证候选miRNA在小菜蛾各发育阶段的表达量;利用软件RNAhybrid和miRanda预测候选miRNA的靶基因，筛选其中与生长发育相关的基因，并通过双荧光素酶报告系统验证靶向关系。【结果】从小菜蛾4个发育阶段中，共获得了2116个已知miRNA和189个新miRNA。经差异表达分析发现，幼虫阶段分别有265、228和132个miRNA的表达量显著高于卵、蛹和成虫。通过荧光定量PCR进一步筛选出了11个幼虫偏好表达的候选miRNA，与miRNA高通量测序结果一致;靶基因预测结果显示，pxy-miR-6094-3p、pxy-miR-750-3p、novelm502、miR-317-3p、miR-1175-3p、miR-750和miR-274这7个miRNA靶向保幼激素代谢通路，体外试验结果表明，pxy-miR-6094-3p、pxy-miR-750-3p、novel-m502和miR-274与保幼激素酯酶基因有靶向关系。【结论】小菜蛾幼虫偏好表达的miRNA可能参与调控了幼虫保幼激素代谢。
Keyword ：
miRNA miRNA 保幼激素 保幼激素 小菜蛾 小菜蛾 幼虫 幼虫 生长发育 生长发育
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| GB/T 7714 | 白建林 , 林桂芳 , 王月 et al. 小菜蛾幼虫偏好表达的microRNA鉴定及功能研究 [J]. | 生物安全学报 , 2022 , 31 (01) : 64-74 . |
| MLA | 白建林 et al. "小菜蛾幼虫偏好表达的microRNA鉴定及功能研究" . | 生物安全学报 31 . 01 (2022) : 64-74 . |
| APA | 白建林 , 林桂芳 , 王月 , 赵茜 , 彭露 , 谢苗 et al. 小菜蛾幼虫偏好表达的microRNA鉴定及功能研究 . | 生物安全学报 , 2022 , 31 (01) , 64-74 . |
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Haplotype-resolved genome assembly of an Oolong tea cultivar Tieguanyin and population genomic analyses of 190 Camellia accessions provide insights into the evolutionary history of the tea plant Camellia sinensis. Tea is an important global beverage crop and is largely clonally propagated. Despite previous studies on the species, its genetic and evolutionary history deserves further research. Here, we present a haplotype-resolved assembly of an Oolong tea cultivar, Tieguanyin. Analysis of allele-specific expression suggests a potential mechanism in response to mutation load during long-term clonal propagation. Population genomic analysis using 190 Camellia accessions uncovered independent evolutionary histories and parallel domestication in two widely cultivated varieties, var. sinensis and var. assamica. It also revealed extensive intra- and interspecific introgressions contributing to genetic diversity in modern cultivars. Strong signatures of selection were associated with biosynthetic and metabolic pathways that contribute to flavor characteristics as well as genes likely involved in the Green Revolution in the tea industry. Our results offer genetic and molecular insights into the evolutionary history of Camellia sinensis and provide genomic resources to further facilitate gene editing to enhance desirable traits in tea crops.
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| GB/T 7714 | Zhang, Xingtan , Chen, Shuai , Shi, Longqing et al. Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis [J]. | NATURE GENETICS , 2021 , 53 (8) : 1250-, . |
| MLA | Zhang, Xingtan et al. "Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis" . | NATURE GENETICS 53 . 8 (2021) : 1250-, . |
| APA | Zhang, Xingtan , Chen, Shuai , Shi, Longqing , Gong, Daping , Zhang, Shengcheng , Zhao, Qian et al. Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis . | NATURE GENETICS , 2021 , 53 (8) , 1250-, . |
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Orphan genes are genes with no sequence homologues in other species. Here, we identified two orphan genes, namely, Tssor-3 and Tssor-4, in Plutella xylostella. Both genes contained a signal peptide sequence, suggesting their functions as secreted proteins. Expression pattern analysis based on real-time quantitative PCR (qPCR) showed that both orphan genes were specifically expressed in all male gonads except the testes. The expression of both the orphan genes peaked at the male adult stage. Immunofluorescence assays suggested that the two proteins were seminal proteins, indicating their potential roles in male reproductive regulation. To further explain their functions, we knocked down the expression of these two genes by RNA interference (RNAi). The results showed that the expression of Tssor-3 and Tssor-4 was significantly downregulated at 24 h after injection compared to that of the controls. Biological assays showed that the number of laid eggs and the hatching rate of offspring eggs were significantly reduced when the expression of Tssor-3 and Tssor-4 was reduced, suggesting that the two orphan genes played a role in male fertility in P. xylostella. Our results provide evidence that orphan genes are involved in male reproductive regulation, which is important for male fitness during evolution.
Keyword ：
male fertility male fertility orphan genes orphan genes Plutella xylostella Plutella xylostella RNA interference RNA interference
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| GB/T 7714 | Tian-pu, Li , Li-wen, Zhang , Ya-qing, Li et al. Functional analysis of the orphan genes Tssor-3 and Tssor-4 in male Plutella xylostella [J]. | JOURNAL OF INTEGRATIVE AGRICULTURE , 2021 , 20 (7) : 1880-1888 . |
| MLA | Tian-pu, Li et al. "Functional analysis of the orphan genes Tssor-3 and Tssor-4 in male Plutella xylostella" . | JOURNAL OF INTEGRATIVE AGRICULTURE 20 . 7 (2021) : 1880-1888 . |
| APA | Tian-pu, Li , Li-wen, Zhang , Ya-qing, Li , Min-sheng, You , Qian, Zhao . Functional analysis of the orphan genes Tssor-3 and Tssor-4 in male Plutella xylostella . | JOURNAL OF INTEGRATIVE AGRICULTURE , 2021 , 20 (7) , 1880-1888 . |
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