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genomics,transcriptomics,and peptidomics of the greater wax moth Galleria mellonella neuropeptides and their expression in response to lead stress

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Insect Science 2024年第3期31卷 773-791页

作者： Li-Lin Luo Yang Lin Jun-Hong Linghu Wei Gong Yuan-Hong Luo Man Liu Dao-Chao Jin Guy Smagghe Tong-Xian Liu Shun-Hua Gui Tian-Ci Yi Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region Institute of EntomologyGuizhou UniversityGuiyangGuizhouChina Guizhou Institute of Biology Guizhou Academy of SciencesGuiyangChina Institute of Plant Health and Medicine Guizhou UniversityGuiyangChina

Neuropeptides are crucial in regulation of a rich variety of developmental,physiological,and behavioral functions throughout the life cycle of *** an integrated approach of multiomics,we identified neuropeptide precursors in the greater wax moth Galleria mellonella,which is a harmful pest of honeybee hives with a worldwide ***,a total of 63 and 67 neuropeptide precursors were predicted and annotated in the *** genome and transcriptome,in which 40 neuropeptide precursors were confirmed in the *** ***,we identified 12 neuropeptide precursor genes present in *** but absent in honeybees,which may be potential novel pesticide target *** hives were contaminated with heavy metals such as lead,enabling its bioaccumulation in *** bodies through the food chain,we performed transcriptome sequencing to analyze the effects of Pb stress on the mRNA expression level of *** neuropeptide *** treatment by Pb,the expression of neuropeptide F1 was found to be significantly downregulated,implying that this neuropeptide might be associated with responding to the heavy metal stress in *** study comprehensively identified neuropeptide precursors in ***,and discussed the effects of heavy metals on insect neuropeptides,with the example of *** results are valuable for future elucidation of how neuropeptides regulate physiological functions in *** and contribute to our understanding of the insect's environmental plasticity and identify potential new biomarkers to assess heavy metal toxicity in insects.

关键词： Galleria mellonella genomics heavy metal stress neuropeptide peptidomics transcriptomics

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Potential and progress of studying mountain biodiversity by means of butterfly genetics and genomics

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Journal of Genetics and genomics 2024年第3期51卷 292-301页

作者： Shuting Wang Marco Girardello Wei Zhang State Key Laboratory of Protein and Plant Gene Research School of Life SciencesPeking UniversityBeijing 100871China Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing 100871China cE3c-Centre for Ecology Evolution and Environmental Changes/Azorean Biodiversity GroupFaculdade de Ciencias Agrarias e do AmbienteUniversidade dos Açores9700-042 Angra do HeroísmoTerceiraPortugal

Mountains are rich in biodiversity,and butterflies are species-rich and have a good ecological and evolutionary research *** review addresses the potential and progress of studying mountain biodiversity using butterflies as a *** discuss the uniqueness of mountain ecosystems,factors influencing the distribution of mountain butterflies,representative genetic and evolutionary models in butterfly research,and evolutionary studies of mountain biodiversity involving butterfly genetics and ***,we demonstrate the necessity of studying mountain butterflies and propose future *** review provides insights for studying the biodiversity of mountain butterflies as well as a summary of research methods for reference.

关键词： Mountain ecosystem Butterfly Biodiversity Adaptation genomics Genetics

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The story of a decade:genomics,functional genomics,and molecular breeding in Brassica napus

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Plant Communications 2024年第4期5卷 94-111页

作者： Jianwei Gu Zhilin Guan Yushun Jiao Kede Liu Dengfeng Hong National Key Laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070HubeiChina College of Life Science and Technology Hubei Engineering UniversityXiaogan 432100 HubeiChina Wuhan Botanical Garden Chinese Academy of SciencesWuhan 430074 HubeiChina Yazhouwan National Laboratory Sanya 572024 HainanChina These authors contributed equally to this article.

Rapeseed(Brassica napus L.)is one of the major global sources of edible vegetable oil and is also used as a feed and pioneer crop and for sightseeing and industrial *** in genome sequencing and molecular marker technology have fueled a boom in functional genomic studies of major agronomic characters such as yield,quality,flowering time,and stress ***,introgression and pyra-miding of key functional genes have greatly accelerated the genetic improvement of important *** we summarize recent progress in rapeseed genomics and genetics,and we discuss effective molecular breeding strategies by exploring thesefindings in *** insights will extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process,ultimately contributing to more sustainable agriculture throughout the world.

关键词： Brassica napus functional genomics genomics molecular breeding agronomic traits

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Accelerating snail vector genomics

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Infectious Diseases of Poverty 2024年第3期13卷 6-10页

作者： Tom Pennance David Rollinson College of Osteopathic Medicine of the Pacific-Northwest Western University of Health SciencesLebanonORUSA Global Schistosomiasis Alliance Ealing Cross85 Uxbridge RoadEalingLondon W55BWUK Science Department Natural History MuseumCromwell RoadLondon SW75BDUK

The three most important genera of snails for the transmission of schistosomes are Bulinus,Biomphalaria and *** of these genera,found in two distantly related families,includes species that act as the intermediate host for one of the three most widespread schistosome species infecting humans,Schistosoma haematobium,*** and ***,*** important step in the fight against schistosomiasis in Asia has been taken with the publication of the article"Chromosome-level genome assembly of Oncomelania hupensis:the intermediate snail host of Schistosoma japonicum",which means that genomes for all three major genera,including species across three continents,are now available in the public *** includes the first genomes of African snail vectors,namely Biomphalaria sudanica,*** and Bulinus truncatus,as well as high-quality chromosome level assemblies for South American *** importantly,the wealth of new genomic and transcriptomic data is helping to establish the specific molecular mechanisms that underly compatibility between snails and their schistosomes,which although diverse and complex,may help to identify potential targets dictating host parasite interactions that can be utilised in future transmission control *** new work on Oncomelania hupensis and indeed studies on other snail vectors,which provide deep insights into the genome,will stimulate research that may well lead to new and much needed control interventions.

关键词： Snail vectors genomics

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Exploring the Unknown: The Application and Prospects of Artificial Intelligence in genomics and Bioinformatics

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Health 2024年第9期16卷 837-848页

作者： Qigang Feng Jie Li Qing Zhang Department of Gastroenterology First Hospital of Yangtze University Jingzhou China Digestive Disease Research Institution of Yangtze University Jingzhou China Clinical Medical College Yangtze University Jingzhou China

This review comprehensively explores the core application of artificial intelligence (AI) in the fields of genomics and bioinformatics, and deeply analyzes how it leads the innovative progress of science. In the cutting-edge fields of genomics and bioinformatics, the application of AI is propelling a deeper understanding of complex genetic mechanisms and the development of innovative therapeutic approaches. The precision of AI in genomic sequence analysis, coupled with breakthroughs in precise gene editing, such as AI-designed gene editors, significantly enhances our comprehension of gene functions and disease associations . Moreover, AI’s capabilities in disease prediction, assessing individual disease risks through genomic data analysis, provide robust support for personalized medicine. AI applications extend beyond gene identification, gene expression pattern prediction, and genomic structural variant analysis, encompassing key areas such as epigenetics, multi-omics data integration, genetic disease diagnosis, evolutionary genomics, and non-coding RNA function prediction. Despite challenges including data privacy, algorithm transparency, and bioethical issues, the future of AI is expected to continue revolutionizing genomics and bioinformatics, ushering in a new era of personalized medicine and precision treatments.

关键词： AI genomics Disease Prediction Gene Editing Multi-Omics Data Fusion

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genomics and morphometrics reveal the adaptive evolution of pikas

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Zoological Research 2022年第5期43卷 813-826页

作者： Rui-Xiang Tang Jiao Wang Yi-Fei Li Cheng-Ran Zhou Guan-Liang Meng Feng-Jun Li Yue Lan Megan Price Lars Podsiadlowski Yan Yu Xu-Ming Wang Yin-Xun Liu Bi-Song Yue Shan-Lin Liu Zhen-Xin Fan Shao-Ying Liu Key Laboratory of Bioresources and Ecoenvironment(Ministry of Education) College of Life SciencesSichuan UniversityChengduSichuan 610065China Sichuan Academy of Forestry ChengduSichuan 610081China Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE Department of PediatricsWest China Second University HospitalSichuan UniversityChengduSichuan 610041China BGI-Shenzhen ShenzhenGuangdong 518083China Zoological Research Museum Alexander Koenig Bonn D-53113Germany Department of Entomology China Agriculture UniversityBeijing 100193China Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife College of Life SciencesSichuan UniversityChengduSichuan 610065China

Pikas(Lagomorpha: Ochotonidae) are small mouselike lagomorphs. To investigate their adaptation to different ecological environments during their dispersal from the Qinghai-Xizang(Tibet) Plateau(QTP), we collected 226 pikas and measured 20 morphological characteristics and recorded habitat information. We also sequenced the genome of 81specimens, representing 27 putative pika *** genome-wide tree based on 4?090 coding genes identified five subgenera, i.e., Alienauroa, Conothoa,Lagotona, Ochotona, and Pika, consistent with morphometric data. Morphologically, Alienauroa and Ochotona had similar traits, including smaller size and earlier divergence time compared to other ***, the habitats of Alienauroa and Ochotona differed from those of the remaining subgenera. Phylogenetic signal analysis detected 83 genes significantly related to morphological characteristics, including several visual and hearingrelated genes. Analysis of shared amino acid substitutions and positively selected genes(PSGs) in Alienauroa and Ochotona identified two genes, i.e.,mitochondrial function-related TSFM(p.Q155E) and low-light visual sensitivity-related PROM1(p.H419Y).Functional experiments demonstrated that TSFM-155E significantly enhanced mitochondrial function compared to TSFM-155Q in other pikas, and PROM1-419Y decreased the modeling of dynamic intracellular chloride efflux upon calcium uptake. Alienauroa and Ochotona individuals mostly inhabit different environments(e.g., subtropical forests) than other pikas, suggesting that a shift from the larger ancestral type and changes in sensory acuity and energy enhancement may have been required in their new environments. This study increases our understanding of the evolutionary history of pikas.

关键词： Pikas genomics Morphometrics Adaptive evolution Sensory and energy functions

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genomics,metagenomics,and microbial oceanography—A sea of opportunities

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Science China Earth Sciences 2011年第4期54卷 473-480页

作者： FANG JiaSong 1,2 &ZHANG Li 3 1 State Key Laboratory of Marine Geology,Tongji University,Shanghai 200092,China 2 College of Natural and Computational Sciences,Hawaii Pacific University,Kaneohe,HI 96744,USA 3State Key Laboratory of Geological Processes and Mineral Resources,Faculty of Earth Sciences,China University of Geosciences,Wuhan 430074,China State Key Laboratory of Marine Geology Tongji University Shanghai China College of Natural and Computational Sciences Hawaii Pacific University Kaneohe USA State Key Laboratory of Geological Processes and Mineral Resources Faculty of Earth Sciences China University of Geosciences Wuhan China

Microbial oceanography is an emerging discipline resulted from the interaction,cross-fertilization and integration of life science and ocean *** oceanography integrates the principles of marine microbiology,microbial ecology and oceanography to study the role of microorganisms in the biogeochemical dynamics of natural marine *** application of genomics tools to study marine microbes is resulting in rapid advancements in microbial oceanography that has important implications in global carbon cycle,climate change,and ecosystem *** we review the application of genomics and metagenomics in microbial oceanography and suggest future directions in microbial oceanography research.

关键词： microbial oceanography genomics metagenomics genes biomass bacteria archaea eukarya phylogeny physiology metabolism ecology biogeochemistry microbiology ecosystem function

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genomics-based plant germplasm research(GPGR)

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The Crop Journal 2017年第2期5卷 166-174页

作者： Jizeng Jia Hongjie Li Xueyong Zhang Zichao Li Lijuan Qiu Key Laboratory of Crop Germplasm & Biotechnology Ministry of AgricultureInstitute of Crop ScienceChinese Academy of Agricultural SciencesThe National Key Facility for Crop Gene Resources and Genetic ImprovementNFCRGI Beijing Key Laboratory of Crop Genetic Improvement Key Laboratory of Crop Heterosis and UtilizationMinistry of EducationChina Agricultural University

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 ＂Cenoplasmics＂ 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.

关键词： Plant germplasm genomics genomics-based plant germplasm research(GPGR) Genoplasmics

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genomics revolution on andrology： genetic testing for male infertility

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Asian Journal of Andrology 2010年第3期12卷 449-450页

作者： Marumudi Eunice Ariachery Chinnama Ammini Department of Endocrinology and Metabolism All lndia Institute of Medical Sciences New Delhi 110029 lndia

Dear Editor, We would like to write to you on the era of＇omics-- genomics revolution on andrology, the way that has taken into a new dimension for tackling the emerging pressure on male infertility and for normal successful fertility outcome. In the Special Issue on Semen Analysis of Asian Journal ofAndrology, Aitken [1] has extensively discussed the causes of male infertility,

关键词： genomics genetic infertility

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Recent progress in alfalfa(Medicago sativa L.)genomics and genomic selection

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The Crop Journal 2018年第6期6卷 565-575页

作者： Charles Hawkins Long-Xi Yu United States Department of Agriculture-Agricultural Research Service Plant Germplasm Introduction and Testing Research

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.

关键词： Alfalfa genomics GWAS GBS Breeding

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