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Group-specific discriminant analysis enhances detection of sex differences in brain functional network lateralization. 群体特异性判别分析增强了对脑功能网络侧化的性别差异的检测。
IF 11.8 2区 生物学
GigaScience Pub Date : 2025-01-06 DOI: 10.1093/gigascience/giaf082
Shuo Zhou, Junhao Luo, Yaya Jiang, Haolin Wang, Haiping Lu, Gaolang Gong
{"title":"Group-specific discriminant analysis enhances detection of sex differences in brain functional network lateralization.","authors":"Shuo Zhou, Junhao Luo, Yaya Jiang, Haolin Wang, Haiping Lu, Gaolang Gong","doi":"10.1093/gigascience/giaf082","DOIUrl":"https://doi.org/10.1093/gigascience/giaf082","url":null,"abstract":"<p><strong>Background: </strong>Lateralization is the asymmetry in function and cognition between the brain hemispheres, with notable sex differences. Conventional neuroscience studies on lateralization use univariate statistical comparisons between male and female groups, with limited and ineffective validation for group specificity. This article proposes to model sex differences in brain functional network lateralization as a dual-classification problem: first-order classification of left versus right hemispheres and second-order classification of male versus female models. To capture sex-specific patterns, we developed an interpretable group-specific discriminant analysis (GSDA) for first-order classification, followed by logistic regression for second-order classification.</p><p><strong>Findings: </strong>Evaluations on 2 large-scale neuroimaging datasets show GSDA's effectiveness in learning sex-specific patterns, significantly improving model group specificity over baseline methods. Major sex differences were identified in the strength of lateralization and interaction patterns within and between lobes.</p><p><strong>Conclusions: </strong>The GSDA-based analysis challenges the conventional approach to investigating group-specific lateralization and indicates that previous findings on sex-specific lateralization will need revisits and revalidation. This method is generic and can be adapted for other group-specific analyses, such as treatment-specific or disease-specific studies.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12398281/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144950490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
BVSim: A benchmarking variation simulator mimicking human variation spectrum. BVSim:模拟人类变异谱的基准变异模拟器。
IF 11.8 2区 生物学
GigaScience Pub Date : 2025-01-06 DOI: 10.1093/gigascience/giaf095
Yongyi Luo, Zhen Zhang, Shu Wang, Jiandong Shi, Jingyu Hao, Sheng Lian, Taobo Hu, Toyotaka Ishibashi, Depeng Wang, Weichuan Yu, Xiaodan Fan
{"title":"BVSim: A benchmarking variation simulator mimicking human variation spectrum.","authors":"Yongyi Luo, Zhen Zhang, Shu Wang, Jiandong Shi, Jingyu Hao, Sheng Lian, Taobo Hu, Toyotaka Ishibashi, Depeng Wang, Weichuan Yu, Xiaodan Fan","doi":"10.1093/gigascience/giaf095","DOIUrl":"https://doi.org/10.1093/gigascience/giaf095","url":null,"abstract":"<p><strong>Background: </strong>Genomic variations, including single-nucleotide polymorphisms, small insertions and deletions, and structural variations, are crucial for understanding evolution and disease. However, comprehensive simulation tools for benchmarking genomic analysis methods are lacking. Existing simulators do not accurately represent the nonuniform distribution and length patterns of structural variations in human genomes, and simulating complex structural variations remains challenging.</p><p><strong>Results: </strong>We present BVSim, a flexible tool that provides probabilistic simulations of genomic variations, primarily focusing on human patterns while accommodating diverse species. BVSim effectively simulates both simple and complex structural variations and small variants by mimicking real-life variation distributions, which often exhibit higher frequencies near telomeres and within tandem repeat regions. Notably, BVSim allows users to input single or multiple benchmark samples from any reference genome, enabling the tool to summarize and represent the unique distribution patterns of structural variation positions and lengths specific to those species. Its compatibility with standard file formats facilitates seamless integration into various genomic research workflows, making it a very useful resource for benchmarking downstream tools such as variant callers. With numerical experiments, we show that BVSim generated more realistic sequences significantly different from other simulators' outputs.</p><p><strong>Conclusions: </strong>BVSim is written in Python and freely available to noncommercial users under the GPL3 license. Source code, application guide, and toy examples are provided on the GitHub page at https://github.com/YongyiLuo98/BVSim. The tool is registered in SciCrunch (RRID:SCR_026926), bio.tools (biotools:BVSim), and WorkflowHub (doi:10.48546/WORKFLOWHUB.WORKFLOW.1361.1).</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12398280/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144950505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes. 通过在参考基因组中隐藏微生物样区域来改进古代环境宏基因组的分类推断。
IF 11.8 2区 生物学
GigaScience Pub Date : 2025-01-06 DOI: 10.1093/gigascience/giaf108
Nikolay Oskolkov, Chenyu Jin, Samantha López Clinton, Benjamin Guinet, Flore Wijnands, Ernst Johnson, Verena E Kutschera, Cormac M Kinsella, Peter D Heintzman, Tom van der Valk
{"title":"Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes.","authors":"Nikolay Oskolkov, Chenyu Jin, Samantha López Clinton, Benjamin Guinet, Flore Wijnands, Ernst Johnson, Verena E Kutschera, Cormac M Kinsella, Peter D Heintzman, Tom van der Valk","doi":"10.1093/gigascience/giaf108","DOIUrl":"10.1093/gigascience/giaf108","url":null,"abstract":"<p><p>Ancient environmental DNA is increasingly vital for reconstructing past ecosystems, particularly when paleontological and archaeological tissue remains are absent. Detecting ancient plant and animal DNA in environmental samples relies on using extensive eukaryotic reference genome databases for profiling metagenomics data. However, many eukaryotic genomes contain regions with high sequence similarity to microbial DNA, which can lead to the misclassification of bacterial and archaeal reads as eukaryotic. This issue is especially problematic in ancient eDNA datasets, where plant and animal DNA is typically present at very low abundance. In this study, we present a method for identifying bacterial- and archaeal-like sequences in eukaryotic genomes and apply it to nearly 3,000 reference genomes from NCBI RefSeq and GenBank (vertebrates, invertebrates, plants) as well as the 1,323 PhyloNorway plant genome assemblies from herbarium material from northern high-latitude regions. We find that microbial-like regions are widespread across eukaryotic genomes and provide a comprehensive resource of their genomic coordinates and taxonomic annotations. This resource enables the masking of microbial-like regions during profiling analyses, thereby improving the reliability of ancient environmental metagenomic datasets for downstream analyses.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12491943/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145212353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A near telomere-to-telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps. 澳大利亚中央胡须龙Pogona vitticeps的近端粒到端粒阶段基因组组装和注释。
IF 11.8 2区 生物学
GigaScience Pub Date : 2025-01-06 DOI: 10.1093/gigascience/giaf085
Hardip R Patel, Kirat Alreja, Andre L M Reis, J King Chang, Zahra A Chew, Hyungtaek Jung, Jillian M Hammond, Ira W Deveson, Aurora Ruiz-Herrera, Laia Marin-Gual, Clare E Holleley, Xiuwen Zhang, Nicholas C Lister, Sarah Whiteley, Lei Xiong, Duminda S B Dissanayake, Paul D Waters, Arthur Georges
{"title":"A near telomere-to-telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps.","authors":"Hardip R Patel, Kirat Alreja, Andre L M Reis, J King Chang, Zahra A Chew, Hyungtaek Jung, Jillian M Hammond, Ira W Deveson, Aurora Ruiz-Herrera, Laia Marin-Gual, Clare E Holleley, Xiuwen Zhang, Nicholas C Lister, Sarah Whiteley, Lei Xiong, Duminda S B Dissanayake, Paul D Waters, Arthur Georges","doi":"10.1093/gigascience/giaf085","DOIUrl":"10.1093/gigascience/giaf085","url":null,"abstract":"<p><strong>Background: </strong>The central bearded dragon (Pogona vitticeps) is widely distributed in central eastern Australia and adapts readily to captivity. Among other attributes, it is distinctive because it undergoes sex reversal from ZZ genotypic males to phenotypic females at high incubation temperatures. Here, we report an annotated near telomere-to-telomere phased assembly of the genome of a female ZW central bearded dragon.</p><p><strong>Results: </strong>Genome assembly length is 1.75 Gbp with a scaffold N50 of 266.2 Mbp, N90 of 28.1 Mbp, 26 gaps, and 42.2% GC content. Most (99.6%) of the reference assembly is scaffolded into 6 macrochromosomes and 10 microchromosomes, including the Z and W microchromosomes, corresponding to the karyotype. The genome assembly exceeds standard recommended by the Earth Biogenome Project (6CQ40): 0.003% collapsed sequence, 0.03% false expansions, 99.8% k-mer completeness, 97.9% complete single-copy BUSCO genes, and an average of 93.5% of transcriptome data mappable back to the genome assembly. The mitochondrial genome (16,731 bp) and the model ribosomal DNA repeat unit (length 9.5 Kbp) were assembled. Male vertebrate sex genes Amh and Amhr2 were discovered as copies in the small non-recombining region of the Z chromosome, absent from the W chromosome. This, coupled with the prior discovery of differential Z and W transcriptional isoform composition arising from pseudo-autosomal sex gene Nr5a1, suggests that complex interactions between these genes, their autosomal copies, and their resultant transcription factors and intermediaries determine sex in the bearded dragon.</p><p><strong>Conclusion: </strong>This high-quality assembly will serve as a resource to enable and accelerate research into the unusual reproductive attributes of this species and for comparative studies across the Agamidae and reptiles more generally.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12360841/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144872646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A comprehensive water buffalo pangenome reveals extensive structural variation linked to population-specific signatures of selection. 一个全面的水牛泛基因组揭示了与种群特异性选择特征相关的广泛结构变异。
IF 11.8 2区 生物学
GigaScience Pub Date : 2025-01-06 DOI: 10.1093/gigascience/giaf099
Fazeela Arshad, Siddharth Jayaraman, Andrea Talenti, Rachel Owen, Muhammad Mohsin, Shahid Mansoor, Muhammad Asif, James Prendergast
{"title":"A comprehensive water buffalo pangenome reveals extensive structural variation linked to population-specific signatures of selection.","authors":"Fazeela Arshad, Siddharth Jayaraman, Andrea Talenti, Rachel Owen, Muhammad Mohsin, Shahid Mansoor, Muhammad Asif, James Prendergast","doi":"10.1093/gigascience/giaf099","DOIUrl":"https://doi.org/10.1093/gigascience/giaf099","url":null,"abstract":"<p><strong>Background: </strong>Water buffalo is a cornerstone livestock species in many low- and middle-income countries, yet major gaps persist in its genomic characterization-complicated by the divergent karyotypes of its two subspecies (swamp and river). Such genomic complexity makes water buffalo a particularly good candidate for the use of graph genomics, which can capture variation missed by linear reference approaches. However, the utility of this approach to improve water buffalo has been largely unexplored.</p><p><strong>Results: </strong>We present a comprehensive pangenome that integrates 4 newly generated, highly contiguous assemblies of Pakistani river buffalo with 8 publicly available assemblies from both subspecies. This doubles the number of accessible high-quality river buffalo genomes and provides the most contiguous assemblies for the subspecies to date. Using the pangenome to assay variation across 711 global samples, we uncovered extensive genomic diversity, including thousands of large structural variants absent from the reference genome, spanning over 140 Mb of additional sequence. We demonstrate the utility of these data by identifying putative functional indels and structural variants linked to selective sweeps in key genes involved in productivity and immune response across 26 populations.</p><p><strong>Conclusions: </strong>This study represents one of the first successful applications of graph genomics in water buffalo and offers valuable insights into how integrating assemblies can transform analyses of water buffalo and other species with complex evolutionary histories. We anticipate that these assemblies, as well as the pangenome and putative functional structural variants we have released, will accelerate efforts to unlock water buffalo's genetic potential, improving productivity and resilience in this economically important species.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12398277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144950483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Artificial intelligence: the human response to approach the complexity of big data in biology. 人工智能:人类对接近生物学大数据复杂性的反应。
IF 11.8 2区 生物学
GigaScience Pub Date : 2025-01-06 DOI: 10.1093/gigascience/giaf057
Giovanni Melandri, Georges R-Radohery, Chloé Beaumont, Sara M de Cripan, Coralie Muller, Luca Piras, Maria Alcina Pereira, Andreia Ferreira Salvador, Xavier Domingo-Almenara, Marie Bolger, Sophie Colombié, Sylvain Prigent, Biotza Gutierrez Arechederra, Nuria Canela Canela, Pierre Pétriacq
{"title":"Artificial intelligence: the human response to approach the complexity of big data in biology.","authors":"Giovanni Melandri, Georges R-Radohery, Chloé Beaumont, Sara M de Cripan, Coralie Muller, Luca Piras, Maria Alcina Pereira, Andreia Ferreira Salvador, Xavier Domingo-Almenara, Marie Bolger, Sophie Colombié, Sylvain Prigent, Biotza Gutierrez Arechederra, Nuria Canela Canela, Pierre Pétriacq","doi":"10.1093/gigascience/giaf057","DOIUrl":"10.1093/gigascience/giaf057","url":null,"abstract":"<p><p>Since the late 2010s, artificial intelligence (AI), encompassing machine learning and propelled by deep learning, has transformed life science research. It has become a crucial tool for advancing the computational analysis of biological processes, the discovery of natural products, and the study of ecosystem dynamics. This review explores how the rapid increase in high-throughput omics data acquisition has driven the need for AI-based analysis in life sciences, with a particular focus on plant sciences, animal sciences, and microbiology. We highlight the role of omics-based predictive analytics in systems biology and innovative AI-based analytical approaches for gaining deeper insights into complex biological systems. Finally, we discuss the importance of FAIR (findable, accessible, interoperable, reusable) principles for omics data, as well as the future challenges and opportunities presented by the increasing use of AI in life sciences.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12160488/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144274679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
SeuratExtend: streamlining single-cell RNA-seq analysis through an integrated and intuitive framework. SeuratExtend:通过集成和直观的框架简化单细胞RNA-seq分析。
IF 11.8 2区 生物学
GigaScience Pub Date : 2025-01-06 DOI: 10.1093/gigascience/giaf076
Yichao Hua, Linqian Weng, Fang Zhao, Florian Rambow
{"title":"SeuratExtend: streamlining single-cell RNA-seq analysis through an integrated and intuitive framework.","authors":"Yichao Hua, Linqian Weng, Fang Zhao, Florian Rambow","doi":"10.1093/gigascience/giaf076","DOIUrl":"10.1093/gigascience/giaf076","url":null,"abstract":"<p><p>Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of cellular heterogeneity, but the rapid expansion of analytical tools has proven to be both a blessing and a curse, presenting researchers with significant challenges. Here, we present SeuratExtend, a comprehensive R package built upon the widely adopted Seurat framework, which streamlines scRNA-seq data analysis by strategically integrating essential tools and databases. SeuratExtend offers a user-friendly and intuitive interface for performing a wide range of analyses, including functional enrichment, trajectory inference, gene regulatory network reconstruction, and denoising. The package integrates multiple databases, such as Gene Ontology and Reactome, and incorporates popular Python tools like scVelo, Palantir, and SCENIC through a unified R interface. We illustrate SeuratExtend's capabilities through case studies investigating tumor-associated high-endothelial venules and autoinflammatory diseases, as well as showcase its novel applications in pathway-level analysis and cluster annotation. SeuratExtend enhances data visualization with optimized plotting functions and carefully curated color schemes, ensuring both aesthetic appeal and scientific rigor. The package's effectiveness has been demonstrated through successful workshops and training programs, establishing its value in both research and educational contexts. SeuratExtend empowers researchers to harness the full potential of scRNA-seq data, making complex analyses accessible to a wider audience. The package, along with comprehensive documentation, tutorials, and educational resources, is freely available at GitHub, providing a valuable resource for the single-cell genomics community.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12236070/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144583587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A framework to mine laser microdissection-based omics data and uncover regulators of pancreatic cancer heterogeneity. 挖掘基于激光显微解剖的组学数据并揭示胰腺癌异质性调节因子的框架。
IF 11.8 2区 生物学
GigaScience Pub Date : 2025-01-06 DOI: 10.1093/gigascience/giaf101
Pierluigi Di Chiaro, Giuseppe R Diaferia, Gioacchino Natoli, Iros Barozzi
{"title":"A framework to mine laser microdissection-based omics data and uncover regulators of pancreatic cancer heterogeneity.","authors":"Pierluigi Di Chiaro, Giuseppe R Diaferia, Gioacchino Natoli, Iros Barozzi","doi":"10.1093/gigascience/giaf101","DOIUrl":"10.1093/gigascience/giaf101","url":null,"abstract":"<p><strong>Background: </strong>Pancreatic ductal adenocarcinoma (PDAC), the most common and aggressive form of pancreatic cancer, exhibits profound intratumor morphological heterogeneity, complicating the elucidation of the underlying molecular mechanisms driving its progression.</p><p><strong>Results: </strong>We present and validate an optimized framework for RNA sequencing (RNA-seq) of multiple spatially resolved laser micro-dissected tumor areas (LMD-seq), along with methodological and analytical details to maximize reproducibility and data mining. This approach enhances sensitivity in detecting lowly expressed genes, outperforming single-cell RNA-seq methods, particularly in identifying rare tumor cell populations and transcriptional programs with low expression. We also present a detailed map of predicted regulatory networks underlying distinct PDAC morpho-biotypes, revealing novel mechanisms and key regulators associated with each subtype.</p><p><strong>Conclusions: </strong>This study provides fully reproducible workflows, including processed data objects, documented code, and computational predictions of the regulatory activities, enabling robust exploration of intratumor heterogeneity of PDAC. The proposed methodology, datasets, and catalog of the molecular and regulatory mechanisms offer a framework for future studies and applications in PDAC and other cancers.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12412123/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145000309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Telomere-to-telomere genome and resequencing of 231 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis. 231个个体的端粒-端粒基因组和重测序揭示了亚洲冰鱼的进化、基因组足迹。
IF 11.8 2区 生物学
GigaScience Pub Date : 2025-01-06 DOI: 10.1093/gigascience/giaf067
Yanfeng Zhou, Chenhe Wang, Binhu Wang, Dongpo Xu, Xizhao Zhang, You Ge, Shulun Jiang, Fujiang Tang, Chunhai Chen, Xuemei Li, Jianbo Jian, Yang You
{"title":"Telomere-to-telomere genome and resequencing of 231 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis.","authors":"Yanfeng Zhou, Chenhe Wang, Binhu Wang, Dongpo Xu, Xizhao Zhang, You Ge, Shulun Jiang, Fujiang Tang, Chunhai Chen, Xuemei Li, Jianbo Jian, Yang You","doi":"10.1093/gigascience/giaf067","DOIUrl":"10.1093/gigascience/giaf067","url":null,"abstract":"<p><p>The Asian icefish, Protosalanx chinensis, has undergone extensive colonization in various waters across China for decades due to its ecological and physiological significance as well as its economic importance in the fishery resource. Here, we decoded a telomereto-telomere (T2T) genome for P. chinensis combining PacBio HiFi long reads and ultra-long ONT (nanopore) reads and Hi-C data. The telomere was identified in both ends of the contig/chromosome. The expanded gene associated with circadian entrainment suggests that P. chinensis may exhibit a high sensitivity to photoperiod. The contracted genes' immune-related families and DNA repair associated with positive selection in P. chinensis suggested the selection pressure during adaptive evolution. The population genetic analysis reported the genetic diversity and genomic footprints in 231 individuals from 7 different locations. The introduced highest alkalinity population (HRCL) exhibited higher values of inbreeding coefficients and clustered different from other groups suggested local environmental adaptation. Thus, the T2T genome and genetic variation can be valuable resources for genomic footprints in P. chinensis, shedding light on its evolution, comparative genomics, and the genetic differences between natural and introduced populations.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"14 ","pages":""},"PeriodicalIF":11.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12266836/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144649193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Chromosome-level genome assembly of Pinus massoniana provides insights into conifer adaptive evolution. 马尾松染色体水平的基因组组装提供了针叶树适应进化的见解。
IF 11.8 2区 生物学
GigaScience Pub Date : 2025-01-06 DOI: 10.1093/gigascience/giaf056
Hu Chen, Xinghu Qin, Yinghao Chen, Haoyu Zhang, Yuanheng Feng, Jianhui Tan, Xinhua Chen, La Hu, Junkang Xie, Jianbo Xie, Zhangqi Yang
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