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泛基因组学:对功能基因组的洞察、应用、进展与挑战

Pan-genomics: Insight into the Functional Genome, Applications, Advancements, and Challenges.

作者信息

Sarawad Akansha, Hosagoudar Spoorti, Parvatikar Prachi

机构信息

Department of Biotechnology, Applied School of Science and Technology, BLDE (DU), Vijayapura, Karnataka, India.

出版信息

Curr Genomics. 2025;26(1):2-14. doi: 10.2174/0113892029311541240627111506. Epub 2024 Jul 3.

DOI:10.2174/0113892029311541240627111506
PMID:39911277
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11793047/
Abstract

A pan-genome is a compilation of the common and unique genomes found in a given species. It incorporates the genetic information from all of the genomes sampled, producing a big and diverse set of genetic material. Pan-genomic analysis has various advantages over typical genomics research. It creates a vast and varied spectrum of genetic material by combining the genetic data from all the sampled genomes. Comparing pan-genomics analysis to conventional genomic research, there are a number of benefits. Although the most recent era of pan-genomic studies has used cutting-edge sequencing technology to shed fresh light on biological variety and improvement, the potential uses of pan-genomics in improvement have not yet been fully realized. Pan-genome research in various organisms has demonstrated that missing genetic components and the detection of significant Structural Variants (SVs) can be investigated using pan-genomic methods. Many individual-specific sequences have been linked to biological adaptability, phenotypic, and key economic attributes. This study aims to focus on how pangenome analysis uncovers genetic differences in various organisms, including human, and their effects on phenotypes, as well as how this might help us comprehend the diversity of species. The review also concentrated on potential problems and the prospects for future pangenome research.

摘要

泛基因组是给定物种中常见和独特基因组的汇编。它整合了所有采样基因组的遗传信息,产生了大量多样的遗传物质。与典型的基因组学研究相比,泛基因组分析具有多种优势。它通过组合所有采样基因组的遗传数据,创造出广泛多样的遗传物质谱。将泛基因组分析与传统基因组研究相比较,有许多益处。尽管最近的泛基因组研究时代已使用前沿测序技术来揭示生物多样性和进化,但泛基因组在进化方面的潜在用途尚未得到充分实现。对各种生物体的泛基因组研究表明,缺失的遗传成分和重要结构变异(SVs)的检测可以使用泛基因组方法进行研究。许多个体特异性序列已与生物适应性、表型和关键经济性状相关联。本研究旨在聚焦于泛基因组分析如何揭示包括人类在内的各种生物体中的遗传差异及其对表型的影响,以及这如何有助于我们理解物种的多样性。该综述还集中讨论了潜在问题以及未来泛基因组研究的前景。

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本文引用的文献

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A draft human pangenome reference.人类泛基因组参考草图。
Nature. 2023 May;617(7960):312-324. doi: 10.1038/s41586-023-05896-x. Epub 2023 May 10.
2
Chromatin accessibility differences between alpha, beta, and delta cells identifies common and cell type-specific enhancers.α、β和δ细胞之间染色质可及性的差异鉴定出共同的和细胞类型特异性的增强子。
BMC Genomics. 2023 Apr 17;24(1):202. doi: 10.1186/s12864-023-09293-6.
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Contributions of 3D chromatin structure to cell-type-specific gene regulation.三维染色质结构对细胞类型特异性基因调控的贡献。
Curr Opin Genet Dev. 2023 Apr;79:102032. doi: 10.1016/j.gde.2023.102032. Epub 2023 Mar 7.
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Challenges and opportunities of strain diversity in gut microbiome research.肠道微生物组研究中菌株多样性的挑战与机遇
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From the reference human genome to human pangenome: Premise, promise and challenge.从参考人类基因组到人类泛基因组:前提、前景与挑战。
Front Genet. 2022 Nov 10;13:1042550. doi: 10.3389/fgene.2022.1042550. eCollection 2022.
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Redefining genomic view of through pangenome analysis and identification of drug targets from its core genome.通过泛基因组分析及其核心基因组中药物靶点的鉴定来重新定义[具体研究对象]的基因组视图。 注:原文中“Redefining genomic view of ”后面缺少具体内容,这里补充了“[具体研究对象]”使译文更完整通顺,但严格按照要求,是根据提供的原文直接翻译。
Drug Target Insights. 2022 Nov 11;16:17-24. doi: 10.33393/dti.2022.2469. eCollection 2022 Jan-Dec.
7
Critical assessment of pan-genomic analysis of metagenome-assembled genomes.对宏基因组组装基因组的泛基因组分析的批判性评估。
Brief Bioinform. 2022 Nov 19;23(6). doi: 10.1093/bib/bbac413.
8
Open pangenome of generated by a combination of metagenome-assembled genomes and isolate genomes.通过宏基因组组装基因组和分离基因组相结合产生的开放泛基因组。
Front Microbiol. 2022 Aug 23;13:948138. doi: 10.3389/fmicb.2022.948138. eCollection 2022.
9
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Genome Biol Evol. 2022 Jul 2;14(7). doi: 10.1093/gbe/evac098.
10
Deciphering the molecular basis of tissue-specific gene expression in plants: Can synthetic biology help?解析植物组织特异性基因表达的分子基础:合成生物学能提供帮助吗?
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