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Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing. 长线程测序揭示癌症基因组中的新端粒和跨端粒染色体臂融合。
IF 11.1 Q1 CELL BIOLOGY Pub Date : 2024-07-10 Epub Date: 2024-06-24 DOI: 10.1016/j.xgen.2024.100588
Kar-Tong Tan, Michael K Slevin, Mitchell L Leibowitz, Max Garrity-Janger, Jidong Shan, Heng Li, Matthew Meyerson

Alterations in the structure and location of telomeres are pivotal in cancer genome evolution. Here, we applied both long-read and short-read genome sequencing to assess telomere repeat-containing structures in cancers and cancer cell lines. Using long-read genome sequences that span telomeric repeats, we defined four types of telomere repeat variations in cancer cells: neotelomeres where telomere addition heals chromosome breaks, chromosomal arm fusions spanning telomere repeats, fusions of neotelomeres, and peri-centromeric fusions with adjoined telomere and centromere repeats. These results provide a framework for the systematic study of telomeric repeats in cancer genomes, which could serve as a model for understanding the somatic evolution of other repetitive genomic elements.

端粒结构和位置的改变是癌症基因组进化的关键。在这里,我们应用长读程和短读程基因组测序技术来评估癌症和癌细胞系中含有端粒重复序列的结构。利用跨越端粒重复序列的长读数基因组序列,我们定义了癌细胞中端粒重复变异的四种类型:端粒添加可修复染色体断裂的新端粒、跨越端粒重复序列的染色体臂融合、新端粒融合以及端粒和中心粒重复序列相邻的近中心粒融合。这些结果为系统研究癌症基因组中的端粒重复序列提供了一个框架,可作为了解其他重复基因组元素体细胞进化的模型。
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引用次数: 0
Rhesus macaque as a model for sex-biased neurological diseases. 将猕猴作为研究性神经疾病的模型。
IF 11.1 Q1 CELL BIOLOGY Pub Date : 2024-07-10 Epub Date: 2024-06-27 DOI: 10.1016/j.xgen.2024.100585
Leticia Rodríguez-Montes, Henrik Kaessmann

Sexual dimorphism, differences between males and females of the same species, is widespread in mammals. However, good animal models to study human sexually dimorphic phenotypes are currently lacking. In this issue, DeCasien et al.1 explore the potential of rhesus macaque as a model for investigating sexually dimorphic traits in the human brain.

哺乳动物普遍存在性二型现象,即同一物种的雌性和雄性之间存在差异。然而,目前还缺乏研究人类性二态表型的良好动物模型。在本期杂志中,DeCasien 等人1 探讨了猕猴作为研究人脑性双态特征模型的潜力。
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引用次数: 0
Exome-wide evidence of compound heterozygous effects across common phenotypes in the UK Biobank. 英国生物库中常见表型的复合杂合效应的全外显子证据。
IF 11.1 Q1 CELL BIOLOGY Pub Date : 2024-07-10 Epub Date: 2024-06-28 DOI: 10.1016/j.xgen.2024.100602
Frederik H Lassen, Samvida S Venkatesh, Nikolas Baya, Barney Hill, Wei Zhou, Alex Bloemendal, Benjamin M Neale, Benedikt M Kessler, Nicola Whiffin, Cecilia M Lindgren, Duncan S Palmer

The phenotypic impact of compound heterozygous (CH) variation has not been investigated at the population scale. We phased rare variants (MAF ∼0.001%) in the UK Biobank (UKBB) exome-sequencing data to characterize recessive effects in 175,587 individuals across 311 common diseases. A total of 6.5% of individuals carry putatively damaging CH variants, 90% of which are only identifiable upon phasing rare variants (MAF < 0.38%). We identify six recessive gene-trait associations (p < 1.68 × 10-7) after accounting for relatedness, polygenicity, nearby common variants, and rare variant burden. Of these, just one is discovered when considering homozygosity alone. Using longitudinal health records, we additionally identify and replicate a novel association between bi-allelic variation in ATP2C2 and an earlier age at onset of chronic obstructive pulmonary disease (COPD) (p < 3.58 × 10-8). Genetic phase contributes to disease risk for gene-trait pairs: ATP2C2-COPD (p = 0.000238), FLG-asthma (p = 0.00205), and USH2A-visual impairment (p = 0.0084). We demonstrate the power of phasing large-scale genetic cohorts to discover phenome-wide consequences of compound heterozygosity.

复合杂合子(CH)变异的表型影响尚未在人群范围内进行调查。我们对英国生物库(UKBB)外显子组测序数据中的罕见变异(MAF ∼0.001%)进行了分阶段分析,以确定311种常见疾病中175,587人的隐性效应特征。共有6.5%的个体携带有可能造成损害的CH变异,其中90%的变异只有在考虑了亲缘关系、多基因性、附近的常见变异和罕见变异负担后,通过分期罕见变异(MAF -7)才能确定。如果只考虑同源性,其中只有一个变异被发现。利用纵向健康记录,我们还发现并复制了 ATP2C2 双等位基因变异与慢性阻塞性肺病(COPD)发病年龄提前之间的新型关联(p -8)。遗传阶段对基因-性状对的疾病风险有影响:ATP2C2-COPD (p = 0.000238)、FLG-哮喘 (p = 0.00205) 和 USH2A-视力障碍 (p = 0.0084)。我们展示了大规模遗传队列分期发现复合杂合子全表型后果的能力。
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引用次数: 0
Sepsis research: Heterogeneity as a foundation rather than an afterthought. 败血症研究:异质性是基础而非事后考虑。
IF 11.1 Q1 CELL BIOLOGY Pub Date : 2024-07-10 DOI: 10.1016/j.xgen.2024.100608
Timothy H Ciesielski

Our understanding of sepsis has been hampered by the implicit assumption that sepsis is a homogeneous disease. In this issue of Cell Genomics, Burnham et al.1 have started to characterize the genetic variants and regulatory networks that underlie variations in the individual response to sepsis; this may eventually enable targeted intervention development.

脓毒症是一种同质性疾病,这一隐含假设阻碍了我们对脓毒症的了解。在本期的《细胞基因组学》(Cell Genomics)杂志上,Burnham 等人1 已开始描述脓毒症个体反应变异的基因变异和调控网络的特征;这可能最终有助于开发有针对性的干预措施。
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引用次数: 0
Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci. 迭代模板切换形成的反向三联体在基因组紊乱位点产生结构变异多样性。
IF 11.1 Q1 CELL BIOLOGY Pub Date : 2024-07-10 Epub Date: 2024-06-21 DOI: 10.1016/j.xgen.2024.100590
Christopher M Grochowski, Jesse D Bengtsson, Haowei Du, Mira Gandhi, Ming Yin Lun, Michele G Mehaffey, KyungHee Park, Wolfram Höps, Eva Benito, Patrick Hasenfeld, Jan O Korbel, Medhat Mahmoud, Luis F Paulin, Shalini N Jhangiani, James Paul Hwang, Sravya V Bhamidipati, Donna M Muzny, Jawid M Fatih, Richard A Gibbs, Matthew Pendleton, Eoghan Harrington, Sissel Juul, Anna Lindstrand, Fritz J Sedlazeck, Davut Pehlivan, James R Lupski, Claudia M B Carvalho

The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a complex genomic rearrangement (CGR). Although it has been identified as an important pathogenic DNA mutation signature in genomic disorders and cancer genomes, its architecture remains unresolved. Here, we studied the genomic architecture of DUP-TRP/INV-DUP by investigating the DNA of 24 patients identified by array comparative genomic hybridization (aCGH) on whom we found evidence for the existence of 4 out of 4 predicted structural variant (SV) haplotypes. Using a combination of short-read genome sequencing (GS), long-read GS, optical genome mapping, and single-cell DNA template strand sequencing (strand-seq), the haplotype structure was resolved in 18 samples. The point of template switching in 4 samples was shown to be a segment of ∼2.2-5.5 kb of 100% nucleotide similarity within inverted repeat pairs. These data provide experimental evidence that inverted low-copy repeats act as recombinant substrates. This type of CGR can result in multiple conformers generating diverse SV haplotypes in susceptible dosage-sensitive loci.

重复-三重/倒置-重复(DUP-TRP/INV-DUP)结构是一种复杂的基因组重排(CGR)。虽然它已被确定为基因组疾病和癌症基因组中重要的致病 DNA 突变特征,但其结构仍未得到解决。在这里,我们研究了 DUP-TRP/INV-DUP 的基因组结构,调查了通过阵列比较基因组杂交(aCGH)确定的 24 名患者的 DNA,在这些患者身上,我们发现了 4 个预测的结构变异(SV)单倍型中存在 4 个结构变异单倍型的证据。通过结合使用短线程基因组测序(GS)、长线程基因组测序、光学基因组图谱和单细胞 DNA 模板链测序(strand-seq),我们确定了 18 个样本的单倍型结构。结果表明,4 个样本的模板切换点是倒置重复对中核苷酸相似度为 100% 的 2.2 至 5.5 kb 的片段。这些数据提供了倒位低拷贝重复序列作为重组底物的实验证据。这种类型的 CGR 可导致多种构象在易感剂量敏感基因座中产生不同的 SV 单倍型。
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引用次数: 0
Mudskipper detects combinatorial RNA binding protein interactions in multiplexed CLIP data. Mudskipper 在多重 CLIP 数据中检测组合 RNA 结合蛋白的相互作用。
IF 11.1 Q1 CELL BIOLOGY Pub Date : 2024-07-10 Epub Date: 2024-07-01 DOI: 10.1016/j.xgen.2024.100603
Hsuanlin Her, Katherine L Rothamel, Grady G Nguyen, Evan A Boyle, Gene W Yeo

The uncovering of protein-RNA interactions enables a deeper understanding of RNA processing. Recent multiplexed crosslinking and immunoprecipitation (CLIP) technologies such as antibody-barcoded eCLIP (ABC) dramatically increase the throughput of mapping RNA binding protein (RBP) binding sites. However, multiplex CLIP datasets are multivariate, and each RBP suffers non-uniform signal-to-noise ratio. To address this, we developed Mudskipper, a versatile computational suite comprising two components: a Dirichlet multinomial mixture model to account for the multivariate nature of ABC datasets and a softmasking approach that identifies and removes non-specific protein-RNA interactions in RBPs with low signal-to-noise ratio. Mudskipper demonstrates superior precision and recall over existing tools on multiplex datasets and supports analysis of repetitive elements and small non-coding RNAs. Our findings unravel splicing outcomes and variant-associated disruptions, enabling higher-throughput investigations into diseases and regulation mediated by RBPs.

揭示蛋白质与 RNA 的相互作用有助于加深对 RNA 加工的理解。最近的多重交联和免疫沉淀(CLIP)技术,如抗体条形码 eCLIP(ABC),极大地提高了绘制 RNA 结合蛋白(RBP)结合位点的通量。然而,多重 CLIP 数据集是多变量的,每个 RBP 的信噪比不均匀。为了解决这个问题,我们开发了 Mudskipper,这是一个多功能计算套件,由两个部分组成:一个是 Dirichlet 多叉混合物模型,用于解释 ABC 数据集的多变量性质;另一个是软掩蔽方法,用于识别和去除信噪比低的 RBP 中的非特异性蛋白质-RNA 相互作用。在多重数据集上,Mudskipper 的精确度和召回率均优于现有工具,并支持对重复元素和小型非编码 RNA 的分析。我们的研究结果揭示了剪接结果和变异相关的破坏,从而能够对由 RBPs 介导的疾病和调控进行更高通量的研究。
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引用次数: 0
Gene-environment interactions within a precision environmental health framework. 精准环境健康框架下的基因-环境相互作用。
IF 11.1 Q1 CELL BIOLOGY Pub Date : 2024-07-10 Epub Date: 2024-06-25 DOI: 10.1016/j.xgen.2024.100591
Alison A Motsinger-Reif, David M Reif, Farida S Akhtari, John S House, C Ryan Campbell, Kyle P Messier, David C Fargo, Tiffany A Bowen, Srikanth S Nadadur, Charles P Schmitt, Kristianna G Pettibone, David M Balshaw, Cindy P Lawler, Shelia A Newton, Gwen W Collman, Aubrey K Miller, B Alex Merrick, Yuxia Cui, Benedict Anchang, Quaker E Harmon, Kimberly A McAllister, Rick Woychik

Understanding the complex interplay of genetic and environmental factors in disease etiology and the role of gene-environment interactions (GEIs) across human development stages is important. We review the state of GEI research, including challenges in measuring environmental factors and advantages of GEI analysis in understanding disease mechanisms. We discuss the evolution of GEI studies from candidate gene-environment studies to genome-wide interaction studies (GWISs) and the role of multi-omics in mediating GEI effects. We review advancements in GEI analysis methods and the importance of large-scale datasets. We also address the translation of GEI findings into precision environmental health (PEH), showcasing real-world applications in healthcare and disease prevention. Additionally, we highlight societal considerations in GEI research, including environmental justice, the return of results to participants, and data privacy. Overall, we underscore the significance of GEI for disease prediction and prevention and advocate for integrating the exposome into PEH omics studies.

了解遗传和环境因素在疾病病因学中的复杂相互作用以及基因-环境相互作用(GEIs)在人类各发育阶段的作用非常重要。我们回顾了基因-环境互作研究的现状,包括测量环境因素所面临的挑战以及基因-环境互作分析在理解疾病机制方面的优势。我们讨论了基因-环境互作研究从候选基因-环境研究到全基因组互作研究(GWIS)的演变过程,以及多组学在介导基因-环境互作效应中的作用。我们回顾了 GEI 分析方法的进展以及大规模数据集的重要性。我们还探讨了将基因互作研究结果转化为精准环境健康(PEH)的问题,展示了在医疗保健和疾病预防方面的实际应用。此外,我们还强调了环境基因组学研究中的社会考虑因素,包括环境正义、将结果返还给参与者以及数据隐私。总之,我们强调了基因组学信息对疾病预测和预防的重要意义,并倡导将暴露组纳入 PEH 全息研究。
{"title":"Gene-environment interactions within a precision environmental health framework.","authors":"Alison A Motsinger-Reif, David M Reif, Farida S Akhtari, John S House, C Ryan Campbell, Kyle P Messier, David C Fargo, Tiffany A Bowen, Srikanth S Nadadur, Charles P Schmitt, Kristianna G Pettibone, David M Balshaw, Cindy P Lawler, Shelia A Newton, Gwen W Collman, Aubrey K Miller, B Alex Merrick, Yuxia Cui, Benedict Anchang, Quaker E Harmon, Kimberly A McAllister, Rick Woychik","doi":"10.1016/j.xgen.2024.100591","DOIUrl":"10.1016/j.xgen.2024.100591","url":null,"abstract":"<p><p>Understanding the complex interplay of genetic and environmental factors in disease etiology and the role of gene-environment interactions (GEIs) across human development stages is important. We review the state of GEI research, including challenges in measuring environmental factors and advantages of GEI analysis in understanding disease mechanisms. We discuss the evolution of GEI studies from candidate gene-environment studies to genome-wide interaction studies (GWISs) and the role of multi-omics in mediating GEI effects. We review advancements in GEI analysis methods and the importance of large-scale datasets. We also address the translation of GEI findings into precision environmental health (PEH), showcasing real-world applications in healthcare and disease prevention. Additionally, we highlight societal considerations in GEI research, including environmental justice, the return of results to participants, and data privacy. Overall, we underscore the significance of GEI for disease prediction and prevention and advocate for integrating the exposome into PEH omics studies.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":null,"pages":null},"PeriodicalIF":11.1,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11293590/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141461133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Synthetic DNA barcodes identify singlets in scRNA-seq datasets and evaluate doublet algorithms. 合成 DNA 条形码识别 scRNA-seq 数据集中的单体并评估双体算法。
IF 11.1 Q1 CELL BIOLOGY Pub Date : 2024-07-10 Epub Date: 2024-06-25 DOI: 10.1016/j.xgen.2024.100592
Ziyang Zhang, Madeline E Melzer, Keerthana M Arun, Hanxiao Sun, Carl-Johan Eriksson, Itai Fabian, Sagi Shaashua, Karun Kiani, Yaara Oren, Yogesh Goyal

Single-cell RNA sequencing (scRNA-seq) datasets contain true single cells, or singlets, in addition to cells that coalesce during the protocol, or doublets. Identifying singlets with high fidelity in scRNA-seq is necessary to avoid false negative and false positive discoveries. Although several methodologies have been proposed, they are typically tested on highly heterogeneous datasets and lack a priori knowledge of true singlets. Here, we leveraged datasets with synthetically introduced DNA barcodes for a hitherto unexplored application: to extract ground-truth singlets. We demonstrated the feasibility of our framework, "singletCode," to evaluate existing doublet detection methods across a range of contexts. We also leveraged our ground-truth singlets to train a proof-of-concept machine learning classifier, which outperformed other doublet detection algorithms. Our integrative framework can identify ground-truth singlets and enable robust doublet detection in non-barcoded datasets.

单细胞 RNA 测序(scRNA-seq)数据集除了包含真正的单细胞(或称单细胞)外,还包含在测序过程中聚合的细胞(或称双细胞)。在 scRNA-seq 中高保真地识别单细胞是避免假阴性和假阳性发现的必要条件。虽然已经提出了几种方法,但它们通常都是在高度异构的数据集上进行测试,缺乏对真正单体的先验知识。在这里,我们利用带有合成引入的 DNA 条形码的数据集进行了一项迄今为止尚未探索过的应用:提取地面真实单体。我们展示了我们的框架 "singletCode "的可行性,以评估各种情况下的现有双码检测方法。我们还利用我们的地面实况单点来训练一个概念验证机器学习分类器,该分类器的性能优于其他双重检测算法。我们的综合框架可以识别地面实况单字,并在非条码数据集中实现稳健的双字检测。
{"title":"Synthetic DNA barcodes identify singlets in scRNA-seq datasets and evaluate doublet algorithms.","authors":"Ziyang Zhang, Madeline E Melzer, Keerthana M Arun, Hanxiao Sun, Carl-Johan Eriksson, Itai Fabian, Sagi Shaashua, Karun Kiani, Yaara Oren, Yogesh Goyal","doi":"10.1016/j.xgen.2024.100592","DOIUrl":"10.1016/j.xgen.2024.100592","url":null,"abstract":"<p><p>Single-cell RNA sequencing (scRNA-seq) datasets contain true single cells, or singlets, in addition to cells that coalesce during the protocol, or doublets. Identifying singlets with high fidelity in scRNA-seq is necessary to avoid false negative and false positive discoveries. Although several methodologies have been proposed, they are typically tested on highly heterogeneous datasets and lack a priori knowledge of true singlets. Here, we leveraged datasets with synthetically introduced DNA barcodes for a hitherto unexplored application: to extract ground-truth singlets. We demonstrated the feasibility of our framework, \"singletCode,\" to evaluate existing doublet detection methods across a range of contexts. We also leveraged our ground-truth singlets to train a proof-of-concept machine learning classifier, which outperformed other doublet detection algorithms. Our integrative framework can identify ground-truth singlets and enable robust doublet detection in non-barcoded datasets.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":null,"pages":null},"PeriodicalIF":11.1,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11293576/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141461134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Evolutionary and biomedical implications of sex differences in the primate brain transcriptome. 灵长类动物大脑转录组性别差异对进化和生物医学的影响。
IF 11.1 Q1 CELL BIOLOGY Pub Date : 2024-07-10 Epub Date: 2024-06-27 DOI: 10.1016/j.xgen.2024.100589
Alex R DeCasien, Kenneth L Chiou, Camille Testard, Arianne Mercer, Josué E Negrón-Del Valle, Samuel E Bauman Surratt, Olga González, Michala K Stock, Angelina V Ruiz-Lambides, Melween I Martínez, Susan C Antón, Christopher S Walker, Jérôme Sallet, Melissa A Wilson, Lauren J N Brent, Michael J Montague, Chet C Sherwood, Michael L Platt, James P Higham, Noah Snyder-Mackler

Humans exhibit sex differences in the prevalence of many neurodevelopmental disorders and neurodegenerative diseases. Here, we generated one of the largest multi-brain-region bulk transcriptional datasets for the rhesus macaque and characterized sex-biased gene expression patterns to investigate the translatability of this species for sex-biased neurological conditions. We identify patterns similar to those in humans, which are associated with overlapping regulatory mechanisms, biological processes, and genes implicated in sex-biased human disorders, including autism. We also show that sex-biased genes exhibit greater genetic variance for expression and more tissue-specific expression patterns, which may facilitate rapid evolution of sex-biased genes. Our findings provide insights into the biological mechanisms underlying sex-biased disease and support the rhesus macaque model for the translational study of these conditions.

人类在许多神经发育障碍和神经退行性疾病的发病率方面存在性别差异。在这里,我们为猕猴生成了一个最大的多脑区批量转录数据集,并描述了性别差异基因表达模式,以研究该物种对性别差异神经疾病的可转化性。我们发现了与人类相似的模式,这些模式与包括自闭症在内的人类性别偏向性疾病的重叠调控机制、生物过程和相关基因有关。我们还发现,性别偏向基因在表达方面表现出更大的遗传变异和更多的组织特异性表达模式,这可能会促进性别偏向基因的快速进化。我们的研究结果为性别偏见疾病的生物学机制提供了见解,并支持将猕猴模型用于这些疾病的转化研究。
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引用次数: 0
Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations. 无论植物寄主或基质特异性如何,真菌的蘑菇基因组总体都在极度扩张。
IF 11.1 Q1 CELL BIOLOGY Pub Date : 2024-07-10 Epub Date: 2024-06-27 DOI: 10.1016/j.xgen.2024.100586
Christoffer Bugge Harder, Shingo Miyauchi, Máté Virágh, Alan Kuo, Ella Thoen, Bill Andreopoulos, Dabao Lu, Inger Skrede, Elodie Drula, Bernard Henrissat, Emmanuelle Morin, Annegret Kohler, Kerrie Barry, Kurt LaButti, Asaf Salamov, Anna Lipzen, Zsolt Merényi, Botond Hegedüs, Petr Baldrian, Martina Stursova, Hedda Weitz, Andy Taylor, Maxim Koriabine, Emily Savage, Igor V Grigoriev, László G Nagy, Francis Martin, Håvard Kauserud

Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.

真菌属(Mycena s.s.)是一种无处不在的蘑菇属,其成员能降解多种死亡植物基质,并伺机侵入活植物根部。在对 24 个真菌属物种的核基因组进行测序后,我们发现它们打破了人们对真菌的预期模式,这种预期模式是基于真菌传统的食腐生态学和基质特化。在新基因家族出现、基因复制、编码多糖降解酶的分泌体增大、转座元件(TE)扩散和水平基因转移的驱动下,真菌的基因组整体上出现了大规模扩张,影响到所有基因家族。主要由于转座元件(TE)的增殖,北极真菌的基因组高达 502 Mbp(是温带真菌的 2 至 8 倍),是形成蘑菇的姬松茸真菌中最大的基因组,这表明在进化过程中可能会出现北极植物基因组扩张的现象。总之,真菌表现出非常不寻常的、多变的、类似马赛克的基因组结构,可适应多种生活方式,为人们日益认识到真菌的生态位适应可能比传统认为的更多变提供了基因组说明。
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引用次数: 0
期刊
Cell genomics
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