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Orphan and de novo Genes in Fungi and Animals: Identification, Origins and Functions. 真菌和动物中的孤儿和新生基因:鉴定、起源和功能。
IF 2.8 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2025-11-28 DOI: 10.1093/gbe/evaf220
Ercan Seçkin, Dominique Colinet, Edoardo Sarti, Etienne G J Danchin

Genes that lack identifiable homologs in other species have been an intriguing and interesting topic of research for many years. These so-called orphan genes were first studied in yeast and since then, they have been found in many other species. This has fostered a whole field of research aiming at tracing back their evolutionary origin and functional significance. Orphan genes represent an important part of protein-coding genes in many species. Their presence was initially mainly hypothesized to result from high divergence from a pre-existing gene, with duplications or horizontal gene transfer facilitating their accelerated evolution. More recently, their possible de novo emergence from nongenic regions has gained particular interest. Several orphan genes are predicted to be involved in reproduction, while others are involved in specific developmental stages, in adaptation mechanisms such as freeze protection or even human disease. However, there is currently no unified resource or synthesis that brings together existing knowledge about how prevalent orphan genes are across different species and what their roles might be. In this review, we focus on orphan genes in animals and fungi. We provide a detailed summary of discoveries over time in terms of orphan gene prevalence in genomes, their origins as well as their roles in different biological contexts.

在其他物种中缺乏可识别的同源基因多年来一直是一个有趣的研究课题。这些所谓的孤儿基因最初是在酵母中研究的,从那以后,在许多其他物种中也发现了它们。这促成了一整个领域的研究,旨在追溯它们的进化起源和功能意义。孤儿基因是许多物种中蛋白质编码基因的重要组成部分。它们的存在最初主要被假设为与先前存在的基因高度分化的结果,复制或水平基因转移促进了它们的加速进化。最近,它们可能从非基因区域重新出现引起了特别的兴趣。据预测,一些孤儿基因与生殖有关,而其他基因则与特定的发育阶段、适应机制(如冷冻保护)甚至人类疾病有关。然而,目前还没有统一的资源或综合来汇集关于孤儿基因在不同物种之间的普遍程度及其可能的作用的现有知识。本文主要对动物和真菌中的孤儿基因进行综述。我们就孤儿基因在基因组中的流行、它们的起源以及它们在不同生物学背景下的作用提供了一份详细的发现摘要。
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引用次数: 0
A Chromosome-level Genome Assembly of the Western Nose-Horned Viper (Vipera ammodytes ammodytes). 西部鼻角蝰(Vipera ammodytes ammodytes)染色体水平的基因组组装。
IF 2.8 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2025-11-28 DOI: 10.1093/gbe/evaf210
Wei-Qiao Rao, Esperanza Rivera-de-Torre, Lorenzo Seneci, Min-Hui Shi, Yao-Lei Zhang, Liang Lin, Tian-Ming Lan, Jože Pungerčar, Si-Qi Liu, Andreas H Laustsen

We present a chromosome-level genome assembly of the western nose-horned viper (Vipera ammodytes ammodytes), the most medically important viper in Europe. Using PacBio Sequel and Illumina HiSeq X Ten sequencing, we generated ∼270 Gb of data, achieving ∼131× coverage of the genome. The final assembly spans 1.55 Gb with a contig N50 of 45.9 Mb and a scaffold N50 of 210 Mb, anchored into 18 pseudo-chromosomes. Completeness was supported by recovery of 97.1% of Vertebrata BUSCOs. A total of 20,775 protein-coding genes were predicted, of which 96.6% were functionally annotated. Repetitive sequences accounted for 53.75% of the genome, dominated by LINEs (41.87%) and LTRs (14.35%). We identified 112 venom-related genes across 15 families, with expansions in SVMPs, Snaclecs, sPLA₂s, SPIs, and SVSPs, together comprising 62.5% of the venom repertoire. Chemosensory genes were also expanded, including 448 olfactory receptors, 72 taste receptors, and 29 vomeronasal receptors. This assembly represents the most complete genome resource for a true viper to date and provides a key resource for investigating venom evolution, chemosensory adaptation, and comparative snake genomics.

我们提出了一个染色体水平的基因组组装的西方鼻角毒蛇(Vipera ammodytes ammodytes),在欧洲最重要的医学毒蛇。使用PacBio Sequel和Illumina HiSeq X Ten测序,我们产生了~ 270 Gb的数据,实现了~ 131倍的基因组覆盖率。最终组装全长1.55 Gb,长N50为45.9 Mb,支架N50为210 Mb,锚定在18条假染色体上。脊椎动物busco的回收率为97.1%,支持了完整性。共预测到20,775个蛋白质编码基因,其中96.6%被功能注释。重复序列占基因组的53.75%,以LINEs(41.87%)和LTRs(14.35%)为主。我们在15个家族中鉴定出112个与毒液相关的基因,在svmp、Snaclecs、sPLA₂s、SPIs和svsp中扩增,共占毒液库的62.5%。化学感觉基因也有所扩展,包括448个嗅觉受体、72个味觉受体和29个犁鼻受体。该组合代表了迄今为止真正毒蛇最完整的基因组资源,并为研究毒液进化,化学感觉适应和比较蛇基因组学提供了一个平台。
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引用次数: 0
Comparative Genomics of the Testacea Group of Drosophila Reveals Introgression and Variation in Chromosome Size and Structure. 果蝇睾丸组的比较基因组学揭示了染色体大小和结构的渗入和变异。
IF 2.8 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2025-11-28 DOI: 10.1093/gbe/evaf225
Theresa Erlenbach, Ryan M R Gawryluk, Steve J Perlman, Robert L Unckless, Kelly A Dyer

Comparative genomic analyses among closely related species provide an opportunity to assess their evolutionary history. The relatedness between species can depend on a variety of factors, including reproductive isolation, introgression, and incomplete lineage sorting, and this can impact divergence across the genome. Here, we use a combination of long- and short-read sequencing and HI-C scaffolding to assemble genomes for each of the four species in the testacea species group of Drosophila, including D. testacea, D. orientacea, D. neotestacea, and D. putrida, and its outgroup, D. bizonata. First, among species, we find many structural rearrangements across the genome as well as a large size difference in the dot chromosome that we infer is due to the expansion of repetitive elements. Second, we assess phylogenetic discordance and uncover a difference in the phylogeny inferred from genes on Muller E and the mitogenome relative to the rest of the genome, which may be due to recent hybridization. Lastly, we assess the rate of molecular evolution of genes shared across all species and identify genes evolving at different rates across the phylogeny. Our results present genomic resources for this species group and begin to probe into some of the evolutionary characteristics that contribute to variation in genome structure, while highlighting the need for high-quality genome resources to fully capture and understand the evolutionary history among closely related species.

在密切相关的物种之间进行比较基因组分析提供了评估其进化史的机会。物种之间的亲缘关系可能取决于多种因素,包括生殖隔离、基因渗入和不完整的谱系分类,这可能会影响整个基因组的分化。在这里,我们使用了长、短序列测序和HI-C支架的组合来组装果蝇睾丸科四种物种的基因组,包括D. testacea、D. orientacea、D. neotestacea和D. putrida及其外群D. bizonata。首先,在物种中,我们发现基因组中的许多结构重排以及点染色体的大尺寸差异,我们推断这是由于重复元素的扩展。其次,我们评估了系统发育的不一致性,并揭示了Muller E上的基因和有丝分裂基因组相对于基因组其余部分的系统发育差异,这可能是由于最近的杂交。最后,我们评估了所有物种共享的基因的分子进化速度,并确定了在整个系统发育中以不同速度进化的基因。我们的研究结果为这一物种群体提供了基因组资源,并开始探索一些导致基因组结构变化的进化特征,同时强调了对高质量基因组资源的需求,以充分捕捉和理解密切相关物种之间的进化史。
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引用次数: 0
Speciation Genomics in the Tiger Whiptail Lizards (Aspidoscelis tigris Complex). 虎鞭尾蜥蜴(Aspidoscelis tigris Complex)的物种形成基因组学研究。
IF 2.8 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2025-11-28 DOI: 10.1093/gbe/evaf218
Anthony J Barley, David V Ho, Peter Baumann, Ian J Wang, H Bradley Shaffer, Robert N Fisher, Levi N Gray, Trevor J Krabbenhoft, Robert E Espinoza, Merly Escalona, Erin Toffelmier, Ruta Sahasrabudhe, Oanh Nguyen, Colin W Fairbairn, Eric Beraut, Robert C Thomson

The transition from small genetic to genome-scale datasets for studying biodiversity has revealed that genetic exchange through introgressive hybridization is a widespread phenomenon in nature. Despite this, a lack of high-quality reference genomes for most non-model species limits our understanding of the impact of this process for many taxonomic groups. This restricts the range of insights that genomic tools can provide for conservation biologists, who often hope to employ genomic datasets to accurately identify historically isolated lineages to protect and to predict their evolutionary fate in the face of environmental change. Tiger whiptail lizards (Aspidoscelis tigris complex) are an abundant and important ecological component of ecosystems across the southwestern United States. In this study, we assembled and annotated a chromosome-level reference genome for A. t. stejnegeri from coastal California. We then used this reference genome to reconstruct patterns of speciation and admixture within the larger species complex, finding evidence that gene flow is widespread both geographically and across the genome.

生物多样性研究从小型遗传数据到基因组数据的转变表明,通过渐进杂交进行的遗传交换是自然界中普遍存在的现象。尽管如此,缺乏大多数非模式物种的高质量参考基因组限制了我们对这一过程对许多分类群体的影响的理解。这限制了基因组工具可以为保护生物学家提供的见解范围,保护生物学家通常希望使用基因组数据集来准确识别历史上孤立的谱系,以保护和预测它们在面对环境变化时的进化命运。虎鞭尾蜥蜴(Aspidoscelis tigris complex)是美国西南部生态系统中丰富而重要的生态组成部分。在这项研究中,我们组装并注释了来自加利福尼亚沿海的a. t. stejnegeri染色体水平的参考基因组。然后,我们使用这个参考基因组来重建更大的物种复合体中的物种形成和混合模式,发现基因流动在地理上和整个基因组中都很广泛的证据。
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引用次数: 0
Acquisition of Spacers from Foreign Prokaryotic Genomes by CRISPR-Cas Systems in Natural Environments. 自然环境下CRISPR-Cas系统从外源原核生物基因组中获取间隔序列。
IF 2.8 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2025-10-29 DOI: 10.1093/gbe/evaf201
Katharina Sures, Sarah P Esser, Till L V Bornemann, Carrie J Moore, André R Soares, Julia Plewka, Perla Abigail Figueroa-Gonzalez, S Emil Ruff, Cristina Moraru, Alexander J Probst

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems of bacteria and archaea provide immunities against mobile genetic elements, like viruses. In addition, protospacer analyses revealed a very specific acquisition of CRISPR spacers derived from genomes of related species or from closely interacting episymbiont genomes as recently shown for subsurface archaea. However, the origin of most of the spacers that can be found in CRISPR-Cas systems from natural environments has not been deciphered. Here, by analyzing CRISPR-Cas systems of metagenome-assembled genomes (MAGs) from two subsurface environments spanning more than 1 Tb of sequencing data, we show that a substantial proportion of CRISPR spacers are acquired from DNA of other prokaryotes inhabiting the same environment. As such, we found that the number of respective spacers can be up to three times higher than the number of self-targeting spacers. Statistical analyses demonstrated that the acquisition of CRISPR spacers from other prokaryotic genomes is partly explained by the relative abundance of the MAG containing the protospacer, as well as by other factors, such as the total number of CRISPR arrays present in a MAG with the respective spacers. Further, we found that spacer acquisition from foreign prokaryotic DNA occurs in almost all types of CRISPR-Cas systems, but shows preferences for subtypes of CRISPR-Cas systems that differ across the investigated ecosystems. Taken together, our results shed new light on the diversity of CRISPR spacers in natural microbial communities and provide an explanation for some of the many unmatched spacers in public databases.

细菌和古细菌的聚集规律间隔短回文重复序列(CRISPR)和CRISPR相关(Cas)系统提供对移动遗传元素(如病毒)的免疫力。此外,原间隔物分析揭示了一种非常特定的CRISPR间隔物的获取,它来自于相关物种的基因组或密切相互作用的附生生物基因组,如最近在地下古细菌中显示的那样。然而,在自然环境中的CRISPR-Cas系统中发现的大多数间隔序列的起源尚未被破译。在这里,通过分析来自两个地下环境的宏基因组组装基因组(MAGs)的CRISPR- cas系统,跨越超过1tb的测序数据,我们发现相当大比例的CRISPR间隔序列来自居住在相同环境中的其他原核生物的DNA。因此,我们发现各自的间隔器的数量可能比自瞄准间隔器的数量高出三倍。统计分析表明,从其他原核生物基因组中获得CRISPR间隔片段的部分原因是含有原间隔片段的MAG的相对丰度,以及其他因素,例如含有相应间隔片段的MAG中存在的CRISPR阵列的总数。此外,研究人员发现,几乎所有类型的CRISPR-Cas系统中都存在来自外源原核DNA的间隔序列获取,但在不同的生态系统中,对CRISPR-Cas系统亚型的偏好有所不同。综上所述,我们的研究结果揭示了天然微生物群落中CRISPR间隔序列的多样性,并为公共数据库中许多不匹配的间隔序列提供了解释。
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引用次数: 0
The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity. 基因组万花筒:物种内基因组多样性的隐藏维度。
IF 2.8 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2025-10-29 DOI: 10.1093/gbe/evaf204
Marina Brasó-Vives, Diego A Hartasánchez, Julien F Ayroles, Christabel F Bucao, Mayra Furlan-Magaril, Paco Majic, Luisa F Pallares, James Phipps-Tan, Thea F Rogers, Aurora Ruiz-Herrera, Gabriela Santos-Rodriguez, Nikolas Vellnow, Justin J S Wilcox, Juan Antonio Rodríguez

Genomic diversity within species encompasses a range of sequence-related, structural, and regulatory features. To illustrate their complexity, we invoke the analogy of a kaleidoscope: while the DNA sequence represents its core, the genome has a dynamic, multidimensional configuration shaped by interactions across these features, generating an array of dimensions of genomic variation. In this perspective, we highlight underexplored dimensions of genomic variation that contribute to phenotypic diversity. We begin by revisiting the existence of noncanonical chromosomes and by emphasizing the role of large-scale structural changes and the 3D genome architecture in modulating genomic function. We then examine the regulatory mechanisms shaping transcriptional activity and genetic variation that, instead of regulating mean trait values, defines the degree of trait variability. Finally, we discuss the influence of sequence composition on its mutational potential. These dimensions, though rooted in sequence, are context dependent, interconnected, and often difficult to disentangle, reflecting a level of structural and regulatory complexity that challenges traditional genotype-phenotype models. By synthesizing recent findings across these dimensions, we argue for a broader framework for studying within-species genomic diversity: one that accounts for the diverse molecular architectures underlying phenotypic output. This expanded view not only deepens our knowledge of the genome itself but also contributes to our understanding of genome evolution and within-species phenotypic variation.

物种内的基因组多样性包括一系列序列相关、结构和调控特征。为了说明它们的复杂性,我们引用了万花筒的类比:当DNA序列代表其核心时,基因组具有动态的多维配置,这些配置由这些特征之间的相互作用形成,从而产生一系列基因组变异维度。从这个角度来看,我们强调了未充分探索的基因组变异维度,有助于表型多样性。我们首先回顾非典型染色体的存在,并强调大规模结构变化和3D基因组结构在调节基因组功能中的作用。然后,我们研究了塑造转录活性和遗传变异的调节机制,而不是调节平均性状值,定义性状变异性的程度。最后讨论了序列组成对其突变势的影响。尽管这些维度根植于序列,但它们依赖于环境,相互关联,并且通常难以解开,反映了对传统基因型-表型模型提出挑战的结构和调控复杂性。通过综合这些方面的最新发现,我们提出了一个更广泛的物种内基因组多样性研究框架:一个解释表型输出背后的不同分子结构的框架。这一扩展的观点不仅加深了我们对基因组本身的认识,而且有助于我们对基因组进化和种内表型变异的理解。
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引用次数: 0
Large Inversion Polymorphisms are Widespread in North American Songbirds. 大型倒置多态性在北美鸣禽中广泛存在。
IF 2.8 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2025-10-29 DOI: 10.1093/gbe/evaf205
Teresa M Pegan, Benjamin M Winger

The prevalence and evolutionary importance of inversion polymorphisms in natural populations is poorly known because of limited genome-wide sequence data availability for most species. Inversion studies in wild populations usually target rare cases of major trait polymorphisms or local adaptation whose genetic basis involves inversions, creating a strong impression that inversions in nature are generally maintained by natural selection through links to ecologically relevant phenotypes. By contrast, genome-wide studies in humans and model organisms suggest that inversion polymorphisms are common, subject to highly complex evolutionary processes, and generally difficult to link with clearly observable cases of phenotypic variation. Using a large comparative population genomic dataset generated from 35 codistributed species of birds, we tested the hypothesis that inversions are common even within populations that lack known phenotypic polymorphisms. We leveraged analytical methods suitable for low-coverage whole genome sequencing to reveal evidence for over 170 putative inversion polymorphisms within 28 species. We find that many polymorphisms are large and present at balanced frequencies, and some are shared across species boundaries. Yet, most polymorphisms do not deviate significantly from Hardy-Weinberg Equilibrium, raising the possibility that many of these massive haploblocks could be segregating neutrally. Our results thereby reveal evidence that inversions show a variety of complex yet largely hidden patterns in natural populations, beyond cases where they contribute to known variation in ecologically relevant traits.

由于大多数物种的全基因组序列数据有限,人们对自然种群中反转多态性的普遍性及其进化重要性知之甚少。野生种群的反转研究通常针对主要性状多态性或局部适应的罕见情况,其遗传基础涉及反转,从而产生一种强烈的印象,即自然界中的反转通常是通过与生态相关表型的联系通过自然选择维持的。相比之下,人类和模式生物的全基因组研究表明,倒置多态性是常见的,受高度复杂的进化过程的影响,通常难以与明显可观察到的表型变异病例联系起来。利用35种共分布鸟类的大型比较种群基因组数据集,我们验证了反转即使在缺乏已知表型多态性的种群中也很常见的假设。我们利用适合低覆盖率全基因组测序的分析方法,揭示了28个物种中170多个假定的倒置多态性的证据。我们发现许多多态性很大,存在于平衡的频率,有些是跨物种边界共享的。然而,大多数多态性并没有明显偏离Hardy-Weinberg平衡,这就提出了这样一种可能性,即许多巨大的单倍体可能是中性分离的。因此,我们的研究结果揭示了逆序在自然种群中显示出各种复杂但很大程度上隐藏的模式的证据,超出了它们对生态相关性状的已知变异的贡献。
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引用次数: 0
Episodic and Ongoing Mechanisms Drive Plastid-Derived Nuclear DNA Evolution in Angiosperms. 在被子植物中,偶发和持续的机制驱动质体衍生的核DNA进化。
IF 2.8 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2025-10-29 DOI: 10.1093/gbe/evaf194
Juan Pablo Marczuk-Rojas, Ana D Maldonado, Lorenzo Carretero-Paulet

NUPTs are DNA sequences of plastid origin that are present in plant nuclear genomes in varying, though typically low, amounts. It is assumed that they are continuously formed and, due to their potentially mutagenic effect, they are removed at a constant turnover rate, which should result in an exponential decay of their age distributions and a negative correlation between age and size. However, these assumptions are based on analyses from a limited number of species and have never been explicitly tested. To gain insight into the mechanisms driving the origin and evolution of NUPTs, here we surveyed the plastid and nuclear genomes of 30 species representing the main angiosperm (flowering plants) lineages. By modeling the distribution of ages and sizes, examining their linear arrangement across the plastid genome, and statistically assessing spatial biases with respect to other genomic features, we showed that NUPTs are: (i) formed by both continuous and episodic mechanisms; (ii) unevenly represented across the plastid genome; (iii) consistently associated with certain classes of RNA genes, in particular rRNA, tRNA, and regulatory RNA genes; (iv) differentially contributing to structural genes; and (v) closer than expected to different superfamilies of transposons in a species-specific manner. Our results reveal the unexpected complexity in the mechanisms driving the origin of NUPTs, which not only involve their continuous formation but also episodic events, highlight their role as a major source of noncoding RNA genes and other genomic features, and provide a more complete picture of the different drivers of evolutionary change at the genome level.

nupt是存在于植物核基因组中质体起源的DNA序列,虽然数量通常很低。假设它们是连续形成的,由于其潜在的诱变作用,它们以恒定的周转率被移除,这应该导致它们的年龄分布呈指数衰减,年龄与尺寸之间呈负相关。然而,这些假设是基于对有限物种的分析,从未经过明确的测试。为了深入了解nupt的起源和进化机制,我们调查了30种主要被子植物(开花植物)谱系的质体和核基因组。通过建模年龄和大小的分布,检查它们在质体基因组中的线性排列,并统计评估相对于其他基因组特征的空间偏差,我们发现nupt是由连续和偶发机制形成的;Ii)在质体基因组中不均匀分布;iii)始终与某些类别的RNA基因相关,特别是rRNA、tRNA和调控RNA基因;Iv)对结构基因的差异贡献;v)以物种特异性的方式与不同的转座子超家族更接近。我们的研究结果揭示了驱动nupt起源机制的意想不到的复杂性,这不仅涉及它们的连续形成,而且还涉及它们的偶发性,突出了它们作为非编码RNA基因和其他基因组特征的主要来源的作用,并提供了基因组水平上进化变化的不同驱动因素的更完整的图景。
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引用次数: 0
Whole-Genome Sequence of Potamopyrgus antipodarum-A Model System for the Maintenance of Sexual Reproduction-Reveals a Recent Whole-Genome Duplication. 一种维持有性生殖的模式系统——马铃薯的全基因组序列揭示了最近的全基因组重复。
IF 2.8 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2025-10-29 DOI: 10.1093/gbe/evaf192
Joseph Jalinsky, Kyle E McElroy, Joel Sharbrough, Laura Bankers, Peter D Fields, Chelsea Higgins, Cynthia Toll, Jeffrey L Boore, John M Logsdon, Maurine Neiman

Key unanswered questions in biology center on the causes, consequences, and maintenance of sexual reproduction ("sex"). Genome-driven processes are central to the evolutionary and genetic mechanisms inherent to sex, making genomic resources a fundamental part of answering these questions. We present the first genome assembly for a species that is uniquely well-suited for the study of (a)sex in nature, Potamopyrgus antipodarum. This New Zealand snail is unusual in featuring multiple separate transitions from obligately sexual to obligately asexual reproduction, leading to the coexistence of phenotypically similar sexual and asexual forms, a feature that is required to directly study the maintenance of sex. These separately derived asexual lineages constitute separate evolutionary experiments, providing a powerful means of characterizing how the absence of sex affects genome evolution. Our genome assembly provides critical steps toward understanding the causes and consequences of sex in this system and important resources for the rapidly growing P. antipodarum and molluscan genomics research community. In characterizing this genome, we uncovered unexpected evidence for a recent whole-genome duplication (WGD) in P. antipodarum. This discovery sets the stage for using P. antipodarum to evaluate processes of rediploidization following WGD and to assess whether WGD might drive transitions to asexuality.

生物学中未解决的关键问题集中在有性生殖(“性”)的原因、后果和维持上。基因组驱动的过程是性别固有的进化和遗传机制的核心,使基因组资源成为回答这些问题的基本部分。我们展示了一个物种的第一个基因组组装,这个物种非常适合研究自然界中的(a)性,Potamopyrgus antipodarum。这只新西兰蜗牛很不寻常,它具有从专一性生殖到专一无性生殖的多次独立转变,导致表型相似的有性和无性形式共存,这是直接研究性维持所必需的特征。这些单独衍生的无性谱系构成了单独的进化实验,为描述性的缺失如何影响基因组进化提供了有力的手段。我们的基因组组装为理解这一系统中性别的原因和后果提供了关键步骤,并为快速增长的反足弓形虫和软体动物基因组学研究界提供了重要资源。在表征这一基因组,我们发现了意想不到的证据,最近全基因组复制(WGD)在p.a antipodarum。这一发现为使用P. antipodarum来评估WGD后的再倍化过程以及评估WGD是否可能驱动向无性行为的转变奠定了基础。
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引用次数: 0
Covering All Bases: A Universal Metazoan UCE Probe Set to Democratize Phylogenomics. 覆盖所有的基础:一个通用的Metazoan UCE探针设置民主化系统基因组学。
IF 2.8 2区 生物学 Q2 EVOLUTIONARY BIOLOGY Pub Date : 2025-10-29 DOI: 10.1093/gbe/evaf193
Shahan Derkarabetian, Arianna Lord, Katherine Angier, Julia G Cosgrove, Ella Frigyik, Sara González-Delgado, Breanna Jordan, Paula C Rodríguez-Flores, Shoyo Sato, Lily Shapiro, Gonzalo Giribet

Biology is in a genomics era, but many researchers may still be alienated from these techniques as a lack of genomic resources remains for many animal groups, necessitating further democratization. Hybrid capture is a popular phylogenomic approach in molecular systematics, with ultraconserved elements being the most popular. However, access to ultraconserved element data is more expensive per sample relative to other commonly used genetic/genomic approaches. Using published genomes, we developed a metazoan ultraconserved element probe set, the universality of which allows multiple research groups working on vastly different animal lineages to share costs and resources across labs. We demonstrated the utility of this probe set both in silico against 58 published metazoan genomes and in vitro with 130 samples representing 33 metazoan phyla, showing that these probes target loci useful for both deep and shallow level relationships. The proportion of target ultraconserved elements sequenced by the Metazoa probe is equivalent to that of taxon-specific probe sets, but from across all animal phyla. We explored general patterns of ultraconserved element recovery across Metazoa using published genomes and the majority of publicly available ultraconserved element probe sets. The Metazoa probe set is available in three forms: the full set, containing 19,986 probes targeting 2,146 loci, a set containing 10,749 probes targeting 1,022 loci, and the reduced cost set, containing 5,098 probes targeting 466 loci. The development of a universal ultraconserved element probe set should expand the use of genomic data to a much larger segment of the zoological community, with strong potential for broad applications in phylogenomics across all animal phyla.

生物学正处于基因组学时代,但由于许多动物群体缺乏基因组资源,许多研究人员可能仍然与这些技术疏远,这需要进一步的民主化。混合捕获是分子系统学中一种流行的系统基因组学方法,其中超保守元件(UCEs)最为流行。然而,与其他常用的遗传/基因组方法相比,获取UCE数据的每个样本成本更高。利用已发表的基因组,我们开发了一套Metazoan UCE探针集,它的通用性允许多个研究小组在实验室中研究截然不同的动物谱系,共享成本和资源。我们证明了该探针集在计算机上对58个已发表的后生动物基因组和代表33个后生动物门的130个样本的体外效用,表明这些探针针对的位点对深层和浅层关系都有用。Metazoa探针测序的目标UCEs的比例与分类群特异性探针集的比例相当,但来自所有动物门。我们使用已发表的基因组和大多数公开可用的UCE探针集探索了跨后生动物的UCE恢复的一般模式。mettazoa探针集在商业上有两种形式:全套,包含19,986个探针,靶向2146个位点;而缩减后的成本集包含5098个探针,目标为466个位点。通用UCE探针集的开发应该将基因组数据的使用扩展到动物群落的更大部分,在所有动物门的系统基因组学中具有广泛应用的强大潜力。
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Genome Biology and Evolution
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