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Interconnected Codons: Unravelling the Epigenetic Significance of Flanking Sequences in CpG Dyads 相互连接的密码子:揭示 CpG Dyads 侧翼序列的表观遗传学意义
IF 3.9 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-04-18 DOI: 10.1007/s00239-024-10172-1
Leo Douglas Creasey, Eran Tauber

Hypothesizing that CpG codon dyads, formed by consecutive codons containing a cytosine-guanine pair (NNC-GNN), may play a crucial role in gene function, we conducted an extensive analysis to investigate their distribution and conservation within mammalian genes. Our findings reveal that genes characterized by a high density of CpG codon dyads are notably associated with homeobox domains and RNA polymerase II transcription factors. Conversely, genes exhibiting low CpG codon dyad density have links to DNA damage repair and mitosis. Importantly, our study identifies a re-markable increase in expressed genes that harbor CpG during embryonic development, suggesting their potential involvement in gene regulation at these developmental stages. These results under-score the functional significance of CpG codon dyads in DNA methylation and gene expression, fur-ther demonstrating the coevolution of consecutive codons and their contribution to codon usage bias.

我们推测,由含有一对胞嘧啶-鸟嘌呤(NNC-GNN)的连续密码子形成的 CpG 密码子二联体可能在基因功能中起着至关重要的作用,因此我们进行了广泛的分析,研究它们在哺乳动物基因中的分布和保存情况。我们的研究结果表明,CpG密码子二元对密度高的基因主要与同源染色体结构域和RNA聚合酶II转录因子有关。相反,CpG密码子二联体密度低的基因则与DNA损伤修复和有丝分裂有关。重要的是,我们的研究发现,在胚胎发育过程中,含有 CpG 的表达基因明显增加,这表明它们可能参与了这些发育阶段的基因调控。这些结果证明了 CpG 密码子二元对在 DNA 甲基化和基因表达中的功能意义,进一步证明了连续密码子的共同进化及其对密码子使用偏倚的贡献。
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引用次数: 0
Genomic Evidence for the Complex Evolutionary History of Macaques (Genus Macaca) 猕猴(猕猴属)复杂进化史的基因组证据
IF 3.9 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-04-18 DOI: 10.1007/s00239-024-10166-z
Zhenxin Fan, Rusong Zhang, Anbo Zhou, Jody Hey, Yang Song, Naoki Osada, Yuzuru Hamada, Bisong Yue, Jinchuan Xing, Jing Li

The genus Macaca is widely distributed, occupies a variety of habitats, shows diverse phenotypic characteristics, and is one of the best-studied genera of nonhuman primates. Here, we reported five re-sequencing Macaca genomes, including one M. cyclopis, one M. fuscata, one M. thibetana, one M. silenus, and one M. sylvanus. Together with published genomes of other macaque species, we combined 20 genome sequences of 10 macaque species to investigate the gene introgression and genetic differences among the species. The network analysis of the SNV-fragment trees indicates a reticular phylogeny of macaque species. Combining the results from various analytical methods, we identified extensive ancient introgression events among macaque species. The multiple introgression signals between different species groups were also observed, such as between fascicularis group species and silenus group species. However, gene flow signals between fascicularis and sinica group were not as strong as those between fascicularis group and silenus group. On the other hand, the unidirect gene flow in M. arctoides probably occurred between the progenitor of M. arctoides and the common ancestor of fascicularis group. Our study also shows that the genetic backgrounds and genetic diversity of different macaques vary dramatically among species, even among populations of the same species. In conclusion, using whole genome sequences and multiple methods, we have studied the evolutionary history of the genus Macaca and provided evidence for extensive introgression among the species.

猕猴属分布广泛,栖息地多样,表现出多种多样的表型特征,是研究最深入的非人灵长类之一。在这里,我们报告了五个重新测序的猕猴基因组,包括一个M. cyclopis、一个M. fuscata、一个M. thibetana、一个M. silenus和一个M. sylvanus。结合已发表的其他猕猴物种的基因组序列,我们对10个猕猴物种的20个基因组序列进行了整合,以研究物种间的基因导入和遗传差异。SNV片段树的网络分析表明,猕猴物种之间存在网状系统发育关系。结合各种分析方法的结果,我们发现了猕猴物种间广泛的古老的基因导入事件。我们还观察到了不同种群之间的多重引种信号,例如在fascicularis种群和silenus种群之间。然而,猕猴群与猕猴群之间的基因流动信号不如猕猴群与猕猴群之间的信号强烈。另一方面,M. arctoides 的单向基因流动可能发生在 M. arctoides 的祖先与 fascicularis 群的共同祖先之间。我们的研究还表明,不同猕猴的遗传背景和遗传多样性在不同物种之间,甚至在同一物种的不同种群之间都存在巨大差异。总之,我们利用全基因组序列和多种方法研究了猕猴属的进化史,并提供了物种间广泛的引种的证据。
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引用次数: 0
Multiple Ecological Axes Drive Molecular Evolution of Cone Opsins in Beloniform Fishes. 多种生态轴驱动贝龙鱼锥形眼色素的分子进化
IF 3.9 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-04-01 Epub Date: 2024-02-28 DOI: 10.1007/s00239-024-10156-1
Katherine D Chau, Frances E Hauser, Alexander Van Nynatten, Jacob M Daane, Matthew P Harris, Belinda S W Chang, Nathan R Lovejoy

Ecological and evolutionary transitions offer an excellent opportunity to examine the molecular basis of adaptation. Fishes of the order Beloniformes include needlefishes, flyingfishes, halfbeaks, and allies, and comprise over 200 species occupying a wide array of habitats-from the marine epipelagic zone to tropical rainforest rivers. These fishes also exhibit a diversity of diets, including piscivory, herbivory, and zooplanktivory. We investigated how diet and habitat affected the molecular evolution of cone opsins, which play a key role in bright light and colour vision and are tightly linked to ecology and life history. We analyzed a targeted-capture dataset to reconstruct the evolutionary history of beloniforms and assemble cone opsin sequences. We implemented codon-based clade models of evolution to examine how molecular evolution was affected by habitat and diet. We found high levels of positive selection in medium- and long-wavelength beloniform opsins, with piscivores showing increased positive selection in medium-wavelength opsins and zooplanktivores showing increased positive selection in long-wavelength opsins. In contrast, short-wavelength opsins showed purifying selection. While marine/freshwater habitat transitions have an effect on opsin molecular evolution, we found that diet plays a more important role. Our study suggests that evolutionary transitions along ecological axes produce complex adaptive interactions that affect patterns of selection on genes that underlie vision.

生态和进化转变为研究适应的分子基础提供了绝佳的机会。贝龙目(Beloniformes)鱼类包括针鱼、飞鱼、半喙鱼和同类,共有 200 多个物种,栖息地广泛,从海洋上层到热带雨林河流。这些鱼类的食性也多种多样,包括鱼食、草食和浮游动物食。我们研究了饮食和栖息地如何影响锥体视蛋白的分子进化,锥体视蛋白在强光和色彩视觉中发挥着关键作用,并且与生态学和生活史密切相关。我们分析了一个定向捕获数据集,以重建白头翁的进化史并组装锥体视蛋白序列。我们采用基于密码子的进化支系模型来研究分子进化如何受到栖息地和饮食的影响。我们发现中波长和长波长的褐腹带动物视蛋白中存在高水平的正选择,食鱼动物在中波长视蛋白中的正选择增加,而浮游动物在长波长视蛋白中的正选择增加。相反,短波长蛋白则表现出净化选择。虽然海洋/淡水栖息地的转换会影响光学蛋白的分子进化,但我们发现饮食在其中扮演了更重要的角色。我们的研究表明,沿生态轴的进化转变会产生复杂的适应性相互作用,从而影响视觉基础基因的选择模式。
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引用次数: 0
Frustration can Limit the Adaptation of Promiscuous Enzymes Through Gene Duplication and Specialisation. 挫折可通过基因复制和特化限制杂合酶的适应性
IF 3.9 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-04-01 Epub Date: 2024-03-12 DOI: 10.1007/s00239-024-10161-4
Michael Schmutzer, Pouria Dasmeh, Andreas Wagner

Virtually all enzymes catalyse more than one reaction, a phenomenon known as enzyme promiscuity. It is unclear whether promiscuous enzymes are more often generalists that catalyse multiple reactions at similar rates or specialists that catalyse one reaction much more efficiently than other reactions. In addition, the factors that shape whether an enzyme evolves to be a generalist or a specialist are poorly understood. To address these questions, we follow a three-pronged approach. First, we examine the distribution of promiscuity in empirical enzymes reported in the BRENDA database. We find that the promiscuity distribution of empirical enzymes is bimodal. In other words, a large fraction of promiscuous enzymes are either generalists or specialists, with few intermediates. Second, we demonstrate that enzyme biophysics is not sufficient to explain this bimodal distribution. Third, we devise a constraint-based model of promiscuous enzymes undergoing duplication and facing selection pressures favouring subfunctionalization. The model posits the existence of constraints between the catalytic efficiencies of an enzyme for different reactions and is inspired by empirical case studies. The promiscuity distribution predicted by our constraint-based model is consistent with the empirical bimodal distribution. Our results suggest that subfunctionalization is possible and beneficial only in certain enzymes. Furthermore, the model predicts that conflicting constraints and selection pressures can cause promiscuous enzymes to enter a 'frustrated' state, in which competing interactions limit the specialisation of enzymes. We find that frustration can be both a driver and an inhibitor of enzyme evolution by duplication and subfunctionalization. In addition, our model predicts that frustration becomes more likely as enzymes catalyse more reactions, implying that natural selection may prefer catalytically simple enzymes. In sum, our results suggest that frustration may play an important role in enzyme evolution.

几乎所有酶都能催化一种以上的反应,这种现象被称为酶的杂交性。目前还不清楚的是,杂合酶通常是以类似速度催化多种反应的通才,还是催化一种反应比催化其他反应更有效的专才。此外,人们对影响酶进化为通性酶还是专性酶的因素也知之甚少。为了解决这些问题,我们采取了三管齐下的方法。首先,我们研究了BRENDA数据库中报告的经验酶的杂合性分布。我们发现,经验酶的杂交分布是双峰的。换句话说,很大一部分滥交酶要么是通才,要么是专才,中间体很少。其次,我们证明酶的生物物理学不足以解释这种双峰分布。第三,我们设计了一个基于约束的模型,说明杂合酶正在经历复制,并面临有利于亚功能化的选择压力。该模型假定酶对不同反应的催化效率之间存在约束,其灵感来自经验案例研究。我们基于约束的模型预测的杂交分布与经验中的双峰分布一致。我们的结果表明,亚功能化是可能的,而且只对某些酶有益。此外,该模型还预测,相互冲突的约束和选择压力会导致滥交的酶进入 "受挫 "状态,在这种状态下,相互竞争的相互作用限制了酶的专业化。我们发现,"受挫 "既是酶通过复制和亚功能化进化的驱动力,也是其抑制因素。此外,我们的模型预测,随着酶催化更多反应,挫折变得更有可能发生,这意味着自然选择可能更倾向于催化简单的酶。总之,我们的研究结果表明,挫折可能在酶的进化中扮演重要角色。
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引用次数: 0
Cyanobacterial Genomes from a Brackish Coastal Lagoon Reveal Potential for Novel Biogeochemical Functions and Their Evolution. 来自咸水海岸泻湖的蓝藻基因组揭示了新的生物地球化学功能及其进化的潜力。
IF 3.9 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-04-01 Epub Date: 2024-03-15 DOI: 10.1007/s00239-024-10159-y
Manisha Ray, Shivakumara Manu, Gurdeep Rastogi, Govindhaswamy Umapathy

Cyanobacteria are recognised for their pivotal roles in aquatic ecosystems, serving as primary producers and major agents in diazotrophic processes. Currently, the primary focus of cyanobacterial research lies in gaining a more detailed understanding of these well-established ecosystem functions. However, their involvement and impact on other crucial biogeochemical cycles remain understudied. This knowledge gap is partially attributed to the challenges associated with culturing cyanobacteria in controlled laboratory conditions and the limited understanding of their specific growth requirements. This can be circumvented partially by the culture-independent methods which can shed light on the genomic potential of cyanobacterial species and answer more profound questions about the evolution of other key biogeochemical functions. In this study, we assembled 83 cyanobacterial genomes from metagenomic data generated from environmental DNA extracted from a brackish water lagoon (Chilika Lake, India). We taxonomically classified these metagenome-assembled genomes (MAGs) and found that about 92.77% of them are novel genomes at the species level. We then annotated these cyanobacterial MAGs for all the encoded functions using KEGG Orthology. Interestingly, we found two previously unreported functions in Cyanobacteria, namely, DNRA (Dissimilatory Nitrate Reduction to Ammonium) and DMSP (Dimethylsulfoniopropionate) synthesis in multiple MAGs using nirBD and dsyB genes as markers. We validated their presence in several publicly available cyanobacterial isolate genomes. Further, we identified incongruities between the evolutionary patterns of species and the marker genes and elucidated the underlying reasons for these discrepancies. This study expands our overall comprehension of the contribution of cyanobacteria to the biogeochemical cycling in coastal brackish ecosystems.

蓝藻在水生生态系统中发挥着举足轻重的作用,既是初级生产者,也是重氮过程中的主要媒介。目前,蓝藻研究的主要重点在于更详细地了解蓝藻的这些既定生态系统功能。然而,蓝藻对其他重要生物地球化学循环的参与和影响仍未得到充分研究。造成这一知识空白的部分原因是在受控实验室条件下培养蓝藻所面临的挑战,以及对蓝藻特定生长要求的了解有限。而独立于培养的方法可以部分解决这一问题,这种方法可以揭示蓝藻物种的基因组潜力,并回答有关其他关键生物地球化学功能进化的更深层次问题。在这项研究中,我们根据从咸水湖(印度奇利卡湖)提取的环境 DNA 生成的元基因组数据,组装了 83 个蓝藻基因组。我们对这些元基因组组装的基因组(MAGs)进行了分类,发现其中约 92.77% 是物种水平的新基因组。然后,我们利用 KEGG 正选法对这些蓝藻 MAGs 的所有编码功能进行了注释。有趣的是,我们以 nirBD 和 dsyB 基因为标记,在多个 MAGs 中发现了两种以前未在蓝藻中报道过的功能,即 DNRA(将硝酸盐还原成铵)和 DMSP(二甲基硫代丙酸盐)合成。我们在几个公开的蓝藻分离基因组中验证了它们的存在。此外,我们还发现了物种进化模式与标记基因之间的不一致性,并阐明了造成这些差异的根本原因。这项研究拓展了我们对蓝藻在沿海咸水生态系统生物地球化学循环中所作贡献的整体理解。
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引用次数: 0
GC Content Across Insect Genomes: Phylogenetic Patterns, Causes and Consequences. 昆虫基因组中的 GC 含量:系统发育模式、原因和后果。
IF 2.1 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-04-01 Epub Date: 2024-03-15 DOI: 10.1007/s00239-024-10160-5
Riccardo G Kyriacou, Peter O Mulhair, Peter W H Holland

The proportions of A:T and G:C nucleotide pairs are often unequal and can vary greatly between animal species and along chromosomes. The causes and consequences of this variation are incompletely understood. The recent release of high-quality genome sequences from the Darwin Tree of Life and other large-scale genome projects provides an opportunity for GC heterogeneity to be compared across a large number of insect species. Here we analyse GC content along chromosomes, and within protein-coding genes and codons, of 150 insect species from four holometabolous orders: Coleoptera, Diptera, Hymenoptera, and Lepidoptera. We find that protein-coding sequences have higher GC content than the genome average, and that Lepidoptera generally have higher GC content than the other three insect orders examined. GC content is higher in small chromosomes in most Lepidoptera species, but this pattern is less consistent in other orders. GC content also increases towards subtelomeric regions within protein-coding genes in Diptera, Coleoptera and Lepidoptera. Two species of Diptera, Bombylius major and B. discolor, have very atypical genomes with ubiquitous increase in AT content, especially at third codon positions. Despite dramatic AT-biased codon usage, we find no evidence that this has driven divergent protein evolution. We argue that the GC landscape of Lepidoptera, Diptera and Coleoptera genomes is influenced by GC-biased gene conversion, strongest in Lepidoptera, with some outlier taxa affected drastically by counteracting processes.

A:T和G:C核苷酸对的比例通常是不相等的,而且在动物物种之间和染色体上会有很大差异。这种变异的原因和后果尚不完全清楚。最近,达尔文生命之树和其他大规模基因组项目发布了高质量的基因组序列,这为比较大量昆虫物种的 GC 异质性提供了机会。在这里,我们分析了来自四个全代谢目 150 个昆虫物种的染色体、蛋白质编码基因和密码子中的 GC 含量:鞘翅目、双翅目、膜翅目和鳞翅目。我们发现蛋白质编码序列的 GC 含量高于基因组的平均水平,而鳞翅目昆虫的 GC 含量普遍高于其他三个昆虫目。在大多数鳞翅目物种中,小染色体中的 GC 含量较高,但这一模式在其他目中不太一致。在双翅目、鞘翅目和鳞翅目中,GC 含量也向蛋白编码基因的次基因组区域增加。双翅目的两个物种--Bombylius major 和 B. discolor--的基因组非常不典型,AT 含量普遍增加,尤其是在第三密码子位置。尽管AT偏倚的密码子使用率很高,但我们没有发现任何证据表明这推动了蛋白质的分化进化。我们认为,鳞翅目、双翅目和鞘翅目昆虫基因组的 GC 分布受 GC 偏向基因转换的影响,其中以鳞翅目的影响最大,而一些离群类群则受到反作用过程的严重影响。
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引用次数: 0
Evolution of Transcript Abundance is Influenced by Indels in Protein Low Complexity Regions. 转录本丰度的进化受蛋白质低复杂性区段中吲哚基因的影响
IF 3.9 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-04-01 Epub Date: 2024-03-14 DOI: 10.1007/s00239-024-10158-z
Zachery W Dickson, G Brian Golding

Protein Protein low complexity regions (LCRs) are compositionally biased amino acid sequences, many of which have significant evolutionary impacts on the proteins which contain them. They are mutationally unstable experiencing higher rates of indels and substitutions than higher complexity regions. LCRs also impact the expression of their proteins, likely through multiple effects along the path from gene transcription, through translation, and eventual protein degradation. It has been observed that proteins which contain LCRs are associated with elevated transcript abundance (TAb), despite having lower protein abundance. We have gathered and integrated human data to investigate the co-evolution of TAb and LCRs through ancestral reconstructions and model inference using an approximate Bayesian calculation based method. We observe that on short evolutionary timescales TAb evolution is significantly impacted by changes in LCR length, with insertions driving TAb down. But in contrast, the observed data is best explained by indel rates in LCRs which are unaffected by shifts in TAb. Our work demonstrates a coupling between LCR and TAb evolution, and the utility of incorporating multiple responses into evolutionary analyses.

蛋白质 蛋白质低复杂性区域(LCR)是氨基酸序列的组成偏差,其中许多对包含它们的蛋白质的进化有重大影响。与复杂度较高的区域相比,低复杂度区域具有突变不稳定性,发生嵌合和置换的比率较高。LCR 还会影响其蛋白质的表达,这可能是通过基因转录、翻译和最终蛋白质降解过程中的多重影响实现的。据观察,尽管蛋白质丰度较低,但含有 LCR 的蛋白质与转录本丰度(TAb)升高有关。我们收集并整合了人类数据,利用基于近似贝叶斯计算的方法,通过祖先重建和模型推断,研究了TAb和LCR的共同进化。我们观察到,在短进化时间尺度上,TAb 的进化受到 LCR 长度变化的显著影响,插入会导致 TAb 下降。但与此相反,观察到的数据最好用 LCR 中的吲哚率来解释,而 LCR 中的吲哚率不受 TAb 变化的影响。我们的工作证明了 LCR 和 TAb 进化之间的耦合关系,以及将多种反应纳入进化分析的实用性。
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引用次数: 0
Assembly Theory: What It Does and What It Does Not Do. 装配理论:它能做什么,不能做什么。
IF 2.1 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-04-01 Epub Date: 2024-03-07 DOI: 10.1007/s00239-024-10163-2
Johannes Jaeger

A recent publication in Nature has generated much heated discussion about evolution, its tendency towards increasing diversity and complexity, and its potential status above and beyond the known laws of fundamental physics. The argument at the heart of this controversy concerns assembly theory, a method to detect and quantify the influence of higher-level emergent causal constraints in computational worlds made of basic objects and their combinations. In this short essay, I briefly review the theory, its basic principles and potential applications. I then go on to critically examine its authors' assertions, concluding that assembly theory has merit but is not nearly as novel or revolutionary as claimed. It certainly does not provide any new explanation of biological evolution or natural selection, or a new grounding of biology in physics. In this regard, the presentation of the paper is starkly distorted by hype, which may explain some of the outrage it created.

自然》(Nature)杂志最近发表的一篇文章引起了人们对进化、进化的多样性和复杂性趋势以及进化超越已知基础物理定律的潜在地位的热烈讨论。这场争论的核心涉及组装理论,这是一种在由基本物体及其组合构成的计算世界中检测和量化高层次突发因果约束影响的方法。在这篇短文中,我将简要回顾该理论及其基本原理和潜在应用。然后,我将批判性地审视其作者的论断,最后得出结论:装配理论有其可取之处,但并不像所宣称的那样新颖或具有革命性。当然,它并没有为生物进化或自然选择提供任何新的解释,也没有为物理学中的生物学提供新的基础。在这方面,该论文的表述明显被炒作所扭曲,这也许是它引起愤怒的部分原因。
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引用次数: 0
Extant Sequence Reconstruction: The Accuracy of Ancestral Sequence Reconstructions Evaluated by Extant Sequence Cross-Validation 外源序列重建:通过外源序列交叉验证评估祖先序列重建的准确性
IF 3.9 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-03-19 DOI: 10.1007/s00239-024-10162-3
Michael A. Sennett, Douglas L. Theobald

Ancestral sequence reconstruction (ASR) is a phylogenetic method widely used to analyze the properties of ancient biomolecules and to elucidate mechanisms of molecular evolution. Despite its increasingly widespread application, the accuracy of ASR is currently unknown, as it is generally impossible to compare resurrected proteins to the true ancestors. Which evolutionary models are best for ASR? How accurate are the resulting inferences? Here we answer these questions using a cross-validation method to reconstruct each extant sequence in an alignment with ASR methodology, a method we term “extant sequence reconstruction” (ESR). We thus can evaluate the accuracy of ASR methodology by comparing ESR reconstructions to the corresponding known true sequences. We find that a common measure of the quality of a reconstructed sequence, the average probability, is indeed a good estimate of the fraction of correct amino acids when the evolutionary model is accurate or overparameterized. However, the average probability is a poor measure for comparing reconstructions from different models, because, surprisingly, a more accurate phylogenetic model often results in reconstructions with lower probability. While better (more predictive) models may produce reconstructions with lower sequence identity to the true sequences, better models nevertheless produce reconstructions that are more biophysically similar to true ancestors. In addition, we find that a large fraction of sequences sampled from the reconstruction distribution may have fewer errors than the single most probable (SMP) sequence reconstruction, despite the fact that the SMP has the lowest expected error of all possible sequences. Our results emphasize the importance of model selection for ASR and the usefulness of sampling sequence reconstructions for analyzing ancestral protein properties. ESR is a powerful method for validating the evolutionary models used for ASR and can be applied in practice to any phylogenetic analysis of real biological sequences. Most significantly, ESR uses ASR methodology to provide a general method by which the biophysical properties of resurrected proteins can be compared to the properties of the true protein.

祖先序列重建(ASR)是一种系统发生学方法,广泛用于分析古代生物大分子的特性和阐明分子进化机制。尽管ASR的应用越来越广泛,但其准确性目前尚不清楚,因为通常无法将复活的蛋白质与真正的祖先进行比较。哪种进化模型最适合 ASR?由此得出的推论准确度如何?在这里,我们用交叉验证的方法来回答这些问题,用 ASR 方法重建排列中的每个现存序列,我们称这种方法为 "现存序列重建"(ESR)。因此,我们可以通过比较 ESR 重建与相应的已知真实序列来评估 ASR 方法的准确性。我们发现,在进化模型准确或过度参数化的情况下,衡量重建序列质量的常用指标--平均概率,确实是对正确氨基酸比例的良好估计。然而,在比较不同模型的重建结果时,平均概率并不是一个好的衡量标准,因为令人惊讶的是,更准确的系统进化模型往往会导致重建结果的概率更低。虽然更好(更具预测性)的模型可能会产生与真实序列具有较低序列同一性的重建结果,但更好的模型所产生的重建结果在生物物理上与真实祖先更为相似。此外,我们还发现,从重建分布中采样的大部分序列可能比单一最可能(SMP)序列重建的误差更小,尽管事实上 SMP 在所有可能序列中具有最低的预期误差。我们的研究结果强调了模型选择对 ASR 的重要性,以及取样序列重建对分析祖先蛋白质特性的有用性。ESR 是验证 ASR 所用进化模型的有力方法,可实际应用于任何真实生物序列的系统发育分析。最重要的是,ESR 利用 ASR 方法提供了一种通用方法,可将复活蛋白质的生物物理特性与真实蛋白质的特性进行比较。
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引用次数: 0
Speciation Features of Ferdinandcohnia quinoae sp. nov to Adapt to the Plant Host Ferdinandcohnia quinoae sp.
IF 3.9 3区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-03-19 DOI: 10.1007/s00239-024-10164-1

Abstract

The bacterial strain SECRCQ15T was isolated from seeds of Chenopodium quinoa in Spain. Phylogenetic, chemotaxonomic, and phenotypic analyses, as well as genome similarity indices, support the classification of the strain into a novel species of the genus Ferdinandcohnia, for which we propose the name Ferdinandcohnia quinoae sp. nov. To dig deep into the speciation features of the strain SECRCQ15T, we performed a comparative genomic analysis of the genome of this strain and those of the type strains of species from the genus Ferdinandcohnia. We found several genes related with plant growth-promoting mechanisms within the SECRCQ15T genome. We also found that singletons of F. quinoae SECRCQ15T are mainly related to the use of carbohydrates, which is a common trait of plant-associated bacteria. To further reveal speciation events in this strain, we revealed genes undergoing diversifying selection (e.g., genes encoding ribosomal proteins) and functions likely lost due to pseudogenization. Also, we found that this novel species contains 138 plant-associated gene-cluster functions that are unique within the genus Ferdinandcohnia. These features may explain both the ecological and taxonomical differentiation of this new taxon.

摘要 从西班牙的藜麦种子中分离出了细菌菌株 SECRCQ15T。系统发生学、化学分类学和表型分析以及基因组相似性指数都支持将该菌株归类为费迪南德氏菌属的一个新种,我们将其命名为费迪南德氏菌藜属新种(Ferdinandcohnia quinoae sp.nov)。为了深入研究 SECRCQ15T 菌株的物种分化特征,我们对该菌株的基因组和 Ferdinandcohnia 属物种的模式菌株的基因组进行了比较基因组分析。我们在 SECRCQ15T 基因组中发现了几个与植物生长促进机制有关的基因。我们还发现,F. quinoae SECRCQ15T 的单子主要与碳水化合物的利用有关,这是植物相关细菌的共同特征。为了进一步揭示该菌株的物种分化事件,我们揭示了正在经历多样化选择的基因(如编码核糖体蛋白的基因)以及可能因假基因化而丧失的功能。此外,我们还发现该新物种含有 138 个植物相关基因簇功能,这在费迪南德梭菌属中是独一无二的。这些特征可能解释了这一新类群在生态学和分类学上的分化。
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引用次数: 0
期刊
Journal of Molecular Evolution
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