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Chrysalis: decoding tissue compartments in spatial transcriptomics with archetypal analysis. 蛹:利用原型分析解码空间转录组学中的组织区划。
IF 5.2 1区 生物学 Q1 BIOLOGY Pub Date : 2024-11-16 DOI: 10.1038/s42003-024-07165-7
Demeter Túrós, Jelica Vasiljevic, Kerstin Hahn, Sven Rottenberg, Alberto Valdeolivas

Dissecting tissue compartments in spatial transcriptomics (ST) remains challenging due to limited spatial resolution and dependence on single-cell reference data. We present Chrysalis, a computational method that rapidly uncovers tissue compartments through spatially variable gene (SVG) detection and archetypal analysis without requiring external reference data. Additionally, it offers a unique visualisation approach for swift tissue characterisation and provides access to the underlying gene expression signatures, enabling the identification of spatially and functionally distinct cellular niches. Chrysalis was evaluated through various benchmarks and validated against deconvolution, independently obtained cell type abundance data, and histopathological annotations, demonstrating superior performance compared to other algorithms on both in silico and real-world test examples. Furthermore, we showcased its versatility across different technologies, such as Visium, Visium HD, Slide-seq, and Stereo-seq.

由于空间分辨率有限且依赖于单细胞参考数据,在空间转录组学(ST)中剖析组织区系仍然具有挑战性。我们介绍的 Chrysalis 是一种计算方法,可通过空间可变基因 (SVG) 检测和原型分析快速揭示组织区系,而无需外部参考数据。此外,它还提供了一种独特的可视化方法,用于快速组织特征描述,并提供了对潜在基因表达特征的访问,从而能够识别空间和功能上不同的细胞壁龛。我们通过各种基准对 Chrysalis 进行了评估,并根据解卷积、独立获得的细胞类型丰度数据和组织病理学注释进行了验证,结果表明 Chrysalis 在硅学和真实世界测试示例中的性能均优于其他算法。此外,我们还展示了它在 Visium、Visium HD、Slide-seq 和 Stereo-seq 等不同技术上的通用性。
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引用次数: 0
NuSAP4 regulates chromosome segregation in Trypanosoma brucei by promoting bipolar spindle assembly. NuSAP4 通过促进双极纺锤体的组装来调节布氏锥虫的染色体分离。
IF 5.2 1区 生物学 Q1 BIOLOGY Pub Date : 2024-11-16 DOI: 10.1038/s42003-024-07248-5
Qing Zhou, Ziyin Li

Faithful chromosome segregation in eukaryotes requires the assembly of a bipolar spindle and the faithful attachment of kinetochores to spindle microtubules, which are regulated by various spindle-associated proteins (SAPs) that play distinct functions in regulating spindle dynamics and microtubule-kinetochore attachment. The protozoan parasite Trypanosoma brucei employs evolutionarily conserved and kinetoplastid-specific proteins, including some kinetoplastid-specific nucleus- and spindle-associated proteins (NuSAPs), to regulate chromosome segregation. Here, we characterized NuSAP4 and its functional interplay with diverse SAPs in promoting chromosome segregation in T. brucei. NuSAP4 associates with the spindle during mitosis and concentrates at spindle poles where it interacts with SPB1 and MAP103. Knockdown of NuSAP4 impairs chromosome segregation by disrupting bipolar spindle assembly and spindle pole protein localization. These results uncover the mechanistic role of NuSAP4 in regulating chromosome segregation by promoting bipolar spindle assembly, and highlight the unusual features of mitotic regulation by spindle-associated proteins in this early divergent microbial eukaryote.

真核生物染色体的忠实分离需要双极纺锤体的组装以及动点系与纺锤体微管的忠实附着,而这些都受到各种纺锤体相关蛋白(SAP)的调控,这些蛋白在调控纺锤体动力学和微管-动点系附着方面发挥着不同的功能。原生动物布氏锥虫(Trypanosoma brucei)利用进化保守和动点细胞特异性蛋白(包括一些动点细胞特异性细胞核和纺锤体相关蛋白(NuSAPs))来调节染色体分离。在这里,我们对 NuSAP4 及其在促进布氏原虫染色体分离过程中与多种 SAP 的功能相互作用进行了表征。NuSAP4 在有丝分裂过程中与纺锤体结合,并集中在纺锤体两极,与 SPB1 和 MAP103 相互作用。通过破坏双极纺锤体组装和纺锤极蛋白定位,敲除NuSAP4会影响染色体分离。这些结果揭示了NuSAP4通过促进双极纺锤体组装来调节染色体分离的机制作用,并突出了这种早期分化的微生物真核细胞中纺锤体相关蛋白对有丝分裂调节的不寻常特征。
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引用次数: 0
Uncovering disease-related multicellular pathway modules on large-scale single-cell transcriptomes with scPAFA. 利用 scPAFA 在大规模单细胞转录组上发现与疾病相关的多细胞通路模块。
IF 5.2 1区 生物学 Q1 BIOLOGY Pub Date : 2024-11-16 DOI: 10.1038/s42003-024-07238-7
Zhuoli Huang, Yuhui Zheng, Weikai Wang, Wenwen Zhou, Yanbo Zhang, Chen Wei, Xiuqing Zhang, Xin Jin, Jianhua Yin

Pathway analysis is a crucial analytical phase in disease research on single-cell RNA sequencing (scRNA-seq) data, offering biological interpretations based on prior knowledge. However, currently available tools for generating cell-level pathway activity scores (PAS) exhibit computational inefficacy in large-scale scRNA-seq datasets. Additionally, disease-related pathways are often identified through cross-condition comparisons within specific cell types, overlooking potential patterns that involve multiple cell types. Here, we present single-cell pathway activity factor analysis (scPAFA), a Python library designed for large-scale single-cell datasets allowing rapid PAS computation and uncovering biologically interpretable disease-related multicellular pathway modules, which are low-dimensional representations of disease-related PAS alterations in multiple cell types. Application on colorectal cancer (CRC) datasets and large-scale lupus atlas over 1.2 million cells demonstrated that scPAFA can achieve over 40-fold reductions in the runtime of PAS computation and further identified reliable and interpretable multicellular pathway modules that capture the heterogeneity of CRC and transcriptional abnormalities in lupus patients, respectively. Overall, scPAFA presents a valuable addition to existing research tools in disease research, with the potential to reveal complex disease mechanisms and support biomarker discovery at the pathway level.

通路分析是单细胞 RNA 测序(scRNA-seq)数据疾病研究中的一个关键分析阶段,它能根据先前的知识提供生物学解释。然而,目前可用来生成细胞级通路活性评分(PAS)的工具在大规模 scRNA-seq 数据集中表现出计算效率低下的问题。此外,疾病相关通路通常是通过特定细胞类型内的跨条件比较来确定的,忽略了涉及多种细胞类型的潜在模式。在这里,我们介绍了单细胞通路活性因子分析(scPAFA),这是一个专为大规模单细胞数据集设计的 Python 库,可以快速计算 PAS 并发现可从生物学角度解释的疾病相关多细胞通路模块,这些模块是多种细胞类型中疾病相关 PAS 改变的低维表示。在结直肠癌(CRC)数据集和超过120万个细胞的大规模狼疮图谱上的应用表明,scPAFA能将PAS计算的运行时间缩短40倍以上,并进一步确定了可靠且可解释的多细胞通路模块,这些模块分别捕捉了CRC和狼疮患者转录异常的异质性。总之,scPAFA 是对现有疾病研究工具的宝贵补充,有望揭示复杂的疾病机制,支持通路水平的生物标记物发现。
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引用次数: 0
Transactivation of the novel 5' cis-acting element of mouse mammary tumor virus (MMTV) by human retroviral transactivators Tat and Tax. 人类逆转录病毒转录因子 Tat 和 Tax 对小鼠乳腺肿瘤病毒 (MMTV) 新型 5' 顺式作用元件的转录激活。
IF 5.2 1区 生物学 Q1 BIOLOGY Pub Date : 2024-11-16 DOI: 10.1038/s42003-024-07139-9
Thanumol Abdul Khader, Waqar Ahmad, Shaima Akhlaq, Neena Gopinathan Panicker, Bushra Gull, Jasmin Baby, Tahir A Rizvi, Farah Mustafa

The mouse mammary tumor virus (MMTV) encodes a 5' element crucial for transcription of its genome along with the Rem/Rem-responsive element (RmRE) responsible for nuclear export of this unspliced RNA. Whether the 5' element is Rem-responsive or has any functional interaction with host/viral factors to facilitate MMTV gene expression was tested in this study. Our results reveal that the 5' element is non-responsive to Rem, but can be transactivated by both HIV Tat and HTLV-1 Tax activators. Reciprocally, MMTV could transactivate not only HIV TAR (similar to HTLV Tax), but also its 5' element. Furthermore, we reveal involvement of pTEFb, a general elongation factor associated with transactivation by Tat/Tax. This makes MMTV the first betaretrovirus to encode both Rem/RRE and Tat/TAR-Tax/TRE-like transcription regulatory systems. This study should enhance not only our understanding of retrovirus replication and virally-induced cancers/immunodeficiency syndromes, but also development of improved retroviral vectors for human gene therapy.

小鼠乳腺肿瘤病毒(MMTV)编码一个对其基因组转录至关重要的 5'元件,以及负责将这种未剪接 RNA 核输出的 Rem/Rem 反应元件(RmRE)。本研究测试了该 5' 元是否具有雷姆响应性,或是否与宿主/病毒因子有任何功能上的相互作用,以促进 MMTV 基因的表达。我们的研究结果表明,5'元件对 Rem 无反应,但可被 HIV Tat 和 HTLV-1 Tax 激活因子转录。反过来,MMTV 不仅能反式激活 HIV TAR(类似于 HTLV Tax),还能反式激活其 5' 元。此外,我们还发现了 pTEFb 的参与,这是一种与 Tat/Tax 的转录活化相关的通用延伸因子。这使 MMTV 成为第一个同时编码 Rem/RRE 和 Tat/TAR-Tax/TRE 类转录调控系统的 betaretrovirus。这项研究不仅加深了我们对逆转录病毒复制和病毒诱导的癌症/免疫缺陷综合征的了解,还有助于开发用于人类基因治疗的改良型逆转录病毒载体。
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引用次数: 0
Mapping cellular stress and lipid dysregulation in Alzheimer-related progressive neurodegeneration using label-free Raman microscopy 利用无标记拉曼显微镜绘制阿尔茨海默氏症相关进行性神经变性的细胞应激和脂质失调图谱
IF 5.2 1区 生物学 Q1 BIOLOGY Pub Date : 2024-11-15 DOI: 10.1038/s42003-024-07182-6
Annika Haessler, Michael Candlish, Jasmin K. Hefendehl, Nathalie Jung, Maike Windbergs
Aβ plaques are a main feature of Alzheimer’s disease, and pathological alterations especially in their microenvironment have recently come into focus. However, a holistic imaging approach unveiling these changes and their biochemical nature is still lacking. In this context, we leverage confocal Raman microscopy as unbiased tool for non-destructive, label-free differentiation of progressive biomolecular changes in the Aβ plaque microenvironment in brain tissue of a murine model of cerebral amyloidosis. By developing a detailed approach, overcoming many challenges of chemical imaging, we identify spatially-resolved molecular signatures of disease-associated structures. Specifically, our study reveals nuclear condensation, indicating cellular degeneration, and increased levels of cytochrome c, showing mitochondrial dysfunction, in the vicinity of Aβ plaques. Further, we observe severe accumulation of especially unsaturated lipids. Thus, our study contributes to a comprehensive understanding of disease progression in the Aβ plaque microenvironment, underscoring the prospective of Raman imaging in neurodegenerative disorder research. Multivariate analysis of hyperspectral Raman imaging data unveils severe cellular toxicity and lipid dysregulation in the chemically complex Aβ plaque microenvironment.
Aβ 斑块是阿尔茨海默病的一个主要特征,其病理改变,尤其是其微环境的改变最近已成为关注的焦点。然而,揭示这些变化及其生化性质的整体成像方法仍然缺乏。在此背景下,我们利用共焦拉曼显微镜这一无偏见的工具,对脑部淀粉样变性模型鼠脑组织中 Aβ 斑块微环境中的渐进式生物分子变化进行无损、无标记的分化。通过开发一种详细的方法,克服了化学成像的许多挑战,我们确定了疾病相关结构的空间分辨分子特征。具体来说,我们的研究揭示了 Aβ 斑块附近细胞核的凝结(表明细胞变性)和细胞色素 c 水平的升高(表明线粒体功能障碍)。此外,我们还观察到特别是不饱和脂质的严重积累。因此,我们的研究有助于全面了解 Aβ 斑块微环境中的疾病进展,凸显了拉曼成像在神经退行性疾病研究中的前景。高光谱拉曼成像数据的多变量分析揭示了化学性质复杂的 Aβ 斑块微环境中严重的细胞毒性和脂质失调。
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引用次数: 0
Age-dependent cerebral vasodilation induced by volatile anesthetics is mediated by NG2+ vascular mural cells 挥发性麻醉剂诱导的年龄依赖性脑血管扩张是由 NG2+ 血管壁细胞介导的。
IF 5.2 1区 生物学 Q1 BIOLOGY Pub Date : 2024-11-15 DOI: 10.1038/s42003-024-07200-7
Hang Zhou, Viola Neudecker, Jose F. Perez-Zoghbi, Ansgar M. Brambrink, Guang Yang
Anesthesia can influence cerebral blood flow by altering vessel diameter. Using in vivo two-photon imaging, we examined the effects of volatile anesthetics, sevoflurane and isoflurane, on vessel diameter in young and adult mice. Our results show that these anesthetics induce robust dilation of cortical arterioles and arteriole-proximate capillaries in adult mice, with milder effects in juveniles and no dilation in infants. This anesthesia-induced vasodilation correlates with decreased cytosolic Ca2+ levels in NG2+ vascular mural cells. Optogenetic manipulation of these cells bidirectionally regulates vessel diameter, and their ablation abolishes the vasodilatory response to anesthetics. In immature brains, NG2+ mural cells are fewer in number and express lower levels of Kir6.1, a subunit of ATP-sensitive potassium channels. This likely contributes to the age-dependent differences in vasodilation, as Kir6.1 activation promotes, while its inhibition reduces, anesthesia-induced vasodilation. These findings highlight the essential role of NG2+ mural cells in mediating anesthesia-induced cerebral vasodilation. Live animal imaging reveals age-dependent cerebral vasodilatory responses to volatile anesthetics, pronounced in adult mice and diminished or absent in developing brains. These effects are mediated by NG2+ mural cells and Kir6.1 signaling.
麻醉可通过改变血管直径来影响脑血流量。我们利用体内双光子成像技术研究了挥发性麻醉剂七氟醚和异氟醚对幼鼠和成年小鼠血管直径的影响。我们的研究结果表明,这些麻醉剂可诱导成年小鼠皮层动脉和动脉近端毛细血管的强烈扩张,对幼鼠的影响较小,而对婴儿则没有扩张作用。这种麻醉诱导的血管扩张与 NG2+ 血管壁细胞的细胞质 Ca2+ 水平下降有关。对这些细胞进行光遗传学操作可双向调节血管直径,而对它们的消减则可消除对麻醉剂的血管扩张反应。在未成熟的大脑中,NG2+ 壁细胞数量较少,表达的 ATP 敏感钾通道亚基 Kir6.1 水平较低。这可能是造成血管扩张的年龄依赖性差异的原因,因为Kir6.1的激活会促进麻醉诱导的血管扩张,而抑制则会减少这种扩张。这些发现凸显了 NG2+ 壁细胞在介导麻醉诱导的脑血管扩张中的重要作用。
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引用次数: 0
Effects of climate and forest development on habitat specialization and biodiversity in Central European mountain forests. 气候和森林发展对中欧山区森林生境专业化和生物多样性的影响。
IF 5.2 1区 生物学 Q1 BIOLOGY Pub Date : 2024-11-15 DOI: 10.1038/s42003-024-07239-6
Tobias Richter, Lisa Geres, Sebastian König, Kristin H Braziunas, Cornelius Senf, Dominik Thom, Claus Bässler, Jörg Müller, Rupert Seidl, Sebastian Seibold

Mountain forests are biodiversity hotspots with competing hypotheses proposed to explain elevational trends in habitat specialization and species richness. The altitudinal-niche-breadth hypothesis suggests decreasing specialization with elevation, which could lead to decreasing species richness and weaker differences in species richness and beta diversity among habitat types with increasing elevation. Testing these predictions for bacteria, fungi, plants, arthropods, and vertebrates, we found decreasing habitat specialization (represented by forest developmental stages) with elevation in mountain forests of the Northern Alps - supporting the altitudinal-niche-breadth hypothesis. Species richness decreased with elevation only for arthropods, whereas changes in beta diversity varied among taxa. Along the forest developmental gradient, species richness mainly followed a U-shaped pattern which remained stable along elevation. This highlights the importance of early and late developmental stages for biodiversity and indicates that climate change may alter community composition not only through distributional shifts along elevation but also across forest developmental stages.

山地森林是生物多样性的热点地区,为解释栖息地专业化和物种丰富度的海拔变化趋势,人们提出了一些相互竞争的假说。海拔-小群-广度假说认为,随着海拔的升高,专业化程度会降低,这可能会导致物种丰富度降低,并且随着海拔的升高,栖息地类型之间物种丰富度和贝塔多样性的差异也会减弱。通过对细菌、真菌、植物、节肢动物和脊椎动物进行测试,我们发现在北阿尔卑斯山的山地森林中,随着海拔的升高,栖息地的专业化程度(以森林发育阶段为代表)也在降低--这支持了海拔-小范围假说。只有节肢动物的物种丰富度随海拔升高而降低,而不同类群的贝塔多样性变化各不相同。在森林发育梯度上,物种丰富度主要呈 "U "型,并随着海拔的升高而保持稳定。这凸显了早期和晚期发育阶段对生物多样性的重要性,并表明气候变化不仅会通过海拔高度的分布变化改变群落组成,也会改变不同森林发育阶段的群落组成。
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引用次数: 0
Feeding postures as indicators of mutable collagenous tissue in extinct echinoderms. 作为已灭绝棘皮动物可变异胶原组织指标的进食姿势。
IF 5.2 1区 生物学 Q1 BIOLOGY Pub Date : 2024-11-15 DOI: 10.1038/s42003-024-07232-z
Johnny A Waters, Jan Bohatý, D Bradford Macurda

Echinoderms are a diverse phylum with a rich fossil record. The five extant classes of echinoderms are characterised by a pentameral (or pseudo-pentameral) symmetry, a water vascular system, a mesodermal skeleton of calcite stereom, and Mutable Collagenous Tissue (MCT), a unique type of connective tissue. Difficulties in tracing the geologic history of these traits complicates phylogenetic analyses of echinoderms. We present evidence herein of MCT in an extinct class of echinoderms, the Blastoidea. Blastoids have composite hair-like structures, brachioles, which formed a feeding filtration fan. Rare specimens from the Devonian of Germany demonstrate the presence of MCT by preserving brachioles as long rigid structures making a feeding fan with MCT in a rigid state. Specimens show brachioles in different configurations in the same specimen, which may indicate nervous control of MCT in individual brachioles. Other specimens appear to indicate the transition of MCT from a rigid to a compliant state as rigid brachioles begin to curve. Still other specimens show a majority of brachioles as limp hair-like structures swept by currents while a minority of brachioles remain rigid. These remarkable specimens could capture MCT transitioning from its rigid to compliant states in individual specimens indicating rapid burial and preservation.

棘皮动物门种类繁多,化石记录丰富。现存的五类棘皮动物具有五体(或假五体)对称、水脉管系统、方解石立体中胚层骨骼以及独特的结缔组织--可变胶原组织(MCT)等特征。由于难以追溯这些特征的地质历史,棘皮动物的系统发育分析变得非常复杂。我们在本文中提出了已灭绝的棘皮动物类--Blastoidea--中MCT的证据。Blastoids具有类似毛发的复合结构--腕管,它形成了一个进食过滤扇。来自德国泥盆纪的罕见标本证明了 MCT 的存在,其保留的腕管是长条形的刚性结构,形成了一个具有 MCT 的刚性进食扇。标本显示,同一标本中的肱骨具有不同的构造,这可能表明单个肱骨中的 MCT 受神经控制。其他标本似乎表明,随着僵硬的肱管开始弯曲,MCT 从僵硬状态过渡到顺从状态。还有一些标本显示,大部分腕管是被水流卷起的软毛状结构,而少数腕管仍然保持刚性。这些非凡的标本可以捕捉到单个标本中的 MCT 从僵硬状态向顺从状态过渡的过程,这表明埋藏和保存的速度很快。
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引用次数: 0
Rapid and objective assessment of auditory temporal processing using dynamic amplitude-modulated stimuli. 利用动态振幅调制刺激对听觉时间处理进行快速客观的评估。
IF 5.2 1区 生物学 Q1 BIOLOGY Pub Date : 2024-11-15 DOI: 10.1038/s42003-024-07187-1
Satyabrata Parida, Kimberly Yurasits, Victoria E Cancel, Maggie E Zink, Claire Mitchell, Meredith C Ziliak, Audrey V Harrison, Edward L Bartlett, Aravindakshan Parthasarathy

Current tests of hearing fail to diagnose pathologies in ~10% of patients seeking help for hearing difficulties. Neural ensemble responses to perceptually relevant cues in the amplitude envelope, termed envelope following responses (EFR), hold promise as an objective diagnostic tool to probe these 'hidden' hearing difficulties. But clinical translation is impeded by current measurement approaches involving static amplitude modulated (AM) tones, which are time-consuming and lack optimal spectrotemporal resolution. Here we develop a framework to rapidly measure EFRs using dynamically varying AMs combined with spectrally specific analyses. These analyses offer 5x improvement in time and 30x improvement in spectrotemporal resolution, and more generally, are optimal for analyzing time-varying signals with known spectral trajectories of interest. We validate this approach across several mammalian species, including humans, and demonstrate robust responses that are highly correlated with traditional static EFRs. Our analytic technique facilitates rapid and objective neural assessment of temporal processing throughout the brain that can be applied to track auditory neurodegeneration using EFRs, as well as tracking recovery after therapeutic interventions.

在因听力困难而寻求帮助的患者中,目前的听力测试无法诊断出约 10% 的病症。对振幅包络中感知相关线索的神经集合反应,即包络跟随反应(EFR),有望成为探查这些 "隐性 "听力障碍的客观诊断工具。但是,由于目前的测量方法涉及静态调幅(AM)音调,既耗时又缺乏最佳的谱时分辨率,因此临床应用受到阻碍。在此,我们开发了一个框架,利用动态变化的调幅音结合特定频谱分析快速测量 EFR。这些分析在时间上提高了 5 倍,在光谱时间分辨率上提高了 30 倍,而且更普遍的是,它们是分析具有已知感兴趣光谱轨迹的时变信号的最佳方法。我们在包括人类在内的多个哺乳动物物种中验证了这种方法,并展示了与传统静态 EFR 高度相关的强大响应。我们的分析技术有助于对整个大脑的时间处理过程进行快速、客观的神经评估,可用于使用 EFRs 跟踪听觉神经变性,以及跟踪治疗干预后的恢复情况。
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引用次数: 0
Phased chromosome-level genome provides insights into the molecular adaptation for migratory lifestyle and population diversity for Pacific saury, Cololabis saira 分阶段染色体级基因组为太平洋秋刀鱼(Cololabis saira)迁徙生活方式的分子适应和种群多样性提供了见解。
IF 5.2 1区 生物学 Q1 BIOLOGY Pub Date : 2024-11-15 DOI: 10.1038/s42003-024-07126-0
Yang Liu, Yanping Luo, Penghao Wang, Wenjia Li, Hao Tian, Chang Cao, Zhiqiang Ye, Hongan Long, Tongtong Lin, Shengjun Wang, Xiaohui Yuan, Shijun Xiao, Yoshiro Watanabe, Yongjun Tian
The Pacific saury (Cololabis saira) is a pelagic fish commonly found in the North Pacific Ocean. Its population diversity and migratory lifestyle have long captured global attention. Despite the inherent complexity of the C. saira genome, characterized by extremely high heterozygosity, we successfully assembled a phased chromosome-level genome. The genome analysis revealed the expansion and natural selection of numerous functional genes, likely contributing to its enduring and extensive migratory lifestyle. Notably, gpr35 and igh genes showed significant expansion in the C. saira genome, potentially associated with regulating the immune response against environmental parasites and pathogens. Moreover, genes involved in DNA repair/replication and peroxisome function, including atm, ercc6, pex14, and pex16, displayed evidence of positive selection. Based on genome-sequencing of 80 individuals from eight sampling sites, we demonstrated that the genomic divergence among C. saira populations is relatively low. However, the sampling sites could be grouped into two distinct clusters, roughly corresponding to the migratory route of C. saira. This suggests a possible genome-wide divergence for C. saira within the open ocean region. Furthermore, the trmu gene, responsible for controlling otolith development and sharpness, exhibited differentiation between the two groups, consistent with previously reported differences in otolith morphology. This study has provided a reference genome and insights into the evolution, ecology, and conservation of Pacific saury and closely-related species. Phased chromosome-level genome provides insights into the molecular adaptation for enduring and extensive migratory lifestyle and population diversity for Pacific saury.
太平洋秋刀鱼(Cololabis saira)是一种常见于北太平洋的中上层鱼类。长期以来,它的种群多样性和洄游生活方式一直吸引着全球的目光。尽管太平洋秋刀鱼基因组本身非常复杂,杂合度极高,但我们还是成功地组装了一个分阶段的染色体级基因组。基因组分析揭示了大量功能基因的扩增和自然选择,这可能是其持久而广泛的迁徙生活方式的原因。值得注意的是,gpr35 和 igh 基因在 C. saira 基因组中有显著扩增,可能与调节对环境寄生虫和病原体的免疫反应有关。此外,参与 DNA 修复/复制和过氧物酶体功能的基因,包括 atm、ercc6、pex14 和 pex16,也显示出正选择的证据。通过对来自八个采样点的 80 个个体进行基因组测序,我们发现赛拉蛙种群间的基因组差异相对较小。然而,采样点可分为两个不同的群组,大致与 C. saira 的迁徙路线相对应。这表明在公海区域内,西拉鱼可能存在全基因组的分化。此外,负责控制耳石发育和尖锐度的 trmu 基因在两组之间表现出分化,这与之前报道的耳石形态差异一致。这项研究为太平洋秋刀鱼及其近缘物种的进化、生态学和保护提供了参考基因组和见解。
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引用次数: 0
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Communications Biology
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