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m6A Profile Dynamics Indicates Regulation of Oyster Development by m6A-RNA Epitranscriptomes. m6A基因谱动态表明m6A- rna表转录组对牡蛎发育的调控。
IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-08-01 Epub Date: 2022-12-07 DOI: 10.1016/j.gpb.2022.12.002
Lorane Le Franc, Bruno Petton, Pascal Favrel, Guillaume Rivière

The N6-methylation of RNA adenosines (N6-methyladenosine, m6A) is an important regulator of gene expression with critical implications in vertebrate and insect development. However, the developmental significance of epitranscriptomes in lophotrochozoan organisms remains unknown. Using methylated RNA immunoprecipitation sequencing (MeRIP-seq), we generated transcriptome-wide m6A-RNA methylomes covering the entire development of the oyster from oocytes to juveniles. Oyster RNA classes display specific m6A signatures, with messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) exhibiting distinct profiles and being highly methylated compared to transposable element (TE) transcripts. Epitranscriptomes are dynamic and correspond to the chronological steps of development (cleavage, gastrulation, organogenesis, and metamorphosis), with minimal mRNA and lncRNA methylation at the morula stage followed by a global increase. mRNA m6A levels are correlated with transcript levels, and shifts in methylation profiles correspond to expression kinetics. Differentially methylated transcripts cluster according to embryo-larval stages and bear the corresponding developmental functions (cell division, signal transduction, morphogenesis, and cell differentiation). The m6A level of TE transcripts is also regulated and peaks during the gastrulation. We demonstrate that m6A-RNA methylomes are dynamic and associated with gene expression regulation during oyster development. The putative epitranscriptome implication in the cleavage, maternal-to-zygotic transition, and cell differentiation in a lophotrochozoan model brings new insights into the control and evolution of developmental processes.

RNA腺苷的n6甲基化(n6 - methylladenosine, m6A)是一个重要的基因表达调控因子,在脊椎动物和昆虫的发育中具有重要意义。然而,表转录组在光藻生物中的发育意义尚不清楚。使用甲基化RNA免疫沉淀测序(MeRIP-seq),我们生成了转录组范围内的m6A-RNA甲基组,涵盖了牡蛎从卵母细胞到幼体的整个发育过程。牡蛎RNA类显示出特定的m6A特征,信使RNA (mrna)和长链非编码RNA (lncRNAs)表现出不同的特征,与转座因子(TE)转录物相比,它们被高度甲基化。表观转录组是动态的,与发育的时间顺序步骤(卵裂、原肠胚形成、器官发生和变态)相对应,在桑葚胚阶段mRNA和lncRNA甲基化最小,随后全球增加。mRNA m6A水平与转录物水平相关,甲基化谱的变化对应于表达动力学。差异甲基化转录物根据胚胎-幼虫阶段聚集,并承担相应的发育功能(细胞分裂、信号转导、形态发生和细胞分化)。TE转录本的m6A水平也受到调控,并在原肠胚形成期间达到峰值。我们证明了m6A-RNA甲基组是动态的,并与牡蛎发育过程中的基因表达调控有关。在光合动物模型中,表观转录组在卵裂、母系到合子的转变和细胞分化中的潜在意义为发育过程的控制和进化提供了新的见解。
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引用次数: 0
The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers. 人类癌症中功能性A-to-I RNA编辑事件的综合研究。
IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-06-01 Epub Date: 2023-01-25 DOI: 10.1016/j.gpb.2022.12.010
Sijia Wu, Zhiwei Fan, Pora Kim, Liyu Huang, Xiaobo Zhou

Adenosine-to-inosine (A-to-I) RNA editing, constituting nearly 90% of all RNA editing events in humans, has been reported to contribute to the tumorigenesis in diverse cancers. However, the comprehensive map for functional A-to-I RNA editing events in cancers is still insufficient. To fill this gap, we systematically and intensively analyzed multiple tumorigenic mechanisms of A-to-I RNA editing events in samples across 33 cancer types from The Cancer Genome Atlas. For individual candidate among ∼ 1,500,000 quantified RNA editing events, we performed diverse types of downstream functional annotations. Finally, we identified 24,236 potentially functional A-to-I RNA editing events, including the cases in APOL1, IGFBP3, GRIA2, BLCAP, and miR-589-3p. These events might play crucial roles in the scenarios of tumorigenesis, due to their tumor-related editing frequencies or probable effects on altered expression profiles, protein functions, splicing patterns, and microRNA regulations of tumor genes. Our functional A-to-I RNA editing events (https://ccsm.uth.edu/CAeditome/) will help better understand the cancer pathology from the A-to-I RNA editing aspect.

腺苷到肌苷(A-to-I)RNA编辑占人类所有RNA编辑事件的近90%,据报道有助于多种癌症的肿瘤发生。然而,癌症中功能性A-to-I RNA编辑事件的全面图谱仍然不足。为了填补这一空白,我们系统深入地分析了癌症基因组图谱中33种癌症类型样本中A-To-I RNA编辑事件的多种致瘤机制。对于约1500000个定量RNA编辑事件中的单个候选者,我们进行了不同类型的下游功能注释。最后,我们确定了24236个潜在的功能性A-to-I RNA编辑事件,包括APOL1、IGFBP3、GRIA2、BLCAP和miR-589-3p中的病例。这些事件可能在肿瘤发生的场景中发挥关键作用,因为它们与肿瘤相关的编辑频率或可能对肿瘤基因的表达谱、蛋白质功能、剪接模式和微小RNA调节的改变产生影响。我们的功能性A-to-I RNA编辑活动(https://ccsm.uth.edu/CAeditome/)将有助于从A-to-I RNA编辑方面更好地理解癌症病理学。
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引用次数: 0
Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities. 新发现的转录本编码潜力揭示了人类蛋白质群落的缺失成员。
IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-06-01 Epub Date: 2022-09-30 DOI: 10.1016/j.gpb.2022.09.008
Sébastien Leblanc, Marie A Brunet, Jean-François Jacques, Amina M Lekehal, Andréa Duclos, Alexia Tremblay, Alexis Bruggeman-Gascon, Sondos Samandi, Mylène Brunelle, Alan A Cohen, Michelle S Scott, Xavier Roucou

Recent proteogenomic approaches have led to the discovery that regions of the transcriptome previously annotated as non-coding regions [i.e., untranslated regions (UTRs), open reading frames overlapping annotated coding sequences in a different reading frame, and non-coding RNAs] frequently encode proteins, termed alternative proteins (altProts). This suggests that previously identified protein-protein interaction (PPI) networks are partially incomplete because altProts are not present in conventional protein databases. Here, we used the proteogenomic resource OpenProt and a combined spectrum- and peptide-centric analysis for the re-analysis of a high-throughput human network proteomics dataset, thereby revealing the presence of 261 altProts in the network. We found 19 genes encoding both an annotated (reference) and an alternative protein interacting with each other. Of the 117 altProts encoded by pseudogenes, 38 are direct interactors of reference proteins encoded by their respective parental genes. Finally, we experimentally validate several interactions involving altProts. These data improve the blueprints of the human PPI network and suggest functional roles for hundreds of altProts.

最近的蛋白质基因组学方法发现,转录组先前被注释为非编码区(即非翻译区(utr),在不同的阅读框中重叠注释编码序列的开放阅读框和非编码rna)的区域经常编码蛋白质,称为替代蛋白质(altProts)。这表明先前确定的蛋白质-蛋白质相互作用(PPI)网络部分不完整,因为altProts不存在于传统的蛋白质数据库中。在这里,我们使用蛋白质基因组资源OpenProt和结合的以光谱和肽为中心的分析对高通量人类网络蛋白质组学数据集进行重新分析,从而揭示了网络中261个altProts的存在。我们发现19个基因编码一个注释(参考)和一个替代蛋白相互作用。在假基因编码的117个altProts中,38个是亲本基因编码的参比蛋白的直接相互作用物。最后,我们通过实验验证了几个涉及altProts的交互作用。这些数据改进了人类PPI网络的蓝图,并建议了数百个altProts的功能角色。
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引用次数: 0
The First Crested Duck Genome Reveals Clues to Genetic Compensation and Crest Cushion Formation. 第一个鸭冠基因组揭示了遗传补偿和冠垫形成的线索。
IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-06-01 Epub Date: 2023-08-29 DOI: 10.1016/j.gpb.2023.08.002
Guobin Chang, Xiaoya Yuan, Qixin Guo, Hao Bai, Xiaofang Cao, Meng Liu, Zhixiu Wang, Bichun Li, Shasha Wang, Yong Jiang, Zhiquan Wang, Yang Zhang, Qi Xu, Qianqian Song, Rui Pan, Lingling Qiu, Tiantian Gu, Xinsheng Wu, Yulin Bi, Zhengfeng Cao, Yu Zhang, Yang Chen, Hong Li, Jianfeng Liu, Wangcheng Dai, Guohong Chen

The Chinese crested (CC) duck is a unique indigenous waterfowl breed, which has a crest cushion that affects its survival rate. Therefore, the CC duck is an ideal model to investigate the genetic compensation response to maintain genetic stability. In the present study, we first generated a chromosome-level genome of CC ducks. Comparative genomics revealed that genes related to tissue repair, immune function, and tumors were under strong positive selection, indicating that these adaptive changes might enhance cancer resistance and immune response to maintain the genetic stability of CC ducks. We also assembled a Chinese spot-billed (Csp-b) duck genome, and detected the structural variations (SVs) in the genome assemblies of three ducks (i.e., CC duck, Csp-b duck, and Peking duck). Functional analysis revealed that several SVs were related to the immune system of CC ducks, further strongly suggesting that genetic compensation in the anti-tumor and immune systems supports the survival of CC ducks. Moreover, we confirmed that the CC duck originated from the mallard ducks. Finally, we revealed the physiological and genetic basis of crest traits and identified a causative mutation in TAS2R40 that leads to crest formation. Overall, the findings of this study provide new insights into the role of genetic compensation in adaptive evolution.

中华凤头鸭是一种独特的本土水禽品种,其羽冠垫影响其成活率。因此,CC鸭是研究遗传补偿反应以保持遗传稳定性的理想模型。在本研究中,我们首先生成了CC鸭的染色体水平基因组。比较基因组学显示,与组织修复、免疫功能和肿瘤相关的基因处于强阳性选择下,表明这些适应性变化可能增强癌症抵抗力和免疫反应,以维持CC鸭的遗传稳定性。我们还组装了中国斑嘴鸭(Csp-b)基因组,并检测了三种鸭(即CC鸭、Csp-b鸭和北京鸭)基因组组装中的结构变异。功能分析表明,几种SV与CC鸭的免疫系统有关,这进一步有力地表明,抗肿瘤和免疫系统中的基因补偿支持CC鸭的生存。此外,我们确认CC鸭源自绿头鸭。最后,我们揭示了嵴性状的生理和遗传基础,并在TAS2R40中鉴定了一个导致嵴形成的致病突变。总的来说,这项研究的发现为遗传补偿在适应性进化中的作用提供了新的见解。
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引用次数: 0
CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network. CNEReg通过发育基因调控网络解释反刍动物特有的保守非编码元件。
IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-06-01 Epub Date: 2022-12-07 DOI: 10.1016/j.gpb.2022.11.007
Xiangyu Pan, Zhaoxia Ma, Xinqi Sun, Hui Li, Tingting Zhang, Chen Zhao, Nini Wang, Rasmus Heller, Wing Hung Wong, Wen Wang, Yu Jiang, Yong Wang

The genetic information coded in DNA leads to trait innovation via a gene regulatory network (GRN) in development. Here, we developed a conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network (CNEReg) to investigate the ruminant multi-chambered stomach innovation. We generated paired expression and chromatin accessibility data during rumen and esophagus development in sheep, and revealed 1601 active ruminant-specific conserved non-coding elements (active-RSCNEs). To interpret the function of these active-RSCNEs, we defined toolkit transcription factors (TTFs) and modeled their regulation on rumen-specific genes via batteries of active-RSCNEs during development. Our developmental GRN revealed 18 TTFs and 313 active-RSCNEs regulating 7 rumen functional modules. Notably, 6 TTFs (OTX1, SOX21, HOXC8, SOX2, TP63, and PPARG), as well as 16 active-RSCNEs, functionally distinguished the rumen from the esophagus. Our study provides a systematic approach to understanding how gene regulation evolves and shapes complex traits by putting evo-devo concepts into practice with developmental multi-omics data.

DNA编码的遗传信息在发育过程中通过基因调控网络(GRN)引导性状创新。在此,我们开发了一种保守的非编码元件解释方法,将多组学数据整合到基因调控网络(gene regulatory network, CNEReg)中,以研究反刍动物多室胃创新。我们生成了绵羊瘤胃和食道发育过程中的配对表达和染色质可及性数据,并揭示了1601个活跃的反刍动物特异性保守非编码元件(active- rscnes)。为了解释这些活性- rscnes的功能,我们定义了工具包转录因子(ttf),并在发育过程中通过活性- rscnes细胞模拟了它们对瘤胃特异性基因的调控。我们的发育GRN发现18个ttf和313个活性rscnes调节7个瘤胃功能模块。值得注意的是,6个ttf (OTX1、SOX21、HOXC8、SOX2、TP63和PPARG)以及16个活性rscnes在功能上区分了瘤胃和食管。我们的研究提供了一种系统的方法来理解基因调控是如何进化和塑造复杂性状的,通过将进化-发展概念与发育多组学数据相结合。
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引用次数: 0
stAPAminer: Mining Spatial Patterns of Alternative Polyadenylation for Spatially Resolved Transcriptomic Studies. stAPAminer:为空间解析转录组学研究挖掘选择性聚腺苷化的空间模式。
IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-06-01 Epub Date: 2023-01-18 DOI: 10.1016/j.gpb.2023.01.003
Guoli Ji, Qi Tang, Sheng Zhu, Junyi Zhu, Pengchao Ye, Shuting Xia, Xiaohui Wu

Alternative polyadenylation (APA) contributes to transcriptome complexity and gene expression regulation and has been implicated in various cellular processes and diseases. Single-cell RNA sequencing (scRNA-seq) has enabled the profiling of APA at the single-cell level; however, the spatial information of cells is not preserved in scRNA-seq. Alternatively, spatial transcriptomics (ST) technologies provide opportunities to decipher the spatial context of the transcriptomic landscape. Pioneering studies have revealed potential spatially variable genes and/or splice isoforms; however, the pattern of APA usage in spatial contexts remains unappreciated. In this study, we developed a toolkit called stAPAminer for mining spatial patterns of APA from spatially barcoded ST data. APA sites were identified and quantified from the ST data. In particular, an imputation model based on the k-nearest neighbors algorithm was designed to recover APA signals, and then APA genes with spatial patterns of APA usage variation were identified. By analyzing well-established ST data of the mouse olfactory bulb (MOB), we presented a detailed view of spatial APA usage across morphological layers of the MOB. We compiled a comprehensive list of genes with spatial APA dynamics and obtained several major spatial expression patterns that represent spatial APA dynamics in different morphological layers. By extending this analysis to two additional replicates of the MOB ST data, we observed that the spatial APA patterns of several genes were reproducible among replicates. stAPAminer employs the power of ST to explore the transcriptional atlas of spatial APA patterns with spatial resolution. This toolkit is available at https://github.com/BMILAB/stAPAminer and https://ngdc.cncb.ac.cn/biocode/tools/BT007320.

选择性多腺苷酸化(APA)有助于转录组的复杂性和基因表达调控,并与各种细胞过程和疾病有关。单细胞RNA测序(scRNA-seq)使APA能够在单细胞水平上进行分析;然而,细胞的空间信息并没有保存在scRNA-seq中。或者,空间转录组学(ST)技术提供了破译转录组学景观的空间背景的机会。开拓性研究揭示了潜在的空间可变基因和/或剪接异构体;然而,APA在空间语境中的使用模式仍然没有得到重视。在这项研究中,我们开发了一个名为stAPAminer的工具包,用于从空间条形码ST数据中挖掘APA的空间模式。APA位点从ST数据中进行鉴定和定量。特别是,设计了一个基于k近邻算法的插补模型来恢复APA信号,然后识别出具有APA使用变异空间模式的APA基因。通过分析小鼠嗅球(MOB)的成熟ST数据,我们提供了跨MOB形态层的空间APA使用的详细视图。我们编制了一份具有空间APA动力学的基因的综合列表,并获得了几个主要的空间表达模式,这些模式代表了不同形态层中的空间APA动态。通过将该分析扩展到MOB ST数据的另外两个重复,我们观察到几个基因的空间APA模式在重复中是可重复的。stAPAminer利用ST的力量以空间分辨率探索空间APA模式的转录图谱。此工具包位于https://github.com/BMILAB/stAPAminer和https://ngdc.cncb.ac.cn/biocode/tools/BT007320.
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引用次数: 0
Recent Advances in Assembly of Complex Plant Genomes. 植物复杂基因组组装的最新进展。
IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-06-01 Epub Date: 2023-04-25 DOI: 10.1016/j.gpb.2023.04.004
Weilong Kong, Yibin Wang, Shengcheng Zhang, Jiaxin Yu, Xingtan Zhang

Over the past 20 years, tremendous advances in sequencing technologies and computational algorithms have spurred plant genomic research into a thriving era with hundreds of genomes decoded already, ranging from those of nonvascular plants to those of flowering plants. However, complex plant genome assembly is still challenging and remains difficult to fully resolve with conventional sequencing and assembly methods due to high heterozygosity, highly repetitive sequences, or high ploidy characteristics of complex genomes. Herein, we summarize the challenges of and advances in complex plant genome assembly, including feasible experimental strategies, upgrades to sequencing technology, existing assembly methods, and different phasing algorithms. Moreover, we list actual cases of complex genome projects for readers to refer to and draw upon to solve future problems related to complex genomes. Finally, we expect that the accurate, gapless, telomere-to-telomere, and fully phased assembly of complex plant genomes could soon become routine.

在过去的20年里,测序技术和计算算法的巨大进步促使植物基因组研究进入了一个繁荣的时代,已经解码了数百个基因组,从无血管植物的基因组到开花植物的基因组。然而,由于复杂基因组的高杂合性、高重复序列或高倍性特征,植物复合体基因组组装仍然具有挑战性,并且仍然难以用传统的测序和组装方法完全解决。在此,我们总结了复杂植物基因组组装的挑战和进展,包括可行的实验策略、测序技术的升级、现有的组装方法和不同的阶段算法。此外,我们列出了复杂基因组项目的实际案例,供读者参考和借鉴,以解决未来与复杂基因组相关的问题。最后,我们预计,复杂植物基因组的准确、无缺口、端粒到端粒的全阶段组装可能很快成为常规。
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引用次数: 0
Dynamic Spatial-temporal Expression Ratio of X Chromosome to Autosomes but Stable Dosage Compensation in Mammals. 哺乳动物X染色体与常染色体的动态时空表达率但具有稳定的剂量补偿。
IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-06-01 Epub Date: 2022-08-27 DOI: 10.1016/j.gpb.2022.08.003
Sheng Hu Qian, Yu-Li Xiong, Lu Chen, Ying-Jie Geng, Xiao-Man Tang, Zhen-Xia Chen

In the evolutionary model of dosage compensation, per-allele expression level of the X chromosome has been proposed to have twofold up-regulation to compensate its dose reduction in males (XY) compared to females (XX). However, the expression regulation of X-linked genes is still controversial, and comprehensive evaluations are still lacking. By integrating multi-omics datasets in mammals, we investigated the expression ratios including X to autosomes (X:AA ratio) and X to orthologs (X:XX ratio) at the transcriptome, translatome, and proteome levels. We revealed a dynamic spatial-temporal X:AA ratio during development in humans and mice. Meanwhile, by tracing the evolution of orthologous gene expression in chickens, platypuses, and opossums, we found a stable expression ratio of X-linked genes in humans to their autosomal orthologs in other species (X:XX ≈ 1) across tissues and developmental stages, demonstrating stable dosage compensation in mammals. We also found that different epigenetic regulations contributed to the high tissue specificity and stage specificity of X-linked gene expression, thus affecting X:AA ratios. It could be concluded that the dynamics of X:AA ratios were attributed to the different gene contents and expression preferences of the X chromosome, rather than the stable dosage compensation.

在剂量补偿的进化模型中,X染色体的每个等位基因表达水平被认为具有两倍的上调,以补偿其在男性(XY)中与女性(XX)相比的剂量减少。然而,X连锁基因的表达调控仍然存在争议,并且仍然缺乏全面的评估。通过整合哺乳动物的多组学数据集,我们研究了转录组、翻译组和蛋白质组水平上的表达比率,包括X与常染色体(X:AA比率)和X与直向同源物(X:XX比率)。我们揭示了人类和小鼠在发育过程中的动态时空X:AA比率。同时,通过追踪鸡、鸭嘴兽和负鼠中同源基因表达的进化,我们发现人类中的X连锁基因与其他物种中的常染色体同源基因在不同组织和发育阶段的稳定表达率(X:XX≈1),表明哺乳动物中有稳定的剂量补偿。我们还发现,不同的表观遗传学调控有助于X连锁基因表达的高组织特异性和阶段特异性,从而影响X:AA比率。可以得出结论,X:AA比值的动态归因于X染色体的不同基因含量和表达偏好,而不是稳定的剂量补偿。
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引用次数: 0
A Chromosome-level Reference Genome of African Oil Palm Provides Insights into Its Divergence and Stress Adaptation. 非洲油棕的染色体水平参考基因组为其分化和应激适应提供了见解。
IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-06-01 Epub Date: 2022-11-24 DOI: 10.1016/j.gpb.2022.11.002
Le Wang, May Lee, Zi Yi Wan, Bin Bai, Baoqing Ye, Yuzer Alfiko, Rahmadsyah Rahmadsyah, Sigit Purwantomo, Zhuojun Song, Antonius Suwanto, Gen Hua Yue

The palm family (Arecaceae), consisting of ∼ 2600 species, is the third most economically important family of plants. The African oil palm (Elaeis guineensis) is one of the most important palms. However, the genome sequences of palms that are currently available are still limited and fragmented. Here, we report a high-quality chromosome-level reference genome of an oil palm, Dura, assembled by integrating long reads with ∼ 150× genome coverage. The assembled genome was 1.7 Gb in size, covering 94.5% of the estimated genome, of which 91.6% was assigned into 16 pseudochromosomes and 73.7% was repetitive sequences. Relying on the conserved synteny with oil palm, the existing draft genome sequences of both date palm and coconut were further assembled into chromosomal level. Transposon burst, particularly long terminal repeat retrotransposons, following the last whole-genome duplication, likely explains the genome size variation across palms. Sequence analysis of the VIRESCENS gene in palms suggests that DNA variations in this gene are related to fruit colors. Recent duplications of highly tandemly repeated pathogenesis-related proteins from the same tandem arrays play an important role in defense responses to Ganoderma. Whole-genome resequencing of both ancestral African and introduced oil palms in Southeast Asia reveals that genes under putative selection are notably associated with stress responses, suggesting adaptation to stresses in the new habitat. The genomic resources and insights gained in this study could be exploited for accelerating genetic improvement and understanding the evolution of palms.

棕榈科(槟榔科)由约2600种植物组成,是经济上第三重要的植物科。非洲油棕(Elaeis guineensis)是最重要的棕榈树之一。然而,目前可用的棕榈树基因组序列仍然有限且支离破碎。在这里,我们报道了一个高质量的染色体水平的参考基因组,油棕榈Dura,通过整合具有约150倍基因组覆盖率的长读数组装而成。组装的基因组大小为1.7Gb,占估计基因组的94.5%,其中91.6%被分配到16个假染色体中,73.7%是重复序列。基于与油棕的保守同源性,将现有的椰枣和椰子基因组序列进一步组装到染色体水平。在最后一次全基因组复制之后,转座子爆发,特别是长末端重复逆转录转座子,可能解释了棕榈树基因组大小的变化。对棕榈树病毒基因的序列分析表明,该基因的DNA变异与果实颜色有关。最近,来自相同串联阵列的高度串联重复的发病机制相关蛋白的重复在对灵芝的防御反应中起着重要作用。对祖先非洲棕榈树和东南亚引进的油棕榈树的全基因组重新测序表明,假定选择下的基因与应激反应显著相关,这表明它们适应了新栖息地的应激。本研究中获得的基因组资源和见解可用于加速遗传改良和了解棕榈的进化。
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引用次数: 0
Whole-genome Duplication Reshaped Adaptive Evolution in A Relict Plant Species, Cyclocarya paliurus. 青钱柳属植物的全基因组复制重塑适应性进化。
IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2023-06-01 Epub Date: 2023-02-11 DOI: 10.1016/j.gpb.2023.02.001
Yinquan Qu, Xulan Shang, Ziyan Zeng, Yanhao Yu, Guoliang Bian, Wenling Wang, Li Liu, Li Tian, Shengcheng Zhang, Qian Wang, Dejin Xie, Xuequn Chen, Zhenyang Liao, Yibin Wang, Jian Qin, Wanxia Yang, Caowen Sun, Xiangxiang Fu, Xingtan Zhang, Shengzuo Fang

Cyclocarya paliurus is a relict plant species that survived the last glacial period and shows a population expansion recently. Its leaves have been traditionally used to treat obesity and diabetes with the well-known active ingredient cyclocaric acid B. Here, we presented three C. paliurus genomes from two diploids with different flower morphs and one haplotype-resolved tetraploid assembly. Comparative genomic analysis revealed two rounds of recent whole-genome duplication events and identified 691 genes with dosage effects that likely contribute to adaptive evolution through enhanced photosynthesis and increased accumulation of triterpenoids. Resequencing analysis of 45 C. paliurus individuals uncovered two bottlenecks, consistent with the known events of environmental changes, and many selectively swept genes involved in critical biological functions, including plant defense and secondary metabolite biosynthesis. We also proposed the biosynthesis pathway of cyclocaric acid B based on multi-omics data and identified key genes, in particular gibberellin-related genes, associated with the heterodichogamy in C. paliurus species. Our study sheds light on evolutionary history of C. paliurus and provides genomic resources to study the medicinal herbs.

青钱柳是最后一次冰川期幸存下来的一种残余植物,最近种群数量有所增加。传统上,它的叶子被众所周知的活性成分环卡酸B用于治疗肥胖和糖尿病。在这里,我们展示了来自两个具有不同花形态的二倍体和一个单倍型解析的四倍体组合的三个青柳基因组。比较基因组分析揭示了最近两轮全基因组复制事件,并鉴定了691个具有剂量效应的基因,这些基因可能通过增强光合作用和增加三萜类化合物的积累来促进适应性进化。对45个青柳个体的重新测序分析发现了两个瓶颈,这与已知的环境变化事件一致,并且许多选择性地扫描了参与关键生物功能的基因,包括植物防御和次生代谢产物生物合成。基于多组学数据,我们还提出了环卡酸B的生物合成途径,并鉴定了与青柳异源二价体相关的关键基因,特别是赤霉素相关基因。我们的研究揭示了青柳的进化史,并为研究中草药提供了基因组资源。
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引用次数: 0
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Genomics, Proteomics & Bioinformatics
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