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Correction: A beginner’s guide to manual curation of transposable elements 更正:一个新手指南手动策展转座元素
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-05-04 DOI: 10.1186/s13100-022-00272-4
Goubert, Clement, Craig, Rory J., Bilat, Agustin F., Peona, Valentina, Vogan, Aaron A., Protasio, Anna V.

Correction to: Mobile DNA 13, 7 (2022)

https://doi.org/10.1186/s13100-021-00259-7

Following the publication of the original article [1] the author reported that Additional files 3, 4 and 5 in the published article are corrupted.

The original article [1] has been updated.

  1. Goubert C, Craig RJ, Bilat AF, et al. A beginner’s guide to manual curation of transposable elements. Mobile DNA. 2022;13:7. https://doi.org/10.1186/s13100-021-00259-7.

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Affiliations

  1. Canadian Center for Computational Genomics, McGill University, Montreal, Québec, Canada

    Clement Goubert

  2. Department of Human Genetics, McGill University, Montreal, Québec, Canada

    Clement Goubert

  3. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK

    Rory J. Craig

  4. Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay

    Agustin F. Bilat

  5. Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden

    Valentina Peona & Aaron A. Vogan

  6. Department of Pathology, Tennis Court Road, Cambridge, CB1 2PQ, UK

    Anna V. Protasio

  7. Christ’s College, St Andrews Street, Cambridge, CB2 3BU, UK

    Anna V. Protasio

Authors
  1. Clement GoubertView author publications

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  2. Rory J. CraigView author publications

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  3. Agustin F. BilatView author publications

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  4. Valentina PeonaView author publications

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  5. Aaron A. VoganView author publications

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  6. Anna V. ProtasioView author publications

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Corresponding author

Correspondence to Anna V. Protasio.

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons lic

更正:Mobile DNA 13,7 (2022)https://doi.org/10.1186/s13100-021-00259-7Following原文发表[1]作者报告发表文章中的附加文件3,4和5被损坏。原文[1]已更新。郭伯特C, Craig RJ, Bilat AF,等。一个初学者的指南手动策展转座元素。移动的DNA。2022年,第13章第7节。https://doi.org/10.1186/s13100-021-00259-7.Article PubMed PubMed Central Google Scholar下载参考资料所属单位加拿大麦吉尔大学计算基因组学中心,蒙特利尔,quacimet,加拿大麦吉尔大学人类遗传学系,蒙特利尔,quacimet,加拿大爱丁堡大学进化生物学研究所,爱丁堡,eh93fl,英国蒙得维的亚,República,蒙得维的亚乌普萨拉大学生物学系,Norbyvägen 18D, 752 36,瑞典乌普萨拉valentina Peona &;Aaron A. vogan病理学系,剑桥网球场路,cb12pq, UKAnna V. ProtasioChrist 's College,剑桥圣安德鲁斯街,cb23bu;UKAnna诉ProtasioAuthorsClement GoubertView publicationsYou作者也可以搜索PubMed的作者在谷歌ScholarRory j . CraigView publicationsYou作者也可以搜索PubMed的作者在谷歌ScholarAgustin f . BilatView publicationsYou作者也可以搜索PubMed的作者在谷歌ScholarValentina PeonaView publicationsYou作者也可以搜索PubMed的作者在谷歌ScholarAaron a VoganView publicationsYou作者也可以搜索这个作者PubMed Google ScholarAnna V. Protasio查看作者出版物你也可以在PubMed Google scholarsearch这个作者对应作者Anna V. Protasio的通信。开放获取本文遵循知识共享署名4.0国际许可协议,该协议允许以任何媒介或格式使用、共享、改编、分发和复制,只要您适当地注明原作者和来源,提供知识共享许可协议的链接,并注明是否进行了更改。本文中的图像或其他第三方材料包含在文章的知识共享许可协议中,除非在材料的署名中另有说明。如果材料未包含在文章的知识共享许可中,并且您的预期用途不被法律法规允许或超过允许的用途,您将需要直接获得版权所有者的许可。要查看本许可的副本,请访问http://creativecommons.org/licenses/by/4.0/。知识共享公共领域免责条款(http://creativecommons.org/publicdomain/zero/1.0/)适用于本文中提供的数据,除非在数据的署名中另有说明。转载及许可转载请注明出处:古伯特,C,克雷格,r.j.,比拉特,A.F.等。更正:一个新手指南手动策展转座元素。移动DNA 13,15(2022)。https://doi.org/10.1186/s13100-022-00272-4Download citation出版日期:2022年5月4日doi: https://doi.org/10.1186/s13100-022-00272-4Share这篇文章任何你分享以下链接的人都可以阅读到这篇文章:获取可共享的链接对不起,本文目前没有可共享的链接。复制到剪贴板由Springer Nature shareit内容共享计划提供
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引用次数: 4
Software evaluation for de novo detection of transposons 转座子从头检测的软件评价
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-04-27 DOI: 10.1186/s13100-022-00266-2
Rodriguez, Matias, Makałowski, Wojciech
Transposable elements (TEs) are major genomic components in most eukaryotic genomes and play an important role in genome evolution. However, despite their relevance the identification of TEs is not an easy task and a number of tools were developed to tackle this problem. To better understand how they perform, we tested several widely used tools for de novo TE detection and compared their performance on both simulated data and well curated genomic sequences. As expected, tools that build TE-models performed better than k-mer counting ones, with RepeatModeler beating competitors in most datasets. However, there is a tendency for most tools to identify TE-regions in a fragmented manner and it is also frequent that small TEs or fragmented TEs are not detected. Consequently, the identification of TEs is still a challenging endeavor and it requires a significant manual curation by an experienced expert. The results will be helpful for identifying common issues associated with TE-annotation and for evaluating how comparable are the results obtained with different tools.
转座因子(te)是真核生物基因组的主要组成部分,在基因组进化中起着重要作用。然而,尽管它们具有相关性,但TEs的识别并不是一项容易的任务,并且开发了许多工具来解决这个问题。为了更好地了解它们的表现,我们测试了几种广泛使用的从头TE检测工具,并比较了它们在模拟数据和精心策划的基因组序列上的表现。正如预期的那样,构建te模型的工具比k-mer计数工具表现得更好,在大多数数据集中,RepeatModeler击败了竞争对手。然而,大多数工具都倾向于以碎片化的方式识别te区域,并且经常无法检测到小te或碎片te。因此,te的识别仍然是一项具有挑战性的工作,需要经验丰富的专家进行大量的手工管理。这些结果将有助于识别与te注释相关的常见问题,并有助于评估使用不同工具获得的结果的可比性。
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引用次数: 13
Subfamily-specific differential contribution of individual monomers and the tether sequence to mouse L1 promoter activity 单个单体和系链序列对小鼠L1启动子活性的亚家族特异性差异贡献
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-04-20 DOI: 10.1186/s13100-022-00269-z
Lingqi Kong, Karabi Saha, Yu-Chen Hu, Jada N. Tschetter, Chase E Habben, Leanne S. Whitmore, Chang-fu Yao, Xi A. Ge, Ping Ye, Simon J. Newkirk, Wenfeng An
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引用次数: 2
Characterization of transposable elements within the Bemisia tabaci species complex 烟粉虱物种复合体内转座因子的表征
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-04-19 DOI: 10.1186/s13100-022-00270-6
Juan Paolo A. Sicat, Paul Visendi, Steven O. Sewe, S. Bouvaine, S. Seal
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引用次数: 4
Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells 透明滑膜炎细胞I型IFN反应中转座元件的转录动力学
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-04-18 DOI: 10.1101/2022.04.18.488675
G. M. Pasquesi, Conor J. Kelly, Andrea D. Ordonez, E. Chuong
Background Bats are a major reservoir of zoonotic viruses, and there has been growing interest in characterizing bat-specific features of innate immunity and inflammation. Recent studies have revealed bat-specific adaptations affecting interferon (IFN) signaling and IFN-stimulated genes (ISGs), but we still have a limited understanding of the genetic mechanisms that have shaped the evolution of bat immunity. Here we investigated the transcriptional and epigenetic dynamics of transposable elements (TEs) during the type I IFN response in little brown bat ( Myotis lucifugus ) primary embryonic fibroblast cells, using RNA-seq and CUT&RUN. Results We found multiple bat-specific TEs that undergo both locus-specific and family-level transcriptional induction in response to IFN. Our transcriptome reassembly identified multiple ISGs that have acquired novel exons from bat-specific TEs, including NLRC5 , SLNF5 and a previously unannotated isoform of the IFITM2 gene. We also identified examples of TE-derived regulatory elements, but did not find strong evidence supporting genome-wide epigenetic activation of TEs in response to IFN. Conclusion Collectively, our study uncovers numerous TE-derived transcripts, proteins, and alternative isoforms that are induced by IFN in Myotis lucifugus cells, highlighting candidate loci that may contribute to bat-specific immune function.
背景蝙蝠是人畜共患病毒的主要宿主,人们对描述蝙蝠先天免疫和炎症的特定特征越来越感兴趣。最近的研究表明,蝙蝠的特异性适应影响干扰素(IFN)信号传导和干扰素刺激基因(ISG),但我们对影响蝙蝠免疫进化的遗传机制的了解仍然有限。在这里,我们使用RNA-seq和CUT&RUN研究了转座子(TE)在小棕蝙蝠(滑鼠)原代胚胎成纤维细胞的I型IFN反应过程中的转录和表观遗传学动力学。结果我们发现多个蝙蝠特异性TE对IFN的反应同时经历基因座特异性和家族水平的转录诱导。我们的转录组重组鉴定了多个ISG,它们从蝙蝠特异性TE中获得了新的外显子,包括NLRC5、SLNF5和IFITM2基因的一种以前未标记的亚型。我们还确定了TE衍生的调节元件的例子,但没有发现强有力的证据支持TE对IFN的全基因组表观遗传学激活。结论总之,我们的研究揭示了IFN在滑膜炎细胞中诱导的许多TE衍生的转录物、蛋白质和替代异构体,突出了可能有助于蝙蝠特异性免疫功能的候选基因座。
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引用次数: 0
RNA sensor MDA5 suppresses LINE-1 retrotransposition by regulating the promoter activity of LINE-1 5′-UTR RNA传感器MDA5通过调节LINE-1 5′-UTR启动子活性抑制LINE-1逆转录转位
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-04-12 DOI: 10.1186/s13100-022-00268-0
Yan, Jiaxiu, Zhao, Yifei, Du, Juan, Wang, Yu, Wang, Shaohua, Wang, Qing, Zhao, Xu, Xu, Wei, Zhao, Ke
Type 1 long interspersed elements, or LINE-1, are the only retroelements that replicate autonomously in human cells. The retrotransposition process of LINE-1 can trigger the activation of the innate immune system and has been proposed to play a role in the development of several autoimmune diseases, including Aicardi-Goutières syndrome (AGS). In contrast, all known AGS-associated proteins, except MDA5, have been reported to affect LINE-1 activity. Thus, MDA5 is likely to also function as a LINE-1 suppressor. MDA5 was found to potently suppress LINE-1 activity in a reporter-based LINE-1 retrotransposition assay. Although MDA5 is an endogenous RNA sensor able to activate the innate immune system, increased interferon (IFN) expression only contributed in part to MDA5-mediated LINE-1 suppression. Instead, MDA5 potently regulated the promoter activity of LINE-1 5′-UTR, as confirmed by transiently expressed myc-tagged MDA5 or knockdown of endogenous MDA5 expression. Consequently, MDA5 effectively reduced the generation of LINE-1 RNA and the subsequent expression of LINE-1 ORF1p and ORF2p. Interestingly, despite MDA5 being a multi-domain protein, the N-terminal 2CARD domain alone is sufficient to interact with LINE-1 5′-UTR and inhibit LINE-1 promoter activity. Our data reveal that MDA5 functions as a promoter regulator; it directly binds to the LINE-1 5′-UTR and suppresses its promoter activity. Consequently, MDA5 reduces LINE-1 RNA and protein levels, and ultimately inhibits LINE-1 retrotransposition. In contrast, MDA5-induced IFN expression only plays a mild role in MDA5-mediated LINE-1 suppression. In addition, the N-terminal 2CARD domain was found to be a functional region for MDA5 upon inhibition of LINE-1 replication. Thus, our data suggest that besides being an initiator of the innate immune system, MDA5 is also an effector against LINE-1 activity, potentially forming a feedback loop by suppressing LINE-1-induced innate immune activation.
1型长穿插元件(LINE-1)是人类细胞中唯一能够自主复制的逆转录因子。LINE-1的逆转录过程可以触发先天免疫系统的激活,并被认为在包括aicardi - gouti综合征(AGS)在内的几种自身免疫性疾病的发展中发挥作用。相反,除了MDA5外,所有已知的ags相关蛋白都影响LINE-1活性。因此,MDA5也可能作为LINE-1抑制因子发挥作用。在基于报告者的LINE-1逆转录试验中,MDA5被发现能有效抑制LINE-1活性。虽然MDA5是一种能够激活先天免疫系统的内源性RNA传感器,但干扰素(IFN)表达的增加仅部分促成了MDA5介导的LINE-1抑制。相反,MDA5可以有效地调节LINE-1 5 ' -UTR的启动子活性,这一点通过myc标记的MDA5的瞬时表达或内源性MDA5的表达下调得到了证实。因此,MDA5有效地减少了LINE-1 RNA的产生和随后LINE-1 ORF1p和ORF2p的表达。有趣的是,尽管MDA5是一个多结构域蛋白,但仅n端2CARD结构域就足以与LINE-1 5 ' -UTR相互作用并抑制LINE-1启动子活性。我们的数据显示MDA5作为启动子调节因子;它直接与LINE-1 5 ' -UTR结合并抑制其启动子活性。因此,MDA5降低了LINE-1 RNA和蛋白质水平,并最终抑制了LINE-1逆转录转位。相比之下,mda5诱导的IFN表达仅在mda5介导的LINE-1抑制中起轻微作用。此外,n端2CARD结构域被发现是MDA5抑制LINE-1复制的功能区域。因此,我们的数据表明,MDA5除了是先天免疫系统的启动器外,也是对抗LINE-1活性的效应物,可能通过抑制LINE-1诱导的先天免疫激活形成反馈回路。
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引用次数: 3
TE Density: a tool to investigate the biology of transposable elements TE密度:一个研究转座因子生物学的工具
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-04-12 DOI: 10.1186/s13100-022-00264-4
Scott J Teresi, Michael B. Teresi, P. Edger
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引用次数: 2
SETMAR, a case of primate co-opted genes: towards new perspectives SETMAR,灵长类动物增选基因的一个案例:走向新的视角
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-04-08 DOI: 10.1186/s13100-022-00267-1
Lié, Oriane, Renault, Sylvaine, Augé-Gouillou, Corinne
We carry out a review of the history and biological activities of one domesticated gene in higher primates, SETMAR, by discussing current controversies. Our purpose is to open a new outlook that will serve as a framework for future work about SETMAR, possibly in the field of cognition development. What is newly important about SETMAR can be summarized as follows: (1) the whole protein sequence is under strong purifying pressure; (2) its role is to strengthen existing biological functions rather than to provide new ones; (3) it displays a tissue-specific pattern of expression, at least for the alternative-splicing it undergoes. Studies reported here demonstrate that SETMAR protein(s) may be involved in essential networks regulating replication, transcription and translation. Moreover, during embryogenesis, SETMAR appears to contribute to brain development. Our review underlines for the first time that SETMAR directly interacts with genes involved in brain functions related to vocalization and vocal learning. These findings pave the way for future works regarding SETMAR and the development of cognitive abilities in higher primates.
我们通过讨论当前的争议,对高等灵长类动物中一个驯化基因SETMAR的历史和生物活性进行了回顾。我们的目的是打开一个新的前景,这将作为未来关于SETMAR工作的框架,可能在认知发展领域。SETMAR的新发现可以概括为:(1)整个蛋白序列处于强大的纯化压力下;(2)其作用是加强现有的生物功能,而不是提供新的功能;(3)它表现出一种组织特异性的表达模式,至少对于它所经历的选择性剪接来说是这样。本文报道的研究表明,SETMAR蛋白可能参与调控复制、转录和翻译的基本网络。此外,在胚胎发生过程中,SETMAR似乎有助于大脑发育。我们的研究首次强调SETMAR直接与与发声和发声学习相关的大脑功能相关的基因相互作用。这些发现为未来有关SETMAR和高等灵长类动物认知能力发展的工作铺平了道路。
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引用次数: 3
The structural diversity of CACTA transposons in genomes of Chenopodium (Amaranthaceae, Caryophyllales) species: specific traits and comparison with the similar elements of angiosperms 藜属植物基因组CACTA转座子的结构多样性:特征及与被子植物相似成分的比较
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-04-04 DOI: 10.1186/s13100-022-00265-3
Belyayev, Alexander, Josefiová, Jiřina, Jandová, Michaela, Kalendar, Ruslan, Mahelka, Václav, Mandák, Bohumil, Krak, Karol
CACTA transposable elements (TEs) comprise one of the most abundant superfamilies of Class 2 (cut-and-paste) transposons. Over recent decades, CACTA elements were widely identified in species from the plant, fungi, and animal kingdoms, but sufficiently studied in the genomes of only a few model species although non-model genomes can bring additional and valuable information. It primarily concerned the genomes of species belonging to clades in the base of large taxonomic groups whose genomes, to a certain extent, can preserve relict and/or possesses specific traits. Thus, we sought to investigate the genomes of Chenopodium (Amaranthaceae, Caryophyllales) species to unravel the structural variability of CACTA elements. Caryophyllales is a separate branch of Angiosperms and until recently the diversity of CACTA elements in this clade was unknown. Application of the short-read genome assembly algorithm followed by analysis of detected complete CACTA elements allowed for the determination of their structural diversity in the genomes of 22 Chenopodium album aggregate species. This approach yielded knowledge regarding: (i) the coexistence of two CACTA transposons subtypes in single genome; (ii) gaining of additional protein conserved domains within the coding sequence; (iii) the presence of captured gene fragments, including key genes for flower development; and (iv)) identification of captured satDNA arrays. Wide comparative database analysis revealed that identified events are scattered through Angiosperms in different proportions. Our study demonstrated that while preserving the basic element structure a wide range of coding and non-coding additions to CACTA transposons occur in the genomes of C. album aggregate species. Ability to relocate additions inside genome in combination with the proposed novel functional features of structural-different CACTA elements can impact evolutionary trajectory of the host genome.
CACTA转座子(TEs)是一类最丰富的2类(剪切-粘贴)转座子超家族之一。近几十年来,CACTA元件在植物、真菌和动物领域的物种中得到了广泛的鉴定,但在少数模式物种的基因组中得到了充分的研究,尽管非模式基因组可以带来额外的有价值的信息。它主要涉及属于大型分类群基础分支的物种的基因组,这些物种的基因组在一定程度上可以保存遗存和/或具有特定特征。因此,我们对藜属植物(苋菜科,石竹科)的基因组进行了研究,以揭示CACTA元件的结构变异性。石竹属植物是被子植物的一个独立分支,直到最近才知道这个分支中CACTA元素的多样性。应用短读基因组组装算法,对检测到的完整CACTA元件进行分析,确定了22种Chenopodium album aggregate种基因组的结构多样性。该方法获得了以下方面的知识:(i)两个CACTA转座子亚型在单个基因组中共存;(ii)在编码序列中获得额外的蛋白质保守结构域;(iii)存在捕获的基因片段,包括花发育的关键基因;(iv)识别捕获的卫星dna阵列。。广泛的比较数据库分析显示,确定的事件以不同的比例分散在被子植物中。我们的研究表明,在保留基本元件结构的同时,CACTA转座子出现了广泛的编码和非编码添加。基因组内添加物的重新定位能力与CACTA元件结构不同的新功能特征相结合,可以影响宿主基因组的进化轨迹。
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引用次数: 1
A beginner’s guide to manual curation of transposable elements 一个初学者的指南手动策展转座元素
IF 4.9 2区 生物学 Q1 Biochemistry, Genetics and Molecular Biology Pub Date : 2022-03-30 DOI: 10.1186/s13100-021-00259-7
Goubert, Clement, Craig, Rory J., Bilat, Agustin F., Peona, Valentina, Vogan, Aaron A., Protasio, Anna V.
In the study of transposable elements (TEs), the generation of a high confidence set of consensus sequences that represent the diversity of TEs found in a given genome is a key step in the path to investigate these fascinating genomic elements. Many algorithms and pipelines are available to automatically identify putative TE families present in a genome. Despite the availability of these valuable resources, producing a library of high-quality full-length TE consensus sequences largely remains a process of manual curation. This know-how is often passed on from mentor-to-mentee within research groups, making it difficult for those outside the field to access this highly specialised skill. Our manuscript attempts to fill this gap by providing a set of detailed computer protocols, software recommendations and video tutorials for those aiming to manually curate TEs. Detailed step-by-step protocols, aimed at the complete beginner, are presented in the Supplementary Methods. The proposed set of programs and tools presented here will make the process of manual curation achievable and amenable to all researchers and in special to those new to the field of TEs.
在转座元件(te)的研究中,产生一组高置信度的共识序列,代表在给定基因组中发现的te的多样性,是研究这些迷人的基因组元件的关键一步。许多算法和管道可用于自动识别假定的TE家族存在于基因组中。尽管这些有价值的资源的可用性,生产一个高质量的全长TE共识序列库在很大程度上仍然是一个手工管理的过程。这种技术诀窍通常是在研究小组内由导师传给学员,这使得该领域以外的人很难获得这种高度专业化的技能。我们的手稿试图通过提供一套详细的计算机协议、软件推荐和视频教程来填补这一空白,为那些旨在手动策划TEs的人提供帮助。详细的一步一步的协议,针对完整的初学者,在补充方法中提出。这里提出的一套程序和工具将使所有研究人员,特别是那些新进入TEs领域的研究人员,能够实现和适应手动策展的过程。
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引用次数: 28
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Mobile DNA
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