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Vela J, Mora P, Montiel EE, Rico-Porras JM, Sanllorente O, Amoasii D, Lorite P, Palomeque T. Exploring horizontal transfer of mariner transposable elements among ants and aphids. Gene 2024; 899:148144. [PMID: 38195050 DOI: 10.1016/j.gene.2024.148144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/11/2024]
Abstract
Aphids and ants are mutualistic species with a close space-time relationship, which may facilitate the occurrence of horizontal transfer events between these insect groups. Myrmar-like mariner elements were previously isolated from two ant (Myrmica ruginodis and Tapinoma ibericum) and two aphid species (Aphis fabae and Aphis hederae). The aim of this work is to determine the presence of Myrmar-like mariner elements in new ant and aphid species, as well as to analyze the likelihood of horizontal transfer events between these taxa. To accomplish this, the Myrmar-like element has been isolated from five aphid species and six ant species. Among these new analyzed species, full-length Myrmar-like mariner elements with very high sequence similarity have been isolated from the aphids Aphis nerii, Aphis spiraecola, Brachycaudus cardui, and Rhopalosiphum maidis as well as from the ants Lasius grandis and Lasius niger, even though aphids and ants belong to two insect orders (Hemiptera and Hymenoptera) that have evolved independently for at least 300 million-years. Both Lasius species establish frequent mutualistic relationships with multiple aphid species, including A. nerii, A. spiraecola, and B. cardui. The study of the putative protein encoded by them and the phylogenetic analysis suggests that they could be active transposons shared by aphids and ants through horizontal transfer events. Additionally, mariner elements with internal deletion were found in several aphids and one ant species, showing a high degree of sequence similarity among them. The characteristics of these elements with internal deletion suggest a complex origin involving various evolutionary processes, possibly including also horizontal transfer events. Myrmar-like elements have also been isolated from the other ant species, although without similarity with the aphid mariner sequences. Myrmar-like elements are also present in phylogenetically distant insect species, as well as in one crustacean species. The phylogenetic study carried out with all Myrmar-like elements suggests the probable occurrence of horizontal transfer events.
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Affiliation(s)
- Jesús Vela
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Pablo Mora
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Eugenia E Montiel
- Departamento de Biología (Genética), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain; Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | - José M Rico-Porras
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Olivia Sanllorente
- Departamento de Zoología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| | - Daniela Amoasii
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Pedro Lorite
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
| | - Teresa Palomeque
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, 23071 Jaén, Spain.
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Pasquesi GIM, Allen H, Ivancevic A, Barbachano-Guerrero A, Joyner O, Guo K, Simpson DM, Gapin K, Horton I, Nguyen L, Yang Q, Warren CJ, Florea LD, Bitler BG, Santiago ML, Sawyer SL, Chuong EB. Regulation of human interferon signaling by transposon exonization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.11.557241. [PMID: 37745311 PMCID: PMC10515820 DOI: 10.1101/2023.09.11.557241] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Innate immune signaling is essential for clearing pathogens and damaged cells, and must be tightly regulated to avoid excessive inflammation or autoimmunity. Here, we found that the alternative splicing of exons derived from transposable elements is a key mechanism controlling immune signaling in human cells. By analyzing long-read transcriptome datasets, we identified numerous transposon exonization events predicted to generate functional protein variants of immune genes, including the type I interferon receptor IFNAR2. We demonstrated that the transposon-derived isoform of IFNAR2 is more highly expressed than the canonical isoform in almost all tissues, and functions as a decoy receptor that potently inhibits interferon signaling including in cells infected with SARS-CoV-2. Our findings uncover a primate-specific axis controlling interferon signaling and show how a transposon exonization event can be co-opted for immune regulation.
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Affiliation(s)
- Giulia Irene Maria Pasquesi
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
- Crnic Institute Boulder Branch, BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303
| | - Holly Allen
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Atma Ivancevic
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Arturo Barbachano-Guerrero
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Olivia Joyner
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Kejun Guo
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045
| | - David M. Simpson
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Keala Gapin
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Isabella Horton
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Lily Nguyen
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045
| | - Qing Yang
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
- Fred Hutchinson Cancer Research Center, Seattle, WA, 98109
| | - Cody J. Warren
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
- The Ohio State University College of Veterinary Medicine, Columbus, OH, 43210
| | - Liliana D. Florea
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205
| | - Benjamin G. Bitler
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045
| | - Mario L. Santiago
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045
| | - Sara L. Sawyer
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Edward B. Chuong
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
- Crnic Institute Boulder Branch, BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303
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Doronina L, Reising O, Clawson H, Churakov G, Schmitz J. Euarchontoglires Challenged by Incomplete Lineage Sorting. Genes (Basel) 2022; 13:774. [PMID: 35627160 PMCID: PMC9141288 DOI: 10.3390/genes13050774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/08/2022] [Accepted: 04/20/2022] [Indexed: 11/17/2022] Open
Abstract
Euarchontoglires, once described as Supraprimates, comprise primates, colugos, tree shrews, rodents, and lagomorphs in a clade that evolved about 90 million years ago (mya) from a shared ancestor with Laurasiatheria. The rapid speciation of groups within Euarchontoglires, and the subsequent inherent incomplete marker fixation in ancestral lineages, led to challenged attempts at phylogenetic reconstructions, particularly for the phylogenetic position of tree shrews. To resolve this conundrum, we sampled genome-wide presence/absence patterns of transposed elements (TEs) from all representatives of Euarchontoglires. This specific marker system has the advantage that phylogenetic diagnostic characters can be extracted in a nearly unbiased fashion genome-wide from reference genomes. Their insertions are virtually free of homoplasy. We simultaneously employed two computational tools, the genome presence/absence compiler (GPAC) and 2-n-way, to find a maximum of diagnostic insertions from more than 3 million TE positions. From 361 extracted diagnostic TEs, 132 provide significant support for the current resolution of Primatomorpha (Primates plus Dermoptera), 94 support the union of Euarchonta (Primates, Dermoptera, plus Scandentia), and 135 marker insertion patterns support a variety of alternative phylogenetic scenarios. Thus, whole genome-level analysis and a virtually homoplasy-free marker system offer an opportunity to finally resolve the notorious phylogenetic challenges that nature produces in rapidly diversifying groups.
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Affiliation(s)
- Liliya Doronina
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany; (O.R.); (G.C.); (J.S.)
| | - Olga Reising
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany; (O.R.); (G.C.); (J.S.)
| | - Hiram Clawson
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA;
| | - Gennady Churakov
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany; (O.R.); (G.C.); (J.S.)
| | - Jürgen Schmitz
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany; (O.R.); (G.C.); (J.S.)
- EvoPAD-RTG, University of Münster, 48149 Münster, Germany
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Hu T, Li J, Long M, Wu J, Zhang Z, Xie F, Zhao J, Yang H, Song Q, Lian S, Shi J, Guo X, Yuan D, Lang D, Yu G, Liang B, Zhou X, Ishibashi T, Fan X, Yu W, Wang D, Wang Y, Peng IF, Wang S. Detection of Structural Variations and Fusion Genes in Breast Cancer Samples Using Third-Generation Sequencing. Front Cell Dev Biol 2022; 10:854640. [PMID: 35493102 PMCID: PMC9043247 DOI: 10.3389/fcell.2022.854640] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/23/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Structural variations (SVs) are common genetic alterations in the human genome that could cause different phenotypes and diseases, including cancer. However, the detection of structural variations using the second-generation sequencing was limited by its short read length, which restrained our understanding of structural variations. Methods: In this study, we developed a 28-gene panel for long-read sequencing and employed it to Oxford Nanopore Technologies and Pacific Biosciences platforms. We analyzed structural variations in the 28 breast cancer-related genes through long-read genomic and transcriptomic sequencing of tumor, para-tumor, and blood samples in 19 breast cancer patients. Results: Our results showed that some somatic SVs were recurring among the selected genes, though the majority of them occurred in the non-exonic region. We found evidence supporting the existence of hotspot regions for SVs, which extended our previous understanding that they exist only for single nucleotide variations. Conclusion: In conclusion, we employed long-read genomic and transcriptomic sequencing to identify SVs from breast cancer patients and proved that this approach holds great potential in clinical application.
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Affiliation(s)
- Taobo Hu
- Department of Breast Surgery, Peking University People’s Hospital, Beijing, China
| | - Jingjing Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
- GrandOmics Inc., Beijing, China
| | - Mengping Long
- Department of Pathology, Peking University Cancer Hospital, Beijing, China
| | - Jinbo Wu
- Department of Breast Surgery, Peking University People’s Hospital, Beijing, China
| | - Zhen Zhang
- Department of Statistics, The Chinese University of Hong Kong, Sha Tin, China
| | - Fei Xie
- Department of Breast Surgery, Peking University People’s Hospital, Beijing, China
| | - Jin Zhao
- Department of Breast Surgery, Peking University People’s Hospital, Beijing, China
| | - Houpu Yang
- Department of Breast Surgery, Peking University People’s Hospital, Beijing, China
| | - Qianqian Song
- Department of Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Sheng Lian
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Jiandong Shi
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | | | | | | | | | - Baosheng Liang
- Department of Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Xiaohua Zhou
- Department of Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Toyotaka Ishibashi
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Xiaodan Fan
- Department of Statistics, The Chinese University of Hong Kong, Sha Tin, China
| | - Weichuan Yu
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | | | - Yang Wang
- GrandOmics Inc., Beijing, China
- *Correspondence: Yang Wang, ; I-Feng Peng, ; Shu Wang,
| | - I-Feng Peng
- GrandOmics Inc., Beijing, China
- *Correspondence: Yang Wang, ; I-Feng Peng, ; Shu Wang,
| | - Shu Wang
- Department of Breast Surgery, Peking University People’s Hospital, Beijing, China
- *Correspondence: Yang Wang, ; I-Feng Peng, ; Shu Wang,
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Doronina L, Feigin CY, Schmitz J. OUP accepted manuscript. Syst Biol 2022; 71:1045-1053. [PMID: 35289914 PMCID: PMC9366447 DOI: 10.1093/sysbio/syac025] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 11/29/2022] Open
Abstract
Although first posited to be of a single origin, the two superfamilies of phalangeriform marsupial possums (Phalangeroidea: brushtail possums and cuscuses and Petauroidea: possums and gliders) have long been considered, based on multiple sequencing studies, to have evolved from two separate origins. However, previous data from these sequence analyses suggested a variety of conflicting trees. Therefore, we reinvestigated these relationships by screening \documentclass[12pt]{minimal}
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}{}$\sim$\end{document}200,000 orthologous short interspersed element (SINE) loci across the newly available whole-genome sequences of phalangeriform species and their relatives. Compared to sequence data, SINE presence/absence patterns are evolutionarily almost neutral molecular markers of the phylogenetic history of species. Their random and highly complex genomic insertion ensures their virtually homoplasy-free nature and enables one to compare hundreds of shared unique orthologous events to determine the true species tree. Here, we identify 106 highly reliable phylogenetic SINE markers whose presence/absence patterns within multiple Australasian possum genomes unexpectedly provide the first significant evidence for the reunification of Australasian possums into one monophyletic group. Together, our findings indicate that nucleotide homoplasy and ancestral incomplete lineage sorting have most likely driven the conflicting signal distributions seen in previous sequence-based studies. [Ancestral incomplete lineage sorting; possum genomes; possum monophyly; retrophylogenomics; SINE presence/absence.]
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Affiliation(s)
- Liliya Doronina
- Institute of Experimental Pathology (ZMBE), University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
| | - Charles Y Feigin
- Department of Molecular Biology, Princeton University, 119 Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544-1014, USA
- School of BioSciences, The University of Melbourne, BioSciences 4, Royal Pde, Parkville, VIC 3010, Australia
| | - Jürgen Schmitz
- Correspondence to be sent to: Institute of Experimental Pathology (ZMBE), University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany; E-mail:
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