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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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Amorim IC, Mello CAA, Félix AP, Xavier C, Wallau GL, Moura RC. Mobilome characterization of the beetle Euchroma gigantea (Buprestidae) uncovers multiple long range Tc1-Mariner horizontal transfer events. Gene 2023; 888:147785. [PMID: 37689222 DOI: 10.1016/j.gene.2023.147785] [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: 03/26/2023] [Revised: 07/05/2023] [Accepted: 09/06/2023] [Indexed: 09/11/2023]
Abstract
Transposable elements (TEs) are mobile repetitive DNA sequences that can transfer horizontally between species. Due to their mutagenic characteristics, TEs are associated with different evolutionary events, including chromosomal rearrangements that are abundant in the beetle Euchroma gigantea. In order to understand more in depth the impact of TEs on the genomic evolution of E. gigantea, we characterized the E. gigantea mobilome and evaluated the horizontal transfer of Tc1-Mariner elements. Genomic sequencing data was generated on the Illumina Hiseq plataform, from a specimen (Northeast lineage) collected in Recife, Pernambuco - Brazil. The TEs were characterized by two independent approaches based on the clustering and assembly of highly repetitive sequences, the RepeatExplorer and dnaPipeTE. The sequences obtained were further characterized using ORFfinder and CD-Search, to obtain the TEs' potential coding proteins and verify the presence and integrity of known TE domains. Evidence for horizontal transfer was evaluated by nucleotide and protein genetic distance between TEs from E. gigantea and other species and phylogenetic incongruences detected between TEs and hosts phylogenetic trees. The mobilome of E. gigantea represents about 21 to 26% of its genome. This mobilome is composed of TEs from 31 superfamilies, belonging to different classes and most known orders of TEs. Several types of TEs with intact domains were observed with emphasis on Tc1-Mariner suggesting the presence of potentially autonomous elements. This superfamily also stands out for having the greatest abundance and diversity, with TEs being classified into four families. When compared to TEs deposited in databases, Mariner TEs stood out as having the highest nucleotide identity (above 90%) with TEs from phylogenetically distant species, such as ants and bees. Altogether these results suggest that E. gigantea Mariner TEs underwent multiple horizontal transfer events to other insect species.
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Affiliation(s)
- Igor C Amorim
- Laboratório de Biodiversidade e Genética de Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco, Recife, Pernambuco, Brazil; Departamento de Tecnologia e Ciências Sociais, Universidade do Estado da Bahia, Juazeiro, BA, Brasil
| | - Catarine A A Mello
- Laboratório de Biodiversidade e Genética de Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco, Recife, Pernambuco, Brazil
| | - Aline P Félix
- Laboratório de Biodiversidade e Genética de Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco, Recife, Pernambuco, Brazil; Pós-Graduação em Genética e Biologia Molecular, Centro de Ciências Biológicas (CB), Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil; Departamento de Entomologia e Núcleo de Bioinformática, Instituto Aggeu Magalhães - Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil
| | - Crislaine Xavier
- Laboratório de Biodiversidade e Genética de Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco, Recife, Pernambuco, Brazil
| | - Gabriel L Wallau
- Departamento de Entomologia e Núcleo de Bioinformática, Instituto Aggeu Magalhães - Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil; Department of Arbovirology and Entomology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany.
| | - Rita C Moura
- Laboratório de Biodiversidade e Genética de Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco, Recife, Pernambuco, Brazil; Pós-Graduação em Genética e Biologia Molecular, Centro de Ciências Biológicas (CB), Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil.
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Yokoi K, Furukawa S, Zhou R, Jouraku A, Bono H. Reference Genome Sequences of the Oriental Armyworm, Mythimna separata (Lepidoptera: Noctuidae). INSECTS 2022; 13:insects13121172. [PMID: 36555082 PMCID: PMC9853324 DOI: 10.3390/insects13121172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 05/05/2023]
Abstract
Lepidopteran insects are an important group of animals, including those used as biochemical and physiological model species in the insect and silk industries as well as others that are major agricultural pests. Therefore, the genome sequences of several lepidopteran insects have been reported. The oriental armyworm, Mythimna separata, is an agricultural pest commonly used to study insect immune reactions and interactions with parasitoid wasps as hosts. To improve our understanding of these research topics, reference genome sequences were constructed in the present study. Using long-read and short-read sequence data, de novo assembly and polishing were performed and haplotigs were purged. Subsequently, gene predictions and functional annotations were performed. To search for orthologs of the Toll and Immune Deficiency (IMD) pathways and for C-type lectins, annotation data analysis, BLASTp, and Hummer scans were performed. The M. separata genome is 682 Mbp; its contig N50 was 2.7 Mbp, with 21,970 genes and 24,452 coding sites predicted. All orthologs of the core components of the Toll and IMD pathways and 105 C-type lectins were identified. These results suggest that the genome data were of sufficient quality for use as reference genome data and could contribute to promoting M. separata and lepidopteran research at the molecular and genome levels.
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Affiliation(s)
- Kakeru Yokoi
- Insect Design Technology Group, Division of Insect Advanced Technology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba 305-0901, Japan;
- Correspondence: ; Tel.: +81-29-838-6129
| | - Seiichi Furukawa
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan;
| | - Rui Zhou
- Degree Program in Agro-Bioresources Science and Technology, University of Tsukuba, Tsukuba 305-8572, Japan;
| | - Akiya Jouraku
- Insect Design Technology Group, Division of Insect Advanced Technology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba 305-0901, Japan;
| | - Hidemasa Bono
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Japan;
- Laboratory of BioDX, Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Japan
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Yokoi K, Wakamiya T, Bono H. Meta-Analysis of the Public RNA-Seq Data of the Western Honeybee Apis mellifera to Construct Reference Transcriptome Data. INSECTS 2022; 13:931. [PMID: 36292879 PMCID: PMC9604386 DOI: 10.3390/insects13100931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/05/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
The Western honeybee (Apis mellifera) is valuable in biological research and agriculture. Its genome sequence was published before those for other insect species. RNA-Seq data for A. mellifera have been applied in several recently published studies. Nevertheless, these data have not been prepared for use in subsequent meta-analyses. To promote A. mellifera transcriptome analysis, we constructed reference transcriptome data using the reference genome sequence and RNA-Seq data curated from about 1,000 runs of public databases. The new reference transcriptome data construct comprised 149,685 transcripts, and 194,174 protein sequences were predicted. Approximately 50-60% of the predicted protein sequences were functionally annotated using the protein sequence data for several model and insect species. Novel candidate immune-related transcripts were searched by meta-analysis using immune-response-related RNA-Seq and reference transcriptome data. Three to twenty candidate transcripts including autophagy-related protein 3 were upregulated or downregulated in response to both viral and bacterial infections. The constructed reference transcriptome data may facilitate future transcriptome analyses of A. mellifera.
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Affiliation(s)
- Kakeru Yokoi
- Insect Design Technology Module, Division of Insect Advanced Technology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba 305-8634, Ibaraki, Japan
| | - Takeshi Wakamiya
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Hiroshima, Japan
| | - Hidemasa Bono
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Hiroshima, Japan
- Laboratory of BioDX, Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Hiroshima, Japan
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