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Martelossi J, Nicolini F, Subacchi S, Pasquale D, Ghiselli F, Luchetti A. Multiple and diversified transposon lineages contribute to early and recent bivalve genome evolution. BMC Biol 2023; 21:145. [PMID: 37365567 DOI: 10.1186/s12915-023-01632-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Transposable elements (TEs) can represent one of the major sources of genomic variation across eukaryotes, providing novel raw materials for species diversification and innovation. While considerable effort has been made to study their evolutionary dynamics across multiple animal clades, molluscs represent a substantially understudied phylum. Here, we take advantage of the recent increase in mollusc genomic resources and adopt an automated TE annotation pipeline combined with a phylogenetic tree-based classification, as well as extensive manual curation efforts, to characterize TE repertories across 27 bivalve genomes with a particular emphasis on DDE/D class II elements, long interspersed nuclear elements (LINEs), and their evolutionary dynamics. RESULTS We found class I elements as highly dominant in bivalve genomes, with LINE elements, despite less represented in terms of copy number per genome, being the most common retroposon group covering up to 10% of their genome. We mined 86,488 reverse transcriptases (RVT) containing LINE coming from 12 clades distributed across all known superfamilies and 14,275 class II DDE/D-containing transposons coming from 16 distinct superfamilies. We uncovered a previously underestimated rich and diverse bivalve ancestral transposon complement that could be traced back to their most recent common ancestor that lived ~ 500 Mya. Moreover, we identified multiple instances of lineage-specific emergence and loss of different LINEs and DDE/D lineages with the interesting cases of CR1- Zenon, Proto2, RTE-X, and Academ elements that underwent a bivalve-specific amplification likely associated with their diversification. Finally, we found that this LINE diversity is maintained in extant species by an equally diverse set of long-living and potentially active elements, as suggested by their evolutionary history and transcription profiles in both male and female gonads. CONCLUSIONS We found that bivalves host an exceptional diversity of transposons compared to other molluscs. Their LINE complement could mainly follow a "stealth drivers" model of evolution where multiple and diversified families are able to survive and co-exist for a long period of time in the host genome, potentially shaping both recent and early phases of bivalve genome evolution and diversification. Overall, we provide not only the first comparative study of TE evolutionary dynamics in a large but understudied phylum such as Mollusca, but also a reference library for ORF-containing class II DDE/D and LINE elements, which represents an important genomic resource for their identification and characterization in novel genomes.
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Affiliation(s)
- Jacopo Martelossi
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Filippo Nicolini
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
- Fano Marine Center, Department of Biological, Geological and Environmental Sciences, University of Bologna, Viale Adriatico 1/N, 61032, Fano, Italy
| | - Simone Subacchi
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Daniela Pasquale
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Fabrizio Ghiselli
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy.
| | - Andrea Luchetti
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
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Novel selectively amplified DNA sequences in the germline genome of the Japanese hagfish, Eptatretus burgeri. Sci Rep 2022; 12:21373. [PMID: 36494570 PMCID: PMC9734144 DOI: 10.1038/s41598-022-26007-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
In the Japanese hagfish Eptatretus burgeri, 16 chromosomes (eliminated [E]-chromosomes) have been lost in somatic cells (2n = 36), which is equivalent to approx. 21% of the genomic DNA in germ cells (2n = 52). At least seven of the 12 eliminated repetitive DNA families isolated in eight hagfish species were selectively amplified in the germline genome of this species. One of them, EEEb1 (eliminated element of E. burgeri 1) is exclusively localized on all E-chromosomes. Herein, we identified four novel eliminated repetitive DNA families (named EEEb3-6) through PCR amplification and suppressive subtractive hybridization (SSH) combined with Southern-blot hybridization. EEEb3 was mosaic for 5S rDNA and SINE elements. EEEb4 was GC-rich repeats and has one pair of direct and inverted repeats, whereas EEEb5 and EEEb6 were AT-rich repeats with one pair and two pairs of sub-repeats, respectively. Interestingly, all repeat classes except EEEb3 were transcribed in the testes, although no open reading frames (ORF) were identified. We conducted fluorescence in situ hybridization (FISH) to examine the chromosomal localizations of EEEb3-6 and EEEb2, which was previously isolated from the germline genome of E. burgeri. All sequences were only found on all EEEb1-positive E-chromosomes. Copy number estimation of the repeated elements by slot-blot hybridization revealed that (i) the EEEb1-6 family members occupied 39.9% of the total eliminated DNA, and (ii) a small number of repeats were retained in somatic cells, suggesting that there is incomplete elimination of the repeated elements. These results provide new insights into the mechanisms involved in the chromosome elimination and the evolution of E-chromosomes.
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3
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Helmprobst F, Kneitz S, Klotz B, Naville M, Dechaud C, Volff JN, Schartl M. Differential expression of transposable elements in the medaka melanoma model. PLoS One 2021; 16:e0251713. [PMID: 34705830 PMCID: PMC8550402 DOI: 10.1371/journal.pone.0251713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/30/2021] [Indexed: 12/16/2022] Open
Abstract
Malignant melanoma incidence is rising worldwide. Its treatment in an advanced state is difficult, and the prognosis of this severe disease is still very poor. One major source of these difficulties is the high rate of metastasis and increased genomic instability leading to a high mutation rate and the development of resistance against therapeutic approaches. Here we investigate as one source of genomic instability the contribution of activation of transposable elements (TEs) within the tumor. We used the well-established medaka melanoma model and RNA-sequencing to investigate the differential expression of TEs in wildtype and transgenic fish carrying melanoma. We constructed a medaka-specific TE sequence library and identified TE sequences that were specifically upregulated in tumors. Validation by qRT- PCR confirmed a specific upregulation of a LINE and an LTR element in malignant melanomas of transgenic fish.
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Affiliation(s)
- Frederik Helmprobst
- Physiological Chemistry, Biocenter, University of Würzburg, Würzburg, Germany
- Department of Neuropathology, Philipps-University Marburg, Marburg, Germany
- * E-mail: (FH); (MS)
| | - Susanne Kneitz
- Physiological Chemistry, Biocenter, University of Würzburg, Würzburg, Germany
- Biochemistry and Cell Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Barbara Klotz
- Physiological Chemistry, Biocenter, University of Würzburg, Würzburg, Germany
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France
| | - Corentin Dechaud
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon, Lyon, France
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, United States of America
- Developmental Biochemistry, University of Würzburg, Würzburg, Germany
- * E-mail: (FH); (MS)
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4
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Chan PP, Lin BY, Mak AJ, Lowe TM. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res 2021; 49:9077-9096. [PMID: 34417604 PMCID: PMC8450103 DOI: 10.1093/nar/gkab688] [Citation(s) in RCA: 515] [Impact Index Per Article: 171.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 12/17/2022] Open
Abstract
tRNAscan-SE has been widely used for transfer RNA (tRNA) gene prediction for over twenty years, developed just as the first genomes were decoded. With the massive increase in quantity and phylogenetic diversity of genomes, the accurate detection and functional prediction of tRNAs has become more challenging. Utilizing a vastly larger training set, we created nearly one hundred specialized isotype- and clade-specific models, greatly improving tRNAscan-SE’s ability to identify and classify both typical and atypical tRNAs. We employ a new comparative multi-model strategy where predicted tRNAs are scored against a full set of isotype-specific covariance models, allowing functional prediction based on both the anticodon and the highest-scoring isotype model. Comparative model scoring has also enhanced the program's ability to detect tRNA-derived SINEs and other likely pseudogenes. For the first time, tRNAscan-SE also includes fast and highly accurate detection of mitochondrial tRNAs using newly developed models. Overall, tRNA detection sensitivity and specificity is improved for all isotypes, particularly those utilizing specialized models for selenocysteine and the three subtypes of tRNA genes encoding a CAU anticodon. These enhancements will provide researchers with more accurate and detailed tRNA annotation for a wider variety of tRNAs, and may direct attention to tRNAs with novel traits.
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Affiliation(s)
- Patricia P Chan
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Brian Y Lin
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Allysia J Mak
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA
| | - Todd M Lowe
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA
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Han G, Zhang N, Jiang H, Meng X, Qian K, Zheng Y, Xu J, Wang J. Diversity of short interspersed nuclear elements (SINEs) in lepidopteran insects and evidence of horizontal SINE transfer between baculovirus and lepidopteran hosts. BMC Genomics 2021; 22:226. [PMID: 33789582 PMCID: PMC8010984 DOI: 10.1186/s12864-021-07543-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 03/22/2021] [Indexed: 11/16/2022] Open
Abstract
Background Short interspersed nuclear elements (SINEs) belong to non-long terminal repeat (non-LTR) retrotransposons, which can mobilize dependent on the help of counterpart long interspersed nuclear elements (LINEs). Although 234 SINEs have been identified so far, only 23 are from insect species (SINEbase: http://sines.eimb.ru/). Results Here, five SINEs were identified from the genome of Plutella xylostella, among which PxSE1, PxSE2 and PxSE3 were tRNA-derived SINEs, PxSE4 and PxSE5 were 5S RNA-derived SINEs. A total of 18 related SINEs were further identified in 13 lepidopteran insects and a baculovirus. The 3′-tail of PxSE5 shares highly identity with that of LINE retrotransposon, PxLINE1. The analysis of relative age distribution profiles revealed that PxSE1 is a relatively young retrotransposon in the genome of P. xylostella and was generated by recent explosive amplification. Integration pattern analysis showed that SINEs in P. xylostella prefer to insert into or accumulate in introns and regions 5 kb downstream of genes. In particular, the PxSE1-like element, SlNPVSE1, in Spodoptera litura nucleopolyhedrovirus II genome is highly identical to SfSE1 in Spodoptera frugiperda, SlittSE1 in Spodoptera littoralis, and SlituSE1 in Spodoptera litura, suggesting the occurrence of horizontal transfer. Conclusions Lepidopteran insect genomes harbor a diversity of SINEs. The retrotransposition activity and copy number of these SINEs varies considerably between host lineages and SINE lineages. Host-parasite interactions facilitate the horizontal transfer of SINE between baculovirus and its lepidopteran hosts. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07543-z.
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Affiliation(s)
- Guangjie Han
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Lixiahe District Institute of Agricultural Sciences, Yangzhou, 225008, China
| | - Nan Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Heng Jiang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Xiangkun Meng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Kun Qian
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Yang Zheng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Jian Xu
- Jiangsu Lixiahe District Institute of Agricultural Sciences, Yangzhou, 225008, China.
| | - Jianjun Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China. .,Joint International Research Laboratory of Agriculture andAgri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
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Colletti A, Savinelli B, Di Muzio G, Rizzo L, Tamburello L, Fraschetti S, Musco L, Danovaro R. The date mussel Lithophaga lithophaga: Biology, ecology and the multiple impacts of its illegal fishery. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 744:140866. [PMID: 32674023 DOI: 10.1016/j.scitotenv.2020.140866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/29/2020] [Accepted: 07/08/2020] [Indexed: 05/26/2023]
Abstract
The date mussel Lithophaga lithophaga is an edible endolithic bivalve, protected by the EU Habitats Directive and other international agreements, living inside carbonate rocks. Its illegal harvesting is carried by breaking the rocks where the bivalve grows. The impact has cascade consequences as it causes permanent changes in the substrate characteristics, the removal of benthic species, a shift from highly complex to structurally simplified habitats. As a result, the rich biodiversity of rocky reefs turns into a biological desert, named "barren". Along with the over exploitation of fish, this practice leads to the increase of sea urchin density and grazing pressure on habitats, hampering the resilience of the associated biodiversity and functions. This paper summarizes the information on date mussel biology, ecology, ecotoxicology, fishery and the legal framework regulating its protection. Evidence indicates that illegal harvesting is still operated and widespread along the Mediterranean and has huge costs in terms of loss of natural capital and ecosystem services, and in terms of active ecological restoration. Two case study areas (the Sorrento and Salento peninsulas) were selected to assess the economic costs of this practice. Tangible economic costs in terms of ecosystems services' loss are huge (from ca. 35,000 to more than 400,000 euros/year in 6.6 km of Sorrento and ca. 1.8 million euros/year along the 69 km of Salento). These costs are, on average, ca. 30 times lower than those of ecosystem restoration. Data mining from websites indicates that date mussels are presently commercialized in hundreds of restaurants in Greece, Balkan countries, Spain and Italy, favoured also by the lack of appropriate consumer information. This practice should be controlled and contrasted at local scale, enforced by national legislations, and implemented by transnational initiatives. Social campaigns are needed to increase public awareness of the serious consequences of date-mussel fishery and consumption.
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Affiliation(s)
- Alberto Colletti
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121 Naples, Italy
| | - Beatrice Savinelli
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121 Naples, Italy
| | - Giorgia Di Muzio
- Department of Life Sciences and Systems Biology, University of Torino, via Accademia Albertina 13, 10123 Torino, Italy
| | - Lucia Rizzo
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121 Naples, Italy
| | - Laura Tamburello
- Department of Integrative Marine Ecology, Ischia Marine Centre, Stazione Zoologica Anton Dohrn, Punta San Pietro, 80077 Ischia, Naples, Italy
| | - Simonetta Fraschetti
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121 Naples, Italy; Department of Biology, University of Naples Federico II, via Cinthia, 80126 Naples, Italy
| | - Luigi Musco
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121 Naples, Italy.
| | - Roberto Danovaro
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121 Naples, Italy; Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131 Ancona, Italy
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Kojima KK. Hagfish genome reveals parallel evolution of 7SL RNA-derived SINEs. Mob DNA 2020; 11:18. [PMID: 32489435 PMCID: PMC7245038 DOI: 10.1186/s13100-020-00210-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/27/2020] [Indexed: 11/26/2022] Open
Abstract
Background Short interspersed elements (SINEs) are ubiquitous components of eukaryotic genomes. SINEs are composite transposable elements that are mobilized by non-long terminal repeat (non-LTR) retrotransposons, also called long interspersed elements (LINEs). The 3′ part of SINEs usually originated from that of counterpart non-LTR retrotransposons. The 5′ part of SINEs mostly originated from small RNA genes. SINE1 is a group of SINEs whose 5′ part originated from 7SL RNA, and is represented by primate Alu and murine B1. Well-defined SINE1 has been found only from Euarchontoglires, a group of mammals, in contrast to the wide distribution of SINE2, which has a tRNA-derived sequence, from animals to plants to protists. Both Alu and B1 are mobilized by L1-type non-LTR retrotransposons, which are the only lineage of autonomous non-LTR retrotransposons active in these mammalian lineages. Results Here a new lineage of SINE1 is characterized from the seashore hagfish Eptatretus burgeri genome. This SINE1 family, designated SINE1-1_EBu, is young, and is transposed by RTE-type non-LTR retrotransposon, not L1-type. Comparison with other SINE families from hagfish indicated the birth of SINE1-1_EBu through chimera formation of a 7SL RNA-derived sequence and an older tRNA-derived SINE family. It reveals parallel evolution of SINE1 in two vertebrate lineages with different autonomous non-LTR retrotransposon partners. The comparison between two SINE1 lineages supports that the RNA secondary structure of the Alu domain of 7SL RNA is required for the efficient retrotransposition. Conclusions The hagfish SINE1 is the first evident SINE1 family found outside of Euarchontoglires. Independent evolution of SINE1 with similar RNA secondary structure originated in 7SL RNA indicates the functional importance of 7SL RNA-derived sequence in the proliferation of SINEs.
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Affiliation(s)
- Kenji K Kojima
- Genetic Information Research Institute, Cupertino, CA 95014 USA
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8
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Nishihara H. Retrotransposons spread potential cis-regulatory elements during mammary gland evolution. Nucleic Acids Res 2020; 47:11551-11562. [PMID: 31642473 PMCID: PMC7145552 DOI: 10.1093/nar/gkz1003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 10/14/2019] [Accepted: 10/17/2019] [Indexed: 12/18/2022] Open
Abstract
Acquisition of cis-elements is a major driving force for rewiring a gene regulatory network. Several kinds of transposable elements (TEs), mostly retrotransposons that propagate via a copy-and-paste mechanism, are known to possess transcription factor binding motifs and have provided source sequences for enhancers/promoters. However, it remains largely unknown whether retrotransposons have spread the binding sites of master regulators of morphogenesis and accelerated cis-regulatory expansion involved in common mammalian morphological features during evolution. Here, I demonstrate that thousands of binding sites for estrogen receptor α (ERα) and three related pioneer factors (FoxA1, GATA3 and AP2γ) that are essential regulators of mammary gland development arose from a spreading of the binding motifs by retrotransposons. The TE-derived functional elements serve primarily as distal enhancers and are enriched around genes associated with mammary gland morphogenesis. The source TEs occurred via a two-phased expansion consisting of mainly L2/MIR in a eutherian ancestor and endogenous retrovirus 1 (ERV1) in simian primates and murines. Thus the build-up of potential sources for cis-elements by retrotransposons followed by their frequent utilization by the host (co-option/exaptation) may have a general accelerating effect on both establishing and diversifying a gene regulatory network, leading to morphological innovation.
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Affiliation(s)
- Hidenori Nishihara
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-S2-17, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
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Seibt KM, Schmidt T, Heitkam T. The conserved 3' Angio-domain defines a superfamily of short interspersed nuclear elements (SINEs) in higher plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:681-699. [PMID: 31610059 DOI: 10.1111/tpj.14567] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
Repetitive sequences are ubiquitous components of eukaryotic genomes affecting genome size and evolution as well as gene regulation. Among them, short interspersed nuclear elements (SINEs) are non-coding retrotransposons usually shorter than 1000 bp. They contain only few short conserved structural motifs, in particular an internal promoter derived from cellular RNAs and a mostly AT-rich 3' tail, whereas the remaining regions are highly variable. SINEs emerge and vanish during evolution, and often diversify into numerous families and subfamilies that are usually specific for only a limited number of species. In contrast, at the 3' end of multiple plant SINEs we detected the highly conserved 'Angio-domain'. This 37 bp segment defines the Angio-SINE superfamily, which encompasses 24 plant SINE families widely distributed across 13 orders within the plant kingdom. We retrieved 28 433 full-length Angio-SINE copies from genome assemblies of 46 plant species, frequently located in genes. Compensatory mutations in and adjacent to the Angio-domain imply selective restraints maintaining its RNA structure. Angio-SINE families share segmental sequence similarities, indicating a modular evolution with strong Angio-domain preservation. We suggest that the conserved domain contributes to the evolutionary success of Angio-SINEs through either structural interactions between SINE RNA and proteins increasing their transpositional efficiency, or by enhancing their accumulation in genes.
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Affiliation(s)
- Kathrin M Seibt
- Faculty of Biology, Technische Universität Dresden, Zellescher Weg 20b, Dresden, 01217, Germany
| | - Thomas Schmidt
- Faculty of Biology, Technische Universität Dresden, Zellescher Weg 20b, Dresden, 01217, Germany
| | - Tony Heitkam
- Faculty of Biology, Technische Universität Dresden, Zellescher Weg 20b, Dresden, 01217, Germany
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Nishihara H. Transposable elements as genetic accelerators of evolution: contribution to genome size, gene regulatory network rewiring and morphological innovation. Genes Genet Syst 2020; 94:269-281. [PMID: 31932541 DOI: 10.1266/ggs.19-00029] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In the current era, as a growing number of genome sequence assemblies have been reported in animals, an in-depth analysis of transposable elements (TEs) is one of the most fundamental and essential studies for evolutionary genomics. Although TEs have, in general, been regarded as non-functional junk/selfish DNA, parasitic elements or harmful mutagens, studies have revealed that TEs have had a substantial and sometimes beneficial impact on host genomes in several ways. First, TEs are themselves diverse and thus provide lineage-specific characteristics to the genomes. Second, because TEs constitute a substantial fraction of animal genomes, they are a major contributing factor to evolutionary changes in genome size and composition. Third, host organisms have co-opted many repetitive sequences as genes, cis-regulatory elements and chromatin domain boundaries, which alter gene regulatory networks and in addition are partly involved in morphological evolution, as has been well documented in mammals. Here, I review the impact of TEs on various aspects of the genome, such as genome size and diversity in animals, as well as the evolution of gene networks and genome architecture in mammals. Given that a number of TE families probably remain to be discovered in many non-model organisms, unknown TEs may have contributed to gene networks in a much wider variety of animals than considered previously.
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Luchetti A, Lomiento M, Mantovani B. Riding the Wave: The SINE-Specific V Highly-Conserved Domain Spread into Mammalian Genomes Exploiting the Replication Burst of the MER6 DNA Transposon. Int J Mol Sci 2019; 20:ijms20225607. [PMID: 31717545 PMCID: PMC6887750 DOI: 10.3390/ijms20225607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 02/06/2023] Open
Abstract
Transposable elements are widely distributed within genomes where they may significantly impact their evolution and cell functions. Short interspersed elements (SINEs) are non-autonomous, fast-evolving elements, but some of them carry a highly conserved domain (HCD), whose sequence remained substantially unchanged throughout the metazoan evolution. SINEs carrying the HCD called V are absent in amniote genomes, but V-like sequences were found within the miniature inverted-repeat transposable element (MITE) MER6 in Homo sapiens. In the present work, the genomic distribution and evolution of MER6 are investigated, in order to reconstruct the origin of human V domain and to envisage its possible functional role. The analysis of 85 tetrapod genomes revealed that MER6 and its variant MER6A are found in primates, while only the MER6A variant was found in bats and eulipotyphlans. These MITEs appeared no longer active, in line with literature data on mammalian DNA transposons. Moreover, they appeared to have originated from a Mariner element found in turtles and from a V-SINE from bony fishes. MER6 insertions were found within genes and conserved in mRNAs: in line with previous hypothesis on functional role of HCDs, the MER6 V domain may be important for cell function also in mammals.
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Affiliation(s)
- Andrea Luchetti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy;
- Correspondence: ; Tel.: +39-051-209-4165
| | - Mariana Lomiento
- Sant’Orsola Malpighi Hospital, University of Bologna, 40138 Bologna Italy;
| | - Barbara Mantovani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy;
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12
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Leclère L, Horin C, Chevalier S, Lapébie P, Dru P, Peron S, Jager M, Condamine T, Pottin K, Romano S, Steger J, Sinigaglia C, Barreau C, Quiroga Artigas G, Ruggiero A, Fourrage C, Kraus JEM, Poulain J, Aury JM, Wincker P, Quéinnec E, Technau U, Manuel M, Momose T, Houliston E, Copley RR. The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle. Nat Ecol Evol 2019; 3:801-810. [PMID: 30858591 DOI: 10.1038/s41559-019-0833-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 01/30/2019] [Indexed: 12/14/2022]
Abstract
Jellyfish (medusae) are a distinctive life-cycle stage of medusozoan cnidarians. They are major marine predators, with integrated neurosensory, muscular and organ systems. The genetic foundations of this complex form are largely unknown. We report the draft genome of the hydrozoan jellyfish Clytia hemisphaerica and use multiple transcriptomes to determine gene use across life-cycle stages. Medusa, planula larva and polyp are each characterized by distinct transcriptome signatures reflecting abrupt life-cycle transitions and all deploy a mixture of phylogenetically old and new genes. Medusa-specific transcription factors, including many with bilaterian orthologues, associate with diverse neurosensory structures. Compared to Clytia, the polyp-only hydrozoan Hydra has lost many of the medusa-expressed transcription factors, despite similar overall rates of gene content evolution and sequence evolution. Absence of expression and gene loss among Clytia orthologues of genes patterning the anthozoan aboral pole, secondary axis and endomesoderm support simplification of planulae and polyps in Hydrozoa, including loss of bilateral symmetry. Consequently, although the polyp and planula are generally considered the ancestral cnidarian forms, in Clytia the medusa maximally deploys the ancestral cnidarian-bilaterian transcription factor gene complement.
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Affiliation(s)
- Lucas Leclère
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Coralie Horin
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Sandra Chevalier
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Pascal Lapébie
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.,Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Marseille, France
| | - Philippe Dru
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Sophie Peron
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Muriel Jager
- Evolution Paris-Seine, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, Paris, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB UMR 7205), Sorbonne Université, MNHN, CNRS, EPHE, Paris, France
| | - Thomas Condamine
- Evolution Paris-Seine, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, Paris, France
| | - Karen Pottin
- Evolution Paris-Seine, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, Paris, France.,Laboratoire de Biologie du Développement (IBPS-LBD, UMR7622), Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Paris, France
| | - Séverine Romano
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Julia Steger
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.,Laboratoire de Biologie du Développement (IBPS-LBD, UMR7622), Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Paris, France
| | - Chiara Sinigaglia
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.,Institut de Génomique Fonctionnelle de Lyon, École Normale Supérieure de Lyon, CNRS UMR 5242-INRA USC 1370, Lyon cedex 07, France
| | - Carine Barreau
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Gonzalo Quiroga Artigas
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.,The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
| | - Antonella Ruggiero
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.,Centre de Recherche de Biologie cellulaire de Montpellier, CNRS UMR 5237, Université de Montpellier, Montpellier Cedex 5, France
| | - Cécile Fourrage
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.,Service de Génétique UMR 781, Hôpital Necker-APHP, Paris, France
| | - Johanna E M Kraus
- Department for Molecular Evolution and Development, Centre of Organismal Systems Biology, University of Vienna, Vienna, Austria.,Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique, Université Paris-Saclay, Evry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Eric Quéinnec
- Evolution Paris-Seine, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, Paris, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB UMR 7205), Sorbonne Université, MNHN, CNRS, EPHE, Paris, France
| | - Ulrich Technau
- Department for Molecular Evolution and Development, Centre of Organismal Systems Biology, University of Vienna, Vienna, Austria
| | - Michaël Manuel
- Evolution Paris-Seine, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, Paris, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB UMR 7205), Sorbonne Université, MNHN, CNRS, EPHE, Paris, France
| | - Tsuyoshi Momose
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Evelyn Houliston
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France
| | - Richard R Copley
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Université, CNRS, Villefranche-sur-mer, France.
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13
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Abstract
Transfer RNAs are the largest, most complex non-coding RNA family, universal to all living organisms. tRNAscan-SE has been the de facto tool for predicting tRNA genes in whole genomes. The newly developed version 2.0 has incorporated advanced methodologies with improved probabilistic search software and a suite of new gene models, enabling better functional classification of predicted genes. This chapter describes the use of the UNIX command-driven and online web versions, illustrating different search modes and options.
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Affiliation(s)
- Patricia P Chan
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.
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14
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Kojima KK. LINEs Contribute to the Origins of Middle Bodies of SINEs besides 3' Tails. Genome Biol Evol 2018; 10:370-379. [PMID: 29325122 PMCID: PMC5786205 DOI: 10.1093/gbe/evy008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2018] [Indexed: 01/06/2023] Open
Abstract
Short interspersed elements (SINEs), which are nonautonomous transposable elements, require the transposition machinery of long interspersed elements (LINEs) to mobilize. SINEs are composed of two or more independently originating parts. The 5′ region is called the “head” and is derived mainly from small RNAs, and the 3′ region (“tail”) originates from the 3′ region of LINEs and is responsible for being recognized by counterpart LINE proteins. The origin of the middle “body” of SINEs is enigmatic, although significant sequence similarities among SINEs from very diverse species have been observed. Here, a systematic analysis of the similarities among SINEs and LINEs deposited on Repbase, a comprehensive database of eukaryotic repeat sequences was performed. Three primary findings are described: 1) The 5′ regions of only two clades of LINEs, RTE and Vingi, were revealed to have contributed to the middle parts of SINEs; 2) The linkage of the 5′ and 3′ parts of LINEs can be lost due to occasional tail exchange of SINEs; and 3) The previously proposed Ceph-domain was revealed to be a fusion of a CORE-domain and a 5′ part of RTE clade of LINE. Based on these findings, a hypothesis that the 5′ parts of bipartite nonautonomous LINEs, which possess only the 5′ and 3′ regions of the original LINEs, can contribute to the undefined middle part of SINEs is proposed.
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Affiliation(s)
- Kenji K Kojima
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.,Genetic Information Research Institute, Mountain View, California
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15
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Biscotti MA, Barucca M, Canapa A. New insights into the genome repetitive fraction of the Antarctic bivalve Adamussium colbecki. PLoS One 2018; 13:e0194502. [PMID: 29590185 PMCID: PMC5874043 DOI: 10.1371/journal.pone.0194502] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/05/2018] [Indexed: 11/29/2022] Open
Abstract
Repetitive DNA represents the major component of the genome in both plant and animal species. It includes transposable elements (TEs), which are dispersed throughout the genome, and satellite DNAs (satDNAs), which are tandemly organized in long arrays. The study of the structure and organization of repetitive DNA contributes to our understanding of genome architecture and the mechanisms leading to its evolution. Molluscs represent one of the largest groups of invertebrates and include organisms with a wide variety of morphologies and lifestyles. To increase our knowledge of bivalves at the genome level, we analysed the Antarctic scallop Adamussium colbecki. The screening of the genomic library evidenced the presence of two novel satDNA elements and the CvA transposon. The interspecific investigation performed in this study demonstrated that one of the two satDNAs isolated in A. colbecki is widespread in polar molluscan species, indicating a possible link between repetitive DNA and abiotic factors. Moreover, the transcriptional activity of CvA and its presence in long-diverged bivalves suggests a possible role for this ancient element in shaping the genome architecture of this clade.
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Affiliation(s)
- Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Marco Barucca
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
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16
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Suh A, Bachg S, Donnellan S, Joseph L, Brosius J, Kriegs JO, Schmitz J. De-novo emergence of SINE retroposons during the early evolution of passerine birds. Mob DNA 2017; 8:21. [PMID: 29255493 PMCID: PMC5729268 DOI: 10.1186/s13100-017-0104-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/29/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Passeriformes ("perching birds" or passerines) make up more than half of all extant bird species. The genome of the zebra finch, a passerine model organism for vocal learning, was noted previously to contain thousands of short interspersed elements (SINEs), a group of retroposons that is abundant in mammalian genomes but considered largely inactive in avian genomes. RESULTS Here we resolve the deep phylogenetic relationships of passerines using presence/absence patterns of SINEs. The resultant retroposon-based phylogeny provides a powerful and independent corroboration of previous sequence-based analyses. Notably, SINE activity began in the common ancestor of Eupasseres (passerines excluding the New Zealand wrens Acanthisittidae) and ceased before the rapid diversification of oscine passerines (suborder Passeri - songbirds). Furthermore, we find evidence for very recent SINE activity within suboscine passerines (suborder Tyranni), following the emergence of a SINE via acquisition of a different tRNA head as we suggest through template switching. CONCLUSIONS We propose that the early evolution of passerines was unusual among birds in that it was accompanied by de-novo emergence and activity of SINEs. Their genomic and transcriptomic impact warrants further study in the light of the massive diversification of passerines.
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Affiliation(s)
- Alexander Suh
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
- Department of Evolutionary Biology (EBC), Uppsala University, SE-75236 Uppsala, Sweden
| | - Sandra Bachg
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
| | - Stephen Donnellan
- South Australian Museum, Adelaide, SA 5000 Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, 5005 Australia
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601 Australia
| | - Jürgen Brosius
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
- Brandenburg Medical School (MHB), D-16816 Neuruppin, Germany
| | - Jan Ole Kriegs
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
- LWL-Museum für Naturkunde, Westfälisches Landesmuseum mit Planetarium, D-48161 Münster, Germany
| | - Jürgen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
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17
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Luchetti A, Plazzi F, Mantovani B. Evolution of Two Short Interspersed Elements in Callorhinchus milii (Chondrichthyes, Holocephali) and Related Elements in Sharks and the Coelacanth. Genome Biol Evol 2017; 9:3824762. [PMID: 28505260 PMCID: PMC5499810 DOI: 10.1093/gbe/evx094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2017] [Indexed: 12/11/2022] Open
Abstract
Short interspersed elements (SINEs) are non-autonomous retrotransposons. Although they usually show fast evolutionary rates, in some instances highly conserved domains (HCDs) have been observed in elements with otherwise divergent sequences and from distantly related species. Here, we document the life history of two HCD-SINE families in the elephant shark Callorhinchus milii, one specific to the holocephalan lineage (CmiSINEs) and another one (SacSINE1-CM) with homologous elements in sharks and the coelacanth (SacSINE1s, LmeSINE1s). The analyses of their relationships indicated that these elements share the same 3′-tail, which would have allowed both elements to rise to high copy number by exploiting the C. milii L2-2_CM long interspersed element (LINE) enzymes. Molecular clock analysis on SINE activity in C. milii genome evidenced two replication bursts occurring right after two major events in the holocephalan evolution: the end-Permian mass extinction and the radiation of modern Holocephali. Accordingly, the same analysis on the coelacanth homologous elements, LmeSINE1, identified a replication wave close to the split age of the two extant Latimeria species. The genomic distribution of the studied SINEs pointed out contrasting results: some elements were preferentially sorted out from gene regions, but accumulated in flanking regions, while others appear more conserved within genes. Moreover, data from the C. milii transcriptome suggest that these SINEs could be involved in miRNA biogenesis and may be targets for miRNA-based regulation.
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Affiliation(s)
- Andrea Luchetti
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali - Università di Bologna, Italy
| | - Federico Plazzi
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali - Università di Bologna, Italy
| | - Barbara Mantovani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali - Università di Bologna, Italy
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18
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Luchetti A, Mantovani B. Rare horizontal transmission does not hide long-term inheritance of SINE highly conserved domains in the metazoan evolution. Curr Zool 2016; 62:667-674. [PMID: 29491954 PMCID: PMC5804259 DOI: 10.1093/cz/zow095] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 08/05/2016] [Indexed: 12/27/2022] Open
Abstract
Transposable elements (TEs) are self-replicating, mobile DNA sequences which constitute a significant fraction of eukaryotic genomes. They are generally considered selfish DNA, as their replication and random insertion may have deleterious effects on genome functionalities, although some beneficial effects and evolutionary potential have been recognized. Short interspersed elements (SINEs) are non-autonomous TEs with a modular structure: a small RNA-related head, a body, and a long interspersed element-related tail. Despite their high turnover rate and de novo emergence, the body may retain highly conserved domains (HCDs) shared among divergent SINE families: in metazoans, at least nine HCD-SINEs have been recognized. Data mining on public molecular databases allowed the retrieval of 16 new HCD-SINE families from cnidarian, molluscs, arthropods, and vertebrates. Tracking the ancestry of HCDs on the metazoan phylogeny revealed that some of them date back to the Radiata–Bilateria split. Moreover, phylogenetic and age versus divergence analyses of the most ancient HCDs suggested that long-term vertical inheritance is the rule, with few horizontal transfer events. We suggest that the evolutionary conservation of HCDs may be linked to their potential to serve as recombination hotspots. This indirectly affects host genomes by maintaining active and diverse SINE lineages, whose insertions may impact (either positively or negatively) on the evolution of the genome.
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Affiliation(s)
- Andrea Luchetti
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali-Università di Bologna, Via Selmi 3, Bologna 40126, Italy
| | - Barbara Mantovani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali-Università di Bologna, Via Selmi 3, Bologna 40126, Italy
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19
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Fawcett JA, Innan H. High Similarity between Distantly Related Species of a Plant SINE Family Is Consistent with a Scenario of Vertical Transmission without Horizontal Transfers. Mol Biol Evol 2016; 33:2593-604. [PMID: 27436006 DOI: 10.1093/molbev/msw130] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Many transposable element (TE) families show surprisingly high levels of similarity between distantly related species. This high similarity, coupled with a "patchy" phylogenetic distribution, has often been attributed to frequent horizontal transfers of TEs between species, even though the mechanistic basis tends to be speculative. Here, we studied the evolution of the Au SINE (Short INterspersed Element) family, in which high similarity between distantly related plant species has been reported. We were able to identify several copies present in orthologous regions of various species, including species that diverged ∼90 Ma, thereby confirming the presence of Au SINE at multiple evolutionary time points. We also found that the Au SINE has been degenerating and is en route to disappearing in many species, indicating that the loss of Au SINE is common. Our results suggest that the evolution of the Au SINE can be readily explained by a scenario of vertical transmission without having to invoke hypothetical scenarios of rampant horizontal transfers. The Au SINE was likely present in the common ancestor of all angiosperms and was retained in some lineages while lost from others. The high level of conservation is probably because the sequences were important for ensuring their transpositional activity. This model of TE evolution should provide a basic framework for understanding the evolution of TEs in general.
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Affiliation(s)
- Jeffrey A Fawcett
- SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Hideki Innan
- SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
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