Network‐based visualisation reveals new insights into transposable element diversity
Abstract Transposable elements (TEs) are widespread across eukaryotic genomes, yet their content varies widely between different species. Factors shaping the diversity of TEs are poorly understood. Understanding the evolution of TEs is difficult because their sequences diversify rapidly and TEs are...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Springer Nature
2021-06-01
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| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.15252/msb.20209600 |
| _version_ | 1797281726282596352 |
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| author | Lisa Schneider Yi‐Ke Guo David Birch Peter Sarkies |
| author_facet | Lisa Schneider Yi‐Ke Guo David Birch Peter Sarkies |
| author_sort | Lisa Schneider |
| collection | DOAJ |
| description | Abstract Transposable elements (TEs) are widespread across eukaryotic genomes, yet their content varies widely between different species. Factors shaping the diversity of TEs are poorly understood. Understanding the evolution of TEs is difficult because their sequences diversify rapidly and TEs are often transferred through non‐conventional means such as horizontal gene transfer. We developed a method to track TE evolution using network analysis to visualise TE sequence and TE content across different genomes. We illustrate our method by first using a monopartite network to study the sequence evolution of Tc1/mariner elements across focal species. We identify a connection between two subfamilies associated with convergent acquisition of a domain from a protein‐coding gene. Second, we use a bipartite network to study how TE content across species is shaped by epigenetic silencing mechanisms. We show that the presence of Piwi‐interacting RNAs is associated with differences in network topology after controlling for phylogenetic effects. Together, our method demonstrates how a network‐based approach can identify hitherto unknown properties of TE evolution across species. |
| first_indexed | 2024-03-07T17:01:36Z |
| format | Article |
| id | doaj.art-0f31713da41040b48b1bd49e8bf86d2e |
| institution | Directory Open Access Journal |
| issn | 1744-4292 |
| language | English |
| last_indexed | 2024-03-07T17:01:36Z |
| publishDate | 2021-06-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj.art-0f31713da41040b48b1bd49e8bf86d2e2024-03-03T03:19:19ZengSpringer NatureMolecular Systems Biology1744-42922021-06-01176n/an/a10.15252/msb.20209600Network‐based visualisation reveals new insights into transposable element diversityLisa Schneider0Yi‐Ke Guo1David Birch2Peter Sarkies3MRC London Institute of Medical Sciences London UKData Sciences Institute Imperial College London UKData Sciences Institute Imperial College London UKMRC London Institute of Medical Sciences London UKAbstract Transposable elements (TEs) are widespread across eukaryotic genomes, yet their content varies widely between different species. Factors shaping the diversity of TEs are poorly understood. Understanding the evolution of TEs is difficult because their sequences diversify rapidly and TEs are often transferred through non‐conventional means such as horizontal gene transfer. We developed a method to track TE evolution using network analysis to visualise TE sequence and TE content across different genomes. We illustrate our method by first using a monopartite network to study the sequence evolution of Tc1/mariner elements across focal species. We identify a connection between two subfamilies associated with convergent acquisition of a domain from a protein‐coding gene. Second, we use a bipartite network to study how TE content across species is shaped by epigenetic silencing mechanisms. We show that the presence of Piwi‐interacting RNAs is associated with differences in network topology after controlling for phylogenetic effects. Together, our method demonstrates how a network‐based approach can identify hitherto unknown properties of TE evolution across species.https://doi.org/10.15252/msb.20209600epigeneticsevolutionnetworkspiRNAstransposable elements |
| spellingShingle | Lisa Schneider Yi‐Ke Guo David Birch Peter Sarkies Network‐based visualisation reveals new insights into transposable element diversity Molecular Systems Biology epigenetics evolution networks piRNAs transposable elements |
| title | Network‐based visualisation reveals new insights into transposable element diversity |
| title_full | Network‐based visualisation reveals new insights into transposable element diversity |
| title_fullStr | Network‐based visualisation reveals new insights into transposable element diversity |
| title_full_unstemmed | Network‐based visualisation reveals new insights into transposable element diversity |
| title_short | Network‐based visualisation reveals new insights into transposable element diversity |
| title_sort | network based visualisation reveals new insights into transposable element diversity |
| topic | epigenetics evolution networks piRNAs transposable elements |
| url | https://doi.org/10.15252/msb.20209600 |
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