Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion.
Structural differences between genomes are a major source of genetic variation that contributes to phenotypic differences. Transposable elements, mobile genetic sequences capable of increasing their copy number and propagating themselves within genomes, can generate structural variation. However, th...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2023-12-01
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| Series: | PLoS Genetics |
| Online Access: | https://doi.org/10.1371/journal.pgen.1011086 |
| _version_ | 1797356364664668160 |
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| author | Manisha Munasinghe Andrew Read Michelle C Stitzer Baoxing Song Claire C Menard Kristy Yubo Ma Yaniv Brandvain Candice N Hirsch Nathan Springer |
| author_facet | Manisha Munasinghe Andrew Read Michelle C Stitzer Baoxing Song Claire C Menard Kristy Yubo Ma Yaniv Brandvain Candice N Hirsch Nathan Springer |
| author_sort | Manisha Munasinghe |
| collection | DOAJ |
| description | Structural differences between genomes are a major source of genetic variation that contributes to phenotypic differences. Transposable elements, mobile genetic sequences capable of increasing their copy number and propagating themselves within genomes, can generate structural variation. However, their repetitive nature makes it difficult to characterize fine-scale differences in their presence at specific positions, limiting our understanding of their impact on genome variation. Domesticated maize is a particularly good system for exploring the impact of transposable element proliferation as over 70% of the genome is annotated as transposable elements. High-quality transposable element annotations were recently generated for de novo genome assemblies of 26 diverse inbred maize lines. We generated base-pair resolved pairwise alignments between the B73 maize reference genome and the remaining 25 inbred maize line assemblies. From this data, we classified transposable elements as either shared or polymorphic in a given pairwise comparison. Our analysis uncovered substantial structural variation between lines, representing both simple and complex connections between TEs and structural variants. Putative insertions in SNP depleted regions, which represent recently diverged identity by state blocks, suggest some TE families may still be active. However, our analysis reveals that within these recently diverged genomic regions, deletions of transposable elements likely account for more structural variation events and base pairs than insertions. These deletions are often large structural variants containing multiple transposable elements. Combined, our results highlight how transposable elements contribute to structural variation and demonstrate that deletion events are a major contributor to genomic differences. |
| first_indexed | 2024-03-08T14:25:33Z |
| format | Article |
| id | doaj.art-cb3777760daf403796ec92959ed765e6 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-03-08T14:25:33Z |
| publishDate | 2023-12-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-cb3777760daf403796ec92959ed765e62024-01-13T05:31:15ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042023-12-011912e101108610.1371/journal.pgen.1011086Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion.Manisha MunasingheAndrew ReadMichelle C StitzerBaoxing SongClaire C MenardKristy Yubo MaYaniv BrandvainCandice N HirschNathan SpringerStructural differences between genomes are a major source of genetic variation that contributes to phenotypic differences. Transposable elements, mobile genetic sequences capable of increasing their copy number and propagating themselves within genomes, can generate structural variation. However, their repetitive nature makes it difficult to characterize fine-scale differences in their presence at specific positions, limiting our understanding of their impact on genome variation. Domesticated maize is a particularly good system for exploring the impact of transposable element proliferation as over 70% of the genome is annotated as transposable elements. High-quality transposable element annotations were recently generated for de novo genome assemblies of 26 diverse inbred maize lines. We generated base-pair resolved pairwise alignments between the B73 maize reference genome and the remaining 25 inbred maize line assemblies. From this data, we classified transposable elements as either shared or polymorphic in a given pairwise comparison. Our analysis uncovered substantial structural variation between lines, representing both simple and complex connections between TEs and structural variants. Putative insertions in SNP depleted regions, which represent recently diverged identity by state blocks, suggest some TE families may still be active. However, our analysis reveals that within these recently diverged genomic regions, deletions of transposable elements likely account for more structural variation events and base pairs than insertions. These deletions are often large structural variants containing multiple transposable elements. Combined, our results highlight how transposable elements contribute to structural variation and demonstrate that deletion events are a major contributor to genomic differences.https://doi.org/10.1371/journal.pgen.1011086 |
| spellingShingle | Manisha Munasinghe Andrew Read Michelle C Stitzer Baoxing Song Claire C Menard Kristy Yubo Ma Yaniv Brandvain Candice N Hirsch Nathan Springer Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion. PLoS Genetics |
| title | Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion. |
| title_full | Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion. |
| title_fullStr | Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion. |
| title_full_unstemmed | Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion. |
| title_short | Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion. |
| title_sort | combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion |
| url | https://doi.org/10.1371/journal.pgen.1011086 |
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