Widespread imprinting of transposable elements and variable genes in the maize endosperm.
Fertilization and seed development is a critical time in the plant life cycle, and coordinated development of the embryo and endosperm are required to produce a viable seed. In the endosperm, some genes show imprinted expression where transcripts are derived primarily from one parental genome. Impri...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2021-04-01
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| Series: | PLoS Genetics |
| Online Access: | https://doi.org/10.1371/journal.pgen.1009491 |
| _version_ | 1818735144259813376 |
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| author | Sarah N Anderson Peng Zhou Kaitlin Higgins Yaniv Brandvain Nathan M Springer |
| author_facet | Sarah N Anderson Peng Zhou Kaitlin Higgins Yaniv Brandvain Nathan M Springer |
| author_sort | Sarah N Anderson |
| collection | DOAJ |
| description | Fertilization and seed development is a critical time in the plant life cycle, and coordinated development of the embryo and endosperm are required to produce a viable seed. In the endosperm, some genes show imprinted expression where transcripts are derived primarily from one parental genome. Imprinted gene expression has been observed across many flowering plant species, though only a small proportion of genes are imprinted. Understanding how imprinted expression arises has been complicated by the reliance on single nucleotide polymorphisms between alleles to enable testing for imprinting. Here, we develop a method to use whole genome assemblies of multiple genotypes to assess for imprinting of both shared and variable portions of the genome using data from reciprocal crosses. This reveals widespread maternal expression of genes and transposable elements with presence-absence variation within maize and across species. Most maternally expressed features are expressed primarily in the endosperm, suggesting that maternal de-repression in the central cell facilitates expression. Furthermore, maternally expressed TEs are enriched for maternal expression of the nearest gene, and read alignments over maternal TE-gene pairs indicate that these are fused rather than independent transcripts. |
| first_indexed | 2024-12-18T00:16:35Z |
| format | Article |
| id | doaj.art-cd12f5be2abc4956988dc26f10d6663d |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-12-18T00:16:35Z |
| publishDate | 2021-04-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-cd12f5be2abc4956988dc26f10d6663d2022-12-21T21:27:31ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042021-04-01174e100949110.1371/journal.pgen.1009491Widespread imprinting of transposable elements and variable genes in the maize endosperm.Sarah N AndersonPeng ZhouKaitlin HigginsYaniv BrandvainNathan M SpringerFertilization and seed development is a critical time in the plant life cycle, and coordinated development of the embryo and endosperm are required to produce a viable seed. In the endosperm, some genes show imprinted expression where transcripts are derived primarily from one parental genome. Imprinted gene expression has been observed across many flowering plant species, though only a small proportion of genes are imprinted. Understanding how imprinted expression arises has been complicated by the reliance on single nucleotide polymorphisms between alleles to enable testing for imprinting. Here, we develop a method to use whole genome assemblies of multiple genotypes to assess for imprinting of both shared and variable portions of the genome using data from reciprocal crosses. This reveals widespread maternal expression of genes and transposable elements with presence-absence variation within maize and across species. Most maternally expressed features are expressed primarily in the endosperm, suggesting that maternal de-repression in the central cell facilitates expression. Furthermore, maternally expressed TEs are enriched for maternal expression of the nearest gene, and read alignments over maternal TE-gene pairs indicate that these are fused rather than independent transcripts.https://doi.org/10.1371/journal.pgen.1009491 |
| spellingShingle | Sarah N Anderson Peng Zhou Kaitlin Higgins Yaniv Brandvain Nathan M Springer Widespread imprinting of transposable elements and variable genes in the maize endosperm. PLoS Genetics |
| title | Widespread imprinting of transposable elements and variable genes in the maize endosperm. |
| title_full | Widespread imprinting of transposable elements and variable genes in the maize endosperm. |
| title_fullStr | Widespread imprinting of transposable elements and variable genes in the maize endosperm. |
| title_full_unstemmed | Widespread imprinting of transposable elements and variable genes in the maize endosperm. |
| title_short | Widespread imprinting of transposable elements and variable genes in the maize endosperm. |
| title_sort | widespread imprinting of transposable elements and variable genes in the maize endosperm |
| url | https://doi.org/10.1371/journal.pgen.1009491 |
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