Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry
Abstract Subgenome dominance has been reported in diverse allopolyploid species, where genes from one subgenome are preferentially retained and are more highly expressed than those from other subgenome(s). However, the molecular mechanisms responsible for subgenome dominance remain poorly understood...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2024-03-01
|
| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-46861-0 |
| _version_ | 1797247234112225280 |
|---|---|
| author | Chao Fang Ning Jiang Scott J. Teresi Adrian E. Platts Gaurav Agarwal Chad Niederhuth Patrick P. Edger Jiming Jiang |
| author_facet | Chao Fang Ning Jiang Scott J. Teresi Adrian E. Platts Gaurav Agarwal Chad Niederhuth Patrick P. Edger Jiming Jiang |
| author_sort | Chao Fang |
| collection | DOAJ |
| description | Abstract Subgenome dominance has been reported in diverse allopolyploid species, where genes from one subgenome are preferentially retained and are more highly expressed than those from other subgenome(s). However, the molecular mechanisms responsible for subgenome dominance remain poorly understood. Here, we develop genome-wide map of accessible chromatin regions (ACRs) in cultivated strawberry (2n = 8x = 56, with A, B, C, D subgenomes). Each ACR is identified as an MNase hypersensitive site (MHS). We discover that the dominant subgenome A contains a greater number of total MHSs and MHS per gene than the submissive B/C/D subgenomes. Subgenome A suffers fewer losses of MHS-related DNA sequences and fewer MHS fragmentations caused by insertions of transposable elements. We also discover that genes and MHSs related to stress response have been preferentially retained in subgenome A. We conclude that preservation of genes and their cognate ACRs, especially those related to stress responses, play a major role in the establishment of subgenome dominance in octoploid strawberry. |
| first_indexed | 2024-04-24T19:55:27Z |
| format | Article |
| id | doaj.art-e8f1d6ed51514ca8bb5579842db48b29 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-04-24T19:55:27Z |
| publishDate | 2024-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-e8f1d6ed51514ca8bb5579842db48b292024-03-24T12:25:36ZengNature PortfolioNature Communications2041-17232024-03-0115111410.1038/s41467-024-46861-0Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberryChao Fang0Ning Jiang1Scott J. Teresi2Adrian E. Platts3Gaurav Agarwal4Chad Niederhuth5Patrick P. Edger6Jiming Jiang7Department of Plant Biology, Michigan State UniversityDepartment of Horticulture, Michigan State UniversityDepartment of Horticulture, Michigan State UniversityDepartment of Horticulture, Michigan State UniversityDepartment of Plant Biology, Michigan State UniversityDepartment of Plant Biology, Michigan State UniversityDepartment of Horticulture, Michigan State UniversityDepartment of Plant Biology, Michigan State UniversityAbstract Subgenome dominance has been reported in diverse allopolyploid species, where genes from one subgenome are preferentially retained and are more highly expressed than those from other subgenome(s). However, the molecular mechanisms responsible for subgenome dominance remain poorly understood. Here, we develop genome-wide map of accessible chromatin regions (ACRs) in cultivated strawberry (2n = 8x = 56, with A, B, C, D subgenomes). Each ACR is identified as an MNase hypersensitive site (MHS). We discover that the dominant subgenome A contains a greater number of total MHSs and MHS per gene than the submissive B/C/D subgenomes. Subgenome A suffers fewer losses of MHS-related DNA sequences and fewer MHS fragmentations caused by insertions of transposable elements. We also discover that genes and MHSs related to stress response have been preferentially retained in subgenome A. We conclude that preservation of genes and their cognate ACRs, especially those related to stress responses, play a major role in the establishment of subgenome dominance in octoploid strawberry.https://doi.org/10.1038/s41467-024-46861-0 |
| spellingShingle | Chao Fang Ning Jiang Scott J. Teresi Adrian E. Platts Gaurav Agarwal Chad Niederhuth Patrick P. Edger Jiming Jiang Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry Nature Communications |
| title | Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry |
| title_full | Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry |
| title_fullStr | Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry |
| title_full_unstemmed | Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry |
| title_short | Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry |
| title_sort | dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry |
| url | https://doi.org/10.1038/s41467-024-46861-0 |
| work_keys_str_mv | AT chaofang dynamicsofaccessiblechromatinregionsandsubgenomedominanceinoctoploidstrawberry AT ningjiang dynamicsofaccessiblechromatinregionsandsubgenomedominanceinoctoploidstrawberry AT scottjteresi dynamicsofaccessiblechromatinregionsandsubgenomedominanceinoctoploidstrawberry AT adrianeplatts dynamicsofaccessiblechromatinregionsandsubgenomedominanceinoctoploidstrawberry AT gauravagarwal dynamicsofaccessiblechromatinregionsandsubgenomedominanceinoctoploidstrawberry AT chadniederhuth dynamicsofaccessiblechromatinregionsandsubgenomedominanceinoctoploidstrawberry AT patrickpedger dynamicsofaccessiblechromatinregionsandsubgenomedominanceinoctoploidstrawberry AT jimingjiang dynamicsofaccessiblechromatinregionsandsubgenomedominanceinoctoploidstrawberry |