Full
Outline
Transposable elements (TEs) are a significant source of genetic diversity in rice and play a crucial role in the domestication process of Asian cultivated rice. However, due to the highly repetitive nature of TE sequences, their identification typically requires high-quality genome sequences. Currently, the limited genomic resources for African cultivated rice (Oryza glaberrima, Og) hinder systematic investigations into TE diversity and its contributions to the Og domestication process.
We constructed a high-resolution pan-TE variation map using the chromosome-level genomes of 21 accessions (11 Og and 10 Oryza barthii [Ob]). We estimated the divergence of each TE variation across the genome using FST analysis and identified 854 selected TE variations putatively involved in the Og domestication process.
The pan-TE variation map comprises 17,097 non-redundant high-quality TE variations with a total length of 39.1 Mb, with 61.7% of the TE variations larger than 1 kb. The total number of TE variations in the Ob accessions was greater than that in the Og accessions. A total of 658 genes harboring selected TE variations were identified as potentially involved in the Og domestication process, which were significantly enriched in biological processes related to basic metabolism. Notably, 30 genes with known functions were involved in the independent domestication of Og.
This study highlights the significant role of TE variations as a source of phenotypic diversity during the Og domestication process. The high-quality pan-TE variation map not only enriches the available variation library for rice breeding but also provides critical theoretical foundations and resource support for the genetic improvement of Og germplasm.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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