Integrative genomics reveals the polygenic basis of seedless in grapevine (Vitis vinifera L.)

The publicly accessible genome data comprises:

1) Haplotype genomes of 'Thompson Seedless' (TS) and 'Black Monukka' (BM) (.fa files) along with annotations (.gff files),

2) Cytoplasmic genomes (mitochondria and chloroplasts),

3) Annotations for tandem repeats,

4) EDTA annotations (available at https://github.com/oushujun/EDTA),

5) panTE (Transposable element) annotations (available at https://github.com/unavailable-2374/TE_Detective-Annotation).

Additionally,

6) Several genomes, such as 'Cabernet Sauvignon', 'Black Corinth Seedless', and 'Black Corinth Seeded', were restructured based on PN_T2T genome similarity using RagTag (https://github.com/malonge/RagTag).

Among these resources,

7) The 'Cabernet Sauvignon' genome was annotated using PN_T2T annotation through Liftoff (https://github.com/agshumate/Liftoff), and it maintains consistent gene IDs between the 'Cabernet Sauvignon' genome and PN_T2T.

Furthermore, we have retained the original data for the protein files of 'Black Corinth Seedless' and 'Black Corinth Seeded'.

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