The codes to assemble two sorghum cultivars.
Due to the strict restrictions on the gff3 file format by the National Genomics Data Center, I was unable to succeed despite my efforts, so I have hosted the data on Figshare. https://figshare.com/articles/dataset/Sorghum_genome/25764612
Regarding the BTx623 gff3 file, after our gene structure annotation pipeline, I utilized the collinearity among genomic sequences to add structural models of genes that we had not discovered but were annotated in BTx623-v3 and BTx623-v5 (completed by Liftoff), and subsequently, I performed two rounds of updates using PASA.
This version of the gff3 file includes more gene models than either BTx623-v3 or BTx623-v5. I will keep refining this annotation file and update it in a timely manner. I continue to see potential for optimization in this annotation, particularly concerning the length issues of UTRs, and I strongly suggest further validation with RNA-seq data before related analyses.
The gene names in BTx623-v3 and BTx623-v5 are identical; however, the gene names in the gff3 file I uploaded do not match those in the annotation files for versions v3/v5. To prevent this misunderstanding, I have deposited the relationship between the amino acid sequences of the BTx623-T2T transcripts and those of the longest transcripts of v3/v5 on figshare.
Should you wish to learn more about optimizing annotation details, or if any issues arise during use, feel free to contact me at weichuanzheng1202@163.com at any time.