We identified 40,341 high-confidence protein-coding genes, and ~4.29% of annotated genes were located in the gap regions of the YL genome. The annotated genes covered 95.9% of the complete BUSCO genes, and ~92.28% of the annotated genes were expressed in at least one tissue or homologous to known proteins, which suggested that our genes annotation was very complete.
Protein-coding genes were predicted from the repeat-masked YL1 genome with the MAKER-P program22 (v2.31.10), which integrates evidence from protein homology, transcripts, and ab initio predictions. The homology-based evidence was derived by aligning protein sequences from 7 plant species to the YL1 genome assembly. Gene functions were annotated using InterProScan27 (v5.24) by searching against publicly available databases, including ProDom, PRINTS, Pfam, SMRT, PANTHER and PROSITE. The Gene Ontology (GO) and KEGG IDs for each gene were assigned according to the corresponding InterPro entry.
Expression data for the genes were calculated from 240 RNA-seq experiments. These reads were mapped to the stem lettuce genome and read counts were generated for the predicted genes. Downstream analysis was done using R to normalize the raw counts with the DESeq2 package. RPKM, Reads per kilo base per million mapped reads. RPKM = numReads / (geneLength/1000 * totalNumReads/1,000,000)
| Show: Chr1: 6424..7434 | Length: 690 |
|
||||||
|
REF +
- AA |
|
Copyright @Yang Lab Institute of Biotechnology, BAAFS, China 京ICP备18005280号-5
