Whole Genome Assembly and Annotation of Asian rice (Zhou et al, 2020)

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit (Chen et al, 2019) and canonical transcripts assigned with TRaCE (Olson and Ware, 2020).

Source : Gramene