Manually annotated gene prediction of the CN14 peach genome

Abstract

Peach (Prunus persica) is a fruit tree in the Rosaceae family and serves as an ideal plant for research on important agronomic characters due to its modest genome size and moderate chromosome number. The high-quality CN14 (from cultivar ‘Zhongyoutao 14′) peach genome was released in 2022. To improve the predicted gene models, RNA-Seq data from 13 individual tissue samples and a tissue mixture were manually compared to the gene models. These newly adjusted gene models (released as CN14 genome, version 2.0) were including total 31546 gene models with a 99.17% BUSCO value. In this v.2.0 annotation, gene models of 3981 transcripts were adjusted, and 742 transcripts were newly added. The number of genes increased from v.1.0 (30181 genes). The newly added and adjusted gene IDs were renamed (Ppv2.XG. XXXXX), while the original names remained for genes with no structural changes. There were 2175 transcription factors/regulators and 1251 protein kinases newly identified. The gene structures of 16 of these genes were verified using RT-PCR, and all were successfully cloned. This updated annotation of the peach genome provides new genes as well as updated gene expression profiles, which will greatly improve gene identification and functional studies in peach.