Identification, characterization and expression analysis of lineage-specific genes within 'Zhongyoutao 14' peach (Prunus persica)

Background: With the development of sequencing technology and the rapid increasing in the number of sequenced genomes, lineage-specific genes (LSGs) have been identified and characterized across various species. Similar to other conserved functional genes, LSGs play a crucial role in biological evolution and development. However, the understanding of LSGs remains limited. This study aims to identify significant gene expression profiles of LSGs in peach, which may contribute to the development of specific tissues and important traits. Methods: Seven peach and 341 exogenous species genomes were used in this study. Firstly, the coding sequences of CN14 peach were compared with other genomes to discover LSGs. Next, the LSGs of CN14 peach were compared with other peach genomes to identify the peach specific genes and orphan genes. Furthermore, the tissue specificity expressed PSGs and orphan genes were identified using transcriptome data. In addition, the genes specific expressed in stem might response to GA3 treatment were identified using RT-qPCR. Result: A total of 74 peach specific genes (PSGs) and 91 Orphan genes were identified. The PSGs and orphan genes had fewer exon numbers, shorter gene lengths and lower molecular weight compared with evolutionarily conserved genes (ECGs). Part of these PSGs and Orphan genes were shown an obvious tissue specificity expression pattern at stem, fruit and flower. Three PSGs and three Orphan genes were identified within the QTLs associated with temperature-sensitive semi-dwarf (TSSD), maturity date (Md), and red flesh around stone (Rfas). Three PSGs and seven Orphan genes were identified in response to GA3, these genes might play important role in stem development of peach. Conclusion: The identification and characterization of PSGs and Orphan genes not only provide valuable peach- specific genetic resources, but also might contribute to peach specific biological process.