Reidentification of hybridization events with transcriptomic data and phylogenomic study in seabuckthorn

Abstract

The natural hybridization of sea buckthorn is widely observed by researchers. While studies have identified the parents of these hybrid offspring, distinguishing between F1 and Fn generations is challenging for natural hybrids. As a result, the genetic composition of these hybrid offspring remains underexplored. In this study, we propose a novel method for identifying hybrid F1 generations using transcriptome data and reference genomes. We successfully identified eight individuals from two natural hybrid populations of sea buckthorn, all of which were confirmed to be hybrid F1 generations. Additionally, we first noted limitations in detecting heterozygous sites during SNP calling in transcriptome data, where allele-specific expression and low expression of genes or transcripts can lead to heterozygous SNPs being incorrectly identified as homozygous. Furthermore, we constructed a phylogenomic tree of the sea buckthorn genus using transcriptome data and compared the relationships among various sea buckthorn species using SNP and indel molecular markers obtained through transcriptome data.