The evolution of multi-gene families and metabolic pathways in the evening primroses (Oenothera: Onagraceae): a comparative transcriptomics approach

The plant genus Oenothera has played an important role in the study of genome evolution and plant defense and reproduction. Here, we built on the 1kp transcriptomic dataset and developed a molecular resource of 63 transcriptomes and present a large-scale comparative study across 29 Oenothera species. We produced 2.3 million transcripts and 25.4 Mb of total length assembly per individual. We used this transcriptome resource to examine genome-wide evolutionary patterns and functional diversification by searching for orthologous genes and performed gene family evolution analysis. We found wide heterogeneity in gene family evolution across the genus, with section Oenothera exhibiting the most pronounced evolutionary changes. Overall, more significant expansions occurred than contractions. We also analyzed the molecular evolution of phenolic metabolism by retrieving proteins annotated for phenolic enzymatic complexes. We identified 1,568 phenolic genes arranged into 83 multigene families tha...月见草属（Oenothera）在基因组进化、植物防御与生殖研究领域始终发挥着重要作用。本研究基于1kp转录组数据集，构建了涵盖63个转录组（transcriptome）的分子资源库，并针对29个月见草属物种开展了大规模比较研究。我们共生成230万条转录本，单个个体的组装总长度可达25.4 Mb。依托该转录组资源，我们通过检索直系同源基因（orthologous genes）并开展基因家族进化分析，解析了全基因组范围的进化模式与功能分化。研究发现该属内基因家族进化呈现广泛异质性，其中月见草组（section Oenothera）的进化改变最为显著。总体而言，基因家族扩张事件显著多于收缩事件。此外，我们通过检索注释为酚类酶复合物的蛋白质序列，分析了酚类代谢的分子进化特征，共鉴定出1568个酚类相关基因，归为83个多基因家族……