The pan-plastome reveals the genetic diversity and genetic divergence of Forsythia suspensa (Oleaceae) from the maternal inheritance perspective

Weeping forsythia ( Forsythia suspensa (Thunb.) Vahl) is one of the 50 essential herbs in Chinese traditional medicine and is valued for its beautiful early spring flowers. The plastome exhibits high genetic variation within species and can be used to reveal species diversity from a maternal perspective. The plastome serves as an effective complement to the nuclear genomic data. In this study, we sequenced and assembled the plastomes of 88 samples covering all of the main distribution regions of F. suspensa to generate a pan-plastomes map and investigate the population structure and genetic diversity of this species. The F. suspensa plastomes exhibited a typical quadripartite structure and 132 annotated genes, with a length of 156,322–156,479 bp. Abundant nucleotide variations were detected among the plastomes, including 734 single nucleotide variations, 211 indels, and 11 small inversions. The three types of indels had significant variations in length. A 1 bp length was the most common for normal-indels and microsatellite-related indels, while 4–6 bp was the most common length of the repeat-related indels. Five well-supported groups were resolved using population structure analysis, the phylogenetic method, and principal component analysis, revealing significant genetic differentiation among the five groups. Genetic divergence was consistent with the geographical pattern, indicating that geographic isolation is one of the factors contributing to the genetic diversity and genetic divergence of F. suspensa. This study evaluated the maternal genetic diversity pattern, generated a pan-plastome map of weeping forsythia, and provided important data for future breeding projects and germplasm preservation. • Pan-plastomes of Forsythia suspensa were constructed and analyzed, identifying 734 SNPs, 211 indels, and 11 small inversions. • Five nutation hotspot regions were identified in plastomes of Forsythia suspensa. • Population structure showed Forsythia suspensa divided into five clusters, with genetic divergence matching geography. • Geographical fragmentation and adaptive evolution promoted genetic differentiation among Forsythia suspensa populations.