Evolutionary dynamics of the chloroplast genome in Daphne (Thymelaeaceae): comparative analysis with related genera and insights into phylogenetics

Abstract

The family Thymelaeaceae Juss., includes numerous botanically and medicinally important species, yet its taxonomy, particularly within the genus Daphne Tourn. ex L., remains unresolved. In the present study, we sequenced and de novo assembled the chloroplast (cp) genome of Daphne mucronata Royle from Pakistan and assembled cp genomes of four additional Daphne species, one Dirca L. species and two Thymelaea Mill. species using public raw data. Comparative analyses across 14 genera, including 17 Daphne species, revealed substantial structural variation in cp genomes. The cp genomes contained 111–112 unique genes, including 77–78 protein-coding genes, 30 tRNA genes and four rRNA genes. When considering duplicated copies in the inverted repeat regions, the total gene count ranged from 128 to 142 (83–96 protein-coding genes, 37–38 tRNA genes and eight rRNA genes). Variability in total gene number was primarily driven by inverted repeat contraction and expansion and pseudogenization of some genes. ndhF was pseudogenized in seven Daphne species, whereas ndhI and ndhG were pseudogenized in one species each. Two large inversion events were detected, involving 19 and 40 genes, respectively; the first inversion was synapomorphic and provided significant phylogenetic signal. Phylogenetic analysis of shared protein-coding sequences from 74 species (87 individuals) recovered Daphne as a strongly supported monophyletic clade when taxa previously proposed for exclusion from the genus were omitted, whereas Wikstroemia Endl. and Gyrinops Gaertn. exhibited paraphyly. This study expands the cp genome resources for Thymelaeaceae and provides new insights into the structural evolution of cp genome.