The complete chloroplast genome sequence of medicinal plant, Daphne tangutica Maxim. (Thymelaeaceae)

Abstract

The complete chloroplast genome sequence of Daphne tangutica Maxim. (Thymelaeaceae), a medicinal plant distributed in northwest alpine region of China, was characterized the complete nucleotide sequence of chloroplast (cp) genome. The total length of cp genome is 169,944 bp, including a large single copy (LSC) region of 84,884 bp, a small single copy (SSC) region of 2248 bp, and a pair of inverted repeats (IRs) of 41,406 bp. The cp genome of D. tangutica contains 137 genes, including 90 protein-coding genes (75 PCG species), 39 transfer RNA genes (31 tRNA species), and eight rRNA genes (four RNA species). A total of 12 genes (tRNA-Lys (UUU), tRNA-Leu (UAA), tRNA-Val (UAC), tRNA-Ile (GAU), tRNA-Ala (UGC), rpl16, rpoC1, petD, rps16, rpl2, ndhB, and ndhA) contains a single intron, and two genes (ycf3 and rps12) contains two introns. The GC content in whole cp genome, LSC region, SSC region, and IR region were 36.8%, 34.8%, 28.6%, and 38.9%, respectively, which are similar to other Thymelaeaceae plants. Phylogenetic analysis suggested that D. tangutica has the closely reltionship with congeneric D. kiusiana.

Comparison of eight complete chloroplast genomes of the endangered Aquilaria tree species (Thymelaeaceae) and their phylogenetic relationships

“…Phylogenetic analysis was performed to determine relatedness of the seven Aquilaria cp genomes sequenced in this study and four publicly available Aquilaria cp genomes: (1) A. crassna (MK779998) 23 , (2) A. sinensis (KT148967) 18 , (3) A. yunnanensis (MG656407) 25 , and (4) A. malaccensis (MH286934) 24 . To place Aquilaria in relation to other species in the family Thymelaeaceae, sequences from G. affinis and P. macrocarpa, and three available accessions: (1) Daphne tangutica (MK455880) 36 , (2) Daphne kiusiana (KY991380) 37 , and (3) Stellera chamaejasme (MK681211) 38 , were included. Neobalanocarpus heimii (MH746730) 39 and Eucalyptus grandis (HM347959) 40 were used as outgroups.…”

Comparative Analysis of Complete Chloroplast Genome Sequences in Edgeworthia (Thymelaeaceae) and New Insights Into Phylogenetic Relationships

“…sinensis , Aquilaria subintegra , and Aquilaria yunnanensis ; 174,693–174,907 bp) from Aquilarieae of subfamily Thymelaeoideae ( Hishamuddin et al, 2020 ), but was longer than the four species of Daphne ( Daphne giraldii , D . kiusiana , Daphne laureola , and Daphne tangutica ; 169,944–171,643 bp) ( Cho et al, 2018 ; Könyves et al, 2019 ; Yan et al, 2019a , b ), two species of Wikstroemia ( W . chamaedaphne and Wikstroemia indica ; 151,731–173,042 bp) from the Daphne group ( Qian and Zhang, 2020 ; Qian et al, 2020 ), and Pimelea aquilonia (172,364 bp) from the Gnidia group ( Foster et al, 2018 ), all belonging to the Daphneae of subfamily Thymelaeoideae.…”

The complete chloroplast genome of Diarthron linifolium (Thymelaeaceae), a species found on a limestone outcrop in eastern Asia

“…1). The SSC region of Diarthron linifolium chloroplast genome is extremely short, which is also found in the chloroplast genomes of neighbor species, including Daphne species (Cho et al, 2018;Yan et al, 2019aYan et al, , 2019bYan et al, , 2021 except Daphne genkwa Siebold & Zucc. (Yoo et al, 2021).…”