The complete chloroplast genome of the traditional medicinal plant <i>Stellera chamaejasme</i> L. (Thymelaeaceae)

Yun, Narae; Park, Jongsun; Oh, Sang‐Hun

doi:10.1080/23802359.2019.1612296

Cited by 8 publications

(6 citation statements)

References 12 publications

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“…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.…”

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confidence: 99%

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

Hishamuddin

Lee

et al. 2020

Sci Rep

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Aquilaria tree species are naturally distributed in the indomalesian region and are protected against over-exploitation. they produce a fragrant non-timber product of high economic value, agarwood. Ambiguous species delimitation and limited genetic information within Aquilaria are among the impediments to conservation efforts. In this study, we conducted comparative analysis on eight Aquilaria species complete chloroplast (cp) genomes, of which seven were newly sequenced using illumina HiSeq X ten platform followed by de novo assembly. Aquilaria cp genomes possess a typical quadripartite structure including gene order and genomic structure. the length of each of the cp genome is about 174 kbp and encoded between 89 and 92 proteins, 38 tRNAs, and 8 rRNAs, with 27 duplicated in the IR (inverted repeat) region. Besides, 832 repeats (forward, reverse, palindrome and complement repeats) and nine highly variable regions were also identified. The phylogenetic analysis suggests that the topology structure of Aquilaria cp genomes were well presented with strong support values based on the cp genomes data set and matches their geographic distribution pattern. In summary, the complete cp genomes will facilitate development of species-specific molecular tools to discriminate Aquilaria species and resolve the evolutionary relationships of members of the thymelaeaceae family. Aquilaria Lam., is a tropical tree genus from the family Thymelaeaceae. Members of this taxon are widely distributed in the Indomalesia region, but their numbers are declining in the wild. Consequentially, they have entered various Red List categories of the International Union for Conservation of Nature (IUCN). The latest IUCN publication placed four species (A. crassna, A. khasiana, A. malaccensis, and A. rostrata) under "Critically Endangered"; one species (A. microcarpa) as "Endangered"; nine species (A.

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confidence: 99%

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

Hishamuddin

Lee

et al. 2020

Sci Rep

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“…By comparing published cp genome reports on members of the Thymelaeaceae, it was determined that the complete cp genome sequence of Edgeworthia is shorter than those of G. affinis of subfamily Octolepidoideae (176,548 bp) and nine species of Aquilaria (Aquilaria beccariana, Aquilaria crassna, Aquilaria hirta, Aquilaria malaccensis, Aquilaria microcarpa, Aquilaria rostrata, A. 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 , and Pimelea aquilonia (172,364 bp) from the Gnidia group (Foster et al, 2018), all belonging to the Daphneae of subfamily Thymelaeoideae. Stellera chamaejasme, from the monospecific Stellera, was the only species from the Daphne group with a total cp genome size within the cp genome size range of Edgeworthia, which was 173,381 bp (Yun et al, 2019). Eventually, rather small size of the SSC region was observed in the cp genome of most species from Thymelaeaceae.…”

Section: Discussionmentioning

confidence: 99%

“…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. Stellera chamaejasme , from the monospecific Stellera , was the only species from the Daphne group with a total cp genome size within the cp genome size range of Edgeworthia , which was 173,381 bp ( Yun et al, 2019 ). Eventually, rather small size of the SSC region was observed in the cp genome of most species from Thymelaeaceae.…”

Section: Discussionmentioning

confidence: 99%

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

2021

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The complete chloroplast genomes of three species of Edgeworthia namely, Edgeworthia albiflora, Edgeworthia chrysantha, and Edgeworthia gardneri (Thymelaeaceae), are reported and characterized. The chloroplast genomes displayed a typical quadripartite structure with conserved genome arrangement and specific divergence. The genomes ranged in length from 172,708 to 173,621 bp and displayed similar GC content of 36.5–36.7%. A total of 138–139 genes were predicted, including 92–93 protein-coding, 38 tRNAs and eight rRNAs genes. Variation in the number of short simple repeats and inverted region boundaries of the three cp genomes were observed. A mutational hotspot was detected along the nucleotide sequence from the ndhF to the trnL-UAG genes. The chloroplast genome-based and internal transcribed spacer (ITS)-based phylogenetic analyses using maximum-likelihood (ML) and Bayesian inference (BI) revealed that E. albiflora diverged before E. chrysantha and E. gardneri and placed the Edgeworthia clade at the base of the Eurasian Daphne group with strong bootstrap support. With an effective taxonomic treatment of the species of Edgeworthia, further molecular analyses of their intra- and interspecific genetic variation are inclined to support the treatment of E. albiflora and E. gardneri as two natural groups. The genetic information obtained from this study will provide valuable genomic resources for the identification of additional species and for deducing the phylogenetic evolution of Edgeworthia.

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“…After getting first draft of chloroplast genome sequences, gap was filled with GapCloser v1.12 (Zhao et al, 2011) and all bases from the assembled sequences were confirmed using BWA v0.7.17 (Li, 2013) and SAMtools v1.9 (Li et al, 2009). All bioinformatic processes for de novo assembly was conducted by the pipeline, Genome Information System (GeIS; http://geis.infoboss.co.kr), which has been efficiently utilized and optimized in the previous studies (Min et al, 2019;Yun et al, 2019;Kim et al, 2021aKim et al, , 2021bPark et al, 2021b).…”

Section: De Novo Assembly and Annotation Of Diarthron Linifolium Chloroplast Genomementioning

confidence: 99%

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

Park²

2021

Korean J. Pl. Taxon

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Diarthron linifolium Turcz. is an annual herb usually found in sandy soil or limestone areas. Plants in the genus Diarthron are known to have toxic chemicals that may, however, be potentially useful as an anticancer treatment. Diarthron linifolium is a unique species among the species of the genus distributed in Korea. Here, we determine the genetic variation of D. linifolium collected in Korea with a full chloroplast genome and investigate its evolutionary status by means of a phylogenetic analysis. The chloroplast genome of Korean D. linifolium has a total length of 172,644 bp with four subregions; 86,158 bp of large single copy and 2,858 bp of small single copy (SSC) regions are separated by 41,814 bp of inverted repeat (IR) regions. We found that the SSC region of D. linifolium is considerably short but that IRs are relatively long in comparison with other chloroplast genomes. Various simple sequence repeats were identified, and our nucleotide diversity analysis suggested potential marker regions near ndhF. The phylogenetic analysis indicated that D. linifolium from Korea is a sister to the group of Daphne species.

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The complete chloroplast genome of the traditional medicinal plant Stellera chamaejasme L. (Thymelaeaceae)

Cited by 8 publications

References 12 publications

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

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

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

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

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