The complete chloroplast genome of Rhododendron kawakamii (Ericaceae)

Abstract Rhododendron kawakamii is endemic in Taiwan island and is a unique and epiphytic species. Here, we report its complete chloroplast genome. The length of the R. kawakamii chloroplast genome is 230,777 bp, with a large single-copy region of 146,155 bp, a small single-copy region of 72,082 bp, and a pair of inverted repeat regions (IRA) of 6,270 bp each. The genome contains 77 protein-coding genes, 29 transfer RNA genes, and four ribosomal RNA genes. In addition, the genome contains 81 simple sequence repeats. Phylogenetic analysis revealed that R. kawakamii is genetically related to R. datiandingense.

Rhododendron kawakamii; chloroplast; genome assembly; next generation sequencing Rhododendron, in the Ericaceae family, is a large and extremely diverse genus, containing more than 1000 species worldwide (Shrestha et al. 2018). Rhododendron kawakamii Hayata is endemic to Taiwan island. Unlike the other Rhododendron species on the island, which are either shrubs or trees, R. kawakamii is epiphytic (Tsai et al. 2012) and naturally distributed in the forest between 1500 and 2600 m. Molecular data supported its uniqueness in the phylogeny and showed that it formed an independent cluster in section Vireya of subgenus Rhododendron (Tsai et al. 2003(Tsai et al. , 2012. Both natural and artificial hybridization among Rhododendron species are common due to their low reproduction barriers (Kaul et al. 1986;Milne et al. 2010), which is particularly true in section Vireya, possibly as a result of adaptive radiation events (Milne et al. 2010). Crossing experiments indicate that R. kawakamii could also hybridize with R. santapaui and produce viable seeds (Kaul et al. 1986). As approximately 70% of Rhododendron are classified as endangered or need conservation (Shrestha et al. 2018), and hybridization presents a grave threat to species integrity (Zhang, Qin, et al. 2020b), we report the complete chloroplast genome of R. kawakamii to provide a germplasm resource for its evolution and conservation studies.
Fresh leaves of R. kawakamii were collected from the Shanlinxi forest recreation area (N23 38 0 7.8 00 , E120 47 0 29.3 00 ). A voucher specimen was deposited at the Herbarium of Taiwan Forest Research Institute (https://taif.tfri.gov.tw/tw/ index.php, Chien-Fan Chen, chenc@tfri.gov.tw) under the voucher number 511025. The genomic DNA of R. kawakamii was extracted by the CTAB (cetyltrimethylammonium bromide) method. The extracted DNA was sequenced using the Illumina HiSeq X Ten system. The sequences were then used to assemble the chloroplast genome of R. kawakamii by Fast-Plast 1.  (Zhang, Gao, et al. 2020a) with the concatenated protein sequences of 77 chloroplast coding genes for R. kawakamii and the other 17 species.
The R. kawakamii chloroplast genome was 230,777 bp in length with a GC content of 35.10%. The genome showed a large single-copy region of 146,155 bp, a small single-copy region of 72,082 bp, and two copies of inverted repeat regions of 6,270 bp each. After annotation, a total of 110 genes were identified in the R. kawakamii chloroplast genome, including 77 protein-coding genes, 29 transfer RNA genes, and four ribosomal RNA genes. Furthermore, a total of 81 simple sequence repeats (SSR) were discovered in the genome. These SSRs included 76 mononucleotides (A/T), 3 dinucleotides (TA) and 2 trinucleotides (AAT/ATT). Phylogenetic analysis revealed that R. kawakamii was genetically related to R. datiandingense (Figure 1).
For the 18 species analyzed in phylogeny, a total of 90 protein-coding genes were annotated in their chloroplast genomes (Table S1), in which clpP, lhbA, orf23, orf28, orf34, orf39, orf46, ORF63, orf64, orf222, ycf1, ycf2, and ycf68 genes were not identified in R. kawakamii chloroplast genome. The orf23, orf28, orf34, orf39, orf46, ORF63, orf64, and orf222 genes were only annotated in two Oryza species, and their functions were unknown. For clpP, lhbA, ycf1, ycf2 and ycf68 genes, they also extensively missed in the other Rhododendron species. clpP gene is a proteolytic subunit of the ATP-dependent Clp protease (Shikanai et al. 2001), may be related to the development of plant (Shikanai et al. 2001;Moreno et al. 2017). lhbA encodes a structural protein of the light-harvesting antenna, may be related to maintenance of stable antenna complexes (Ruf et al. 2000). ycf1, ycf2 and ycf68 genes are in ycf gene family and their functions generally unknown (Logacheva et al. 2017;Slipiko et al. 2020), although ycf2 gene is a putative ATPase (Huang et al. 2017). How these missed genes in R. kawakamii chloroplast are functionally related to the growth of R. kawakamii needs further study in the future.

Disclosure statement
No potential conflict of interest was reported by the author(s).  Data availability statement