The complete chloroplast genome of Ranzania japonica , an endangered species native to Japan
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TECHNICAL NOTE
The complete chloroplast genome of Ranzania japonica, an endangered species native to Japan Minglei Wang1 · Yao Chen1 · Faiza Hina1 · Tetsuo Ohi‑Toma2 · Pan Li1
Received: 19 September 2017 / Accepted: 13 October 2017 © Springer Science+Business Media B.V. 2017
Abstract Ranzania japonica, which has high ornamental value, is an endangered species native to Japan. To better understand its genetic background, here we report the first chloroplast (cp) genome of R. japonica. The complete chloroplast genome is 169,224 bp in length and shares the common feature of comprising two copies of inverted repeats (IRs 37,924 bp) that divide the genome into two single-copy (LSC 74,477 bp and SSC 18,899 bp) regions. The genome contains 113 unique genes, including 68 protein coding gene, 37 tRNA genes, and eight rRNA genes. By comparing cp genomes of R. japonica, Mahonia bealei, Berberis amurensis and B. koreana, an expansion of IRs at their junction with LSC was revealed in Ranzania. Keywords Ranzania japonica · Berberidaceae · Chloroplast genome · Comparative genomics Ranzania japonica (T. Itô ex Maxim.) T. Itô is the only species of the genus Ranzania T. Itô (Berberidaceae; Ohwi 1965). It is a rare perennial herb native to deciduous broadleaves forests with heavy snowfalls in the mountains of Minglei Wang and Yao Chen have contributed equally to this work. * Pan Li [email protected] 1
Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo 112‑0001, Japan
2
central Honshu, Japan. The plant bears a single or a small cluster of drooping cup-shaped mauve flowers, which are very elegant and lovely, so it is occasionally used in shade gardens. The Ministry of Environment of Japan (2017) designated R. japonica as an endangered plant, category near threatened (NT). However, no researches of intraspecific genetic diversity have been reported on this beautiful endangered species to date. Thus, to better understand its genetic background, we determined the first complete chloroplast genome of R. japonica, using next-generation sequencing technology. The complete chloroplast genome sequence was registered into GenBank with the accession number MG234280. Total genomic DNA was isolated from silica-dried leaves of one R. japonica using a modified CTAB method (Doyle and Doyle 1987). Purified DNA was sheared (yielding ≤ 800 bp fragments) and the quality of fragmentation was checked on a Bioanalyzer 2100 (Agilent Technologies). The short-insert (500 bp) paired-end libraries preparation and sequencing were performed on Illumina HiSeq 2500 with the read length of 125 bp (Beijing Genomics Institute, BGI). The raw data (approximately 3.96 Gb) was filtered and high quality reads (Phred scores of
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