Abstract
Alpinia katsumadai (A. katsumadai), Alpinia oxyphylla (A. oxyphylla) and Alpinia pumila (A. pumila), which belong to the family Zingiberaceae, exhibit multiple medicinal properties. The chloroplast genome of a non-model plant provides valuable information for species identification and phylogenetic analysis. Here, we sequenced three complete chloroplast genomes of A. katsumadai, A. oxyphylla sampled from Guangdong and A. pumila, and analyzed the published chloroplast genomes of Alpinia zerumbet (A. zerumbet) and A. oxyphylla sampled from Hainan to retrieve useful chloroplast molecular resources for Alpinia. The five Alpinia chloroplast genomes possessed typical quadripartite structures comprising of a large single copy (LSC, 87,248–87,667 bp), a small single copy (SSC, 15,306–18,295 bp) and a pair of inverted repeats (IR, 26,917–29,707 bp). They had similar gene contents, gene orders and GC contents, but were slightly different in the numbers of small sequence repeats (SSRs) and long repeats. Interestingly, fifteen highly divergent regions (rpl36, ycf1, rps15, rpl22, infA, psbT-psbN, accD-psaI, petD-rpoA, psaC-ndhE, ccsA-ndhD, ndhF-rpl32, rps11-rpl36, infA-rps8, psbC-psbZ, and rpl32-ccsA), which could be suitable for species identification and phylogenetic studies, were detected in the Alpinia chloroplast genomes. Comparative analyses among the five chloroplast genomes indicated that 1891 mutational events, including 304 single nucleotide polymorphisms (SNPs) and 118 insertion/deletions (indels) between A. pumila and A. katsumadai, 367 SNPs and 122 indels between A. pumila and A. oxyphylla sampled from Guangdong, 331 SNPs and 115 indels between A. pumila and A. zerumbet, 371 SNPs and 120 indels between A. pumila and A. oxyphylla sampled from Hainan, and 20 SNPs and 23 indels between the two accessions of A. oxyphylla, were accurately located. Additionally, phylogenetic relationships based on SNP matrix among 28 whole chloroplast genomes showed that Alpinia was a sister branch to Amomum in the family Zingiberaceae, and that the five Alpinia accessions were divided into three groups, one including A. pumila, another including A. zerumbet and A. katsumadai, and the other including two accessions of A. oxyphylla. In conclusion, the complete chloroplast genomes of the three medicinal Alpinia species in this study provided valuable genomic resources for further phylogeny and species identification in the family Zingiberaceae.
Highlights
Alpinia Roxb. is the biggest genus in the family Zingiberaceae, which includes more than 230 species of perennial herb [1,2,3]
All the three species of Alpinia we sequenced had a typical quadripartite structure, with a single circular molecule ranged from 161,410 bp (A. oxyphylla sampled from Guangdong) to 162,387 bp (A. katsumadai) in length
The complete chloroplast genome of A. oxyphylla sampled from Guangdong was 59 bp longer than that of A. oxyphylla sampled from Hainan (Table 1)
Summary
Alpinia Roxb. is the biggest genus in the family Zingiberaceae, which includes more than 230 species of perennial herb [1,2,3]. There are 54 species in China and most of them possess multiple medicinal properties; these species include Alpinia katsumadai K. Schum., Alpinia oxyphylla Miq., Alpinia pumila Hook. F., and others [1,2,4] Of these species, the dried seeds of A. katsumadai and A. oxyphylla, and dried rhizomes of A. pumila can be used as traditional Chinese medicine and folk medicine, respectively [1,2,4]. A. katsumadai is mainly distributed in forests of Southern China (Guangdong, Guangxi, and Hainan provinces) as well as south into neighboring Vietnam [1,3]. A. pumila is native to shady, humid mountain valleys in Guangdong, Guangxi, Hunan and Yunnan provinces at altitudes of
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