The complete chloroplast genome sequence of Actinidia arguta : gene structure and genomic resources
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TECHNICAL NOTE
The complete chloroplast genome sequence of Actinidia arguta: gene structure and genomic resources Wenqing Li1 · Yizeng Lu1,2 · Xiaoman Xie1 · Bin Li2 · Yi Han1 · Tao Sun1 · Deshen Liu1
Received: 22 July 2017 / Accepted: 9 August 2017 © Springer Science+Business Media B.V. 2017
Abstract Actinidia arguta, known as hardy kiwi or bower vine, is a cold-hardy species native to East-Asia. Wild populations of hardy kiwi are now in danger which need urgent conservation. In this study, we sequenced the complete chloroplast genome of A. arguta and used these data to assess its genomic resources. The chloroplast genome size of A. arguta is 156,809 bp with a typical quadripartite structure consisting of a pair of inverted repeats of 23,918 bp separated by small and large single copy regions of 20,475 and 88,497 bp. There were 113 unique representative genes, and 50 simple sequences repeats were discovered. Phylogenetic analyses based on whole chloroplast genome showed that the position of A. arguta was on the base of Actinidia. Thus, the complete A. arguta chloroplast genome provides interesting insights and valuable genomic resources that can be used to reconstruct its phylogeny, evaluate genetic variations, and develop conservation strategy of this specie. Keywords Chloroplast genome · Actinidia arguta · Genomic resources · SSRs Wenqing Li and Yizeng Lu have contributed equally to this work. * Xiaoman Xie [email protected] * Bin Li [email protected] 1
Shandong Provincial Center of Forest Tree Germplasm Resources, Jinan 250102, China
State Key Laboratory of Tree Breeding and Forest Genetics, Key Laboratory of Tree Breeding and Forest Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
2
Actinidia arguta, also called kiwi berry, hardy kiwi fruit or mini kiwi, is naturally distributed in East-Asia (Lai et al. 2015). It contains a large amount of vitamin C and polyphenols, and shows a high activity of a cysteine protease, actinidin (Kataoka et al. 2010). However, largely due to anthropogenic over-exploitation and loss of habitat, this species has been listed in the second category of key protected wild plants, and need urgent protection and restoration. To support conservation of this rare species and its populations, markers variable at the population level need to be developed from genomic resources. Chloroplast genome is a highly conserved circular DNA ranging from 115 to 165 kb with a stable genome, gene content and gene order in angiosperms (Li et al. 2016b). The availability of the chloroplast genome provides a powerful genetic resource for DNA barcoding (Dong et al. 2012), species conservation and genetics engineering studies (Li et al. 2016a). Here, we sequenced and analyzed the chloroplast genome of A. arguta based on the Illumina Hiseq X ten system. Our aim was to retrieve chloroplast genome structure and valuable genomic resources for this species. Fresh leaves of A. arguta were collected from wild plant in situ co
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