Characterization of the complete chloroplast genome of the wild Himalayan pear Pyrus pashia (Rosales: Rosaceae: Maloidea
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TECHNICAL NOTE
Characterization of the complete chloroplast genome of the wild Himalayan pear Pyrus pashia (Rosales: Rosaceae: Maloideae) Lu Bao1 · Ke Li1 · Yuanwen Teng2 · Dong Zhang1
Received: 27 February 2017 / Accepted: 10 March 2017 © Springer Science+Business Media Dordrecht 2017
Abstract Pyrus pashia is a deciduous fruiting tree species of high commercial, scientific, nutritional and therapeutic values. Many of its wild populations are in danger, and need urgent conservation. To contribute to such efforts, its complete chloroplast genome was assembled from high-throughput Illumina sequencing data. The circular genome is 160,153 bp long, and displays a typical quadripartite structure of the large (LSC, 88,129 bp) and small (SSC, 19,252 bp) single-copy regions, separated by a pair of inverted repeat regions (IRs, 26,386 bp each). It harbors 112 gene species, including 78 protein-coding, 30 transfer RNA and 4 ribosomal RNA gene species. Being similar to many other confamilial taxa, it has a biased base composition (31.35% A, 18.63% C, 17.93% G and 32.09% T) with an overall A+T content of 63.44%. Phylogenetic analysis suggested that P. pashia was more closely related to its congeners than to the other confamilial taxa with sequenced chloroplast genomes. Keywords Pyrus pashia · High-throughput sequencing · Chloroplast genome · MITObim The wild Himalayan pear Pyrus pashia is a deciduous fruiting tree species within the family Rosaceae, and is native to Southwest China and the Himalayas, naturally occurring in * Dong Zhang [email protected] 1
College of Horticulture, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, People’s Republic of China
2
College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, People’s Republic of China
valleys with an elevation of 600–3000 m (Lu et al. 2003). This plant possesses high commercial, scientific, nutritional and therapeutic values. It has been widely used as an important germplasm resource for genetic breeding of pears as well as a pear rootstock across its geographic range because of its high adaptation to local environments (Liu et al. 2013; Lu et al. 2003). It is also well-known for its nutritional and therapeutic importance, and has long been used conventionally by many communities in the Himalayas for treating gastrointestinal, respiratory and cardiovascular ailments (reviewed by Janbaz et al. 2015). In addition, it is regarded as an intermediate species between the occidental and oriental pear groups, and thus may have played an important role in the evolution of the genus Pyrus (Challice and Westwood 1973; Rubtsov 1944). Despite these significant values, many of its wild populations are in danger due to the ecological damages caused by global warming and urbanization, and need urgent conservation (Liu et al. 2013). To gain a better insight into its genetics and genomics and thus contribute to its conservation, we assembled its complete chloroplast genome by using high-throughput Illumina sequencing tec
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