Phylogenetic relationships and characterization of the complete chloroplast genome of Actinidia chinensis var. jinshi01
Quality control was performed to remove low-quality reads and adapters using the FastQC (Andrews 2015). A total of 980, 062 clean reads were obtained and the average value of Q30 is 90.88%, indicating the good quality for further analysis. The chloroplast genome was assembled using the SPAdes v 3.5.0 (http://cab.spbu.ru/software/spades/) and annotated using the CpGAVAS (Lapidus et al. 2014; Liu et al. 2012). The tRNA genes were further identified using ARWEN (http://mbio-serv2.mbioekol.lu.se/ARWEN/) and tRNAscan-SE (Lowe and Chan 2016; Laslett and Canback 2008). The physical map of the chloroplast genome of Rosa sterilis was generated using Organellar Genome DRAW. Clean reads were obtained with 150-bp paired-end reads.