Characterization of the complete chloroplast genome sequence of Primula veris (Ericales: Primulaceae)
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TECHNICAL NOTE
Characterization of the complete chloroplast genome sequence of Primula veris (Ericales: Primulaceae) Tao Zhou1 • Jixiang Zhao1 • Chen Chen1 • Xu Meng1 • Guifang Zhao1
Received: 3 August 2016 / Accepted: 16 August 2016 Ó Springer Science+Business Media Dordrecht 2016
Abstract Primula veris is an important spring blooming perennial with high ecological and genetic values. In the present study, the complete chloroplast (cp) genome of Primula veris (Primulaceae) was assembled based on the Illumina sequencing reads. The complete chloroplast genome of P. veris was 150,856 bp in length and contained a pair of IR regions (25,524 bp) separated by a small single copy region (17,760 bp) and a large single copy region (82,048 bp). The cp genome of P. veris encoded 131 genes including 86 protein-coding genes (79 PCG species), 37 tRNA genes (29 tRNA species) and eight ribosomal RNA genes (four rRNA species). The overall AT content of P. veris cp genome is 62.9 %. The maximum likelihood phylogenetic analysis based on 15 chloroplast genomes revealed that P. veris was closely related to that of congeneric P. sinensis. Keywords Primula veris Chloroplast genome Illumina sequencing Phylogenetic analysis Primula veris is an important spring blooming perennial belongs to family Primulaceae and is mainly distributed in fragmented habitats in Europe. As one of Primula species, P. veris is an established model system in the study of the genetics, evolution, and ecology of heterostylous floral polymorphisms (Nowak et al. 2015). However, the wild resources of P. veris were declined due to excessive
& Guifang Zhao [email protected] 1
Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Sciences, Northwest University, Xi’an, China
grazing and ongoing destruction (Brys and Jacquemyn 2009). Thus it is urgent to adopt corresponding measures to protect this valuable species. Obviously, a good knowledge of comprehensive genomics information would definitely contribute to the formulation of conservation strategy. Previous researches about P. veris mainly focused on its ecological and genetic characterizations (Brys et al. 2003; Van Rossum et al. 2004). To date, there is still no complete chloroplast (cp) genome was characterized for P. veris. Here, we assembled the complete chloroplast genome of P. veris by using Illumina sequencing reads. The cp genome sequence of P. veris from this study will not only pave the way for future evolutionary study on this species but also help to clarify phylogenetic relationships of Primula species. The raw reads sequenced by Illumina Hiseq 2000 platform were retrieved from NCBI Sequence Read Archive database under Accession number: SRR1660452 (Nowak et al. 2015). Firstly, the whole genome sequencing reads were aligned to the reference (P. sinensis chloroplast genome) using bowtie2-2.2.6 (Langmead and Salzberg 2012). Secondly, the matched reads (2.5G) were assembled with MIRA 4.0.2 and SPAdes-3.6.0 (Chevreux et
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