Complete chloroplast genome sequence of Magnolia grandiflora and comparative analysis with related species

• DOI: 10.1007/s11427-012-4430-8
• Publication Date: 2013-01-17T17:25:59Z
• Authors: XiWen Li; HuanHuan Gao; YiTao Wang; JingYuan Song; Robert Henry; HeZhen Wu; ZhiGang Hu; Hui Yao; HongMei Luo; Kun Luo; HongLin Pan; ShiLin Chen
• Keywords: 0301 basic medicine; 2300 Environmental Science; 1300 Biochemistry; Inverted repeats; Intron; Genetics and Molecular Biology; Genes, Plant; Magnoliaceae; Evolution, Molecular; 1100 Agricultural and Biological Sciences; 03 medical and health sciences; Species Specificity; Environmental Science(all); Genes, Chloroplast; Genome, Chloroplast; Phylogeny; Base Composition; Agricultural and Biological Sciences(all); Base Sequence; Biochemistry, Genetics and Molecular Biology(all); Inverted Repeat Sequences; DNA, Chloroplast; Chromosome Mapping; High-Throughput Nucleotide Sequencing; Sequence Analysis, DNA; 15. Life on land; SSR; Phylogenetics; Magnolia; Genome, Plant; Microsatellite Repeats

Magnolia grandiflora is an important medicinal, ornamental and horticultural plant species. The chloroplast (cp) genome of M. grandiflora was sequenced using a 454 sequencing platform and the genome structure was compared with other related species. The complete cp genome of M. grandiflora was 159623 bp in length and contained a pair of inverted repeats (IR) of 26563 bp separated by large and small single copy (LSC, SSC) regions of 87757 and 18740 bp, respectively. A total of 129 genes were successfully annotated, 18 of which included introns. The identity, number and GC content of M. grandiflora cp genes were similar to those of other Magnoliaceae species genomes. Analysis revealed 218 simple sequence repeat (SSR) loci, most composed of A or T, contributing to a bias in base composition. The types and abundances of repeat units in Magnoliaceae species were relatively conserved and these loci will be useful for developing M. grandiflora cp genome vectors. In addition, results indicated that the cp genome size in Magnoliaceae species and the position of the IR border were closely related to the length of the ycf1 gene. Phylogenetic analyses based on 66 shared genes from 30 species using maximum parsimony (MP) and maximum likelihood (ML) methods provided strong support for the phylogenetic position of Magnolia. The availability of the complete cp genome sequence of M. grandiflora provides valuable information for breeding of desirable varieties, cp genetic engineering, developing useful molecular markers and phylogenetic analyses in Magnoliaceae.