title: Intraspecific and heteroplasmic variations, gene losses and inversions in the chloroplast genome of Astragalus membranaceus.
abstract: Astragalus membranaceus is an important medicinal plant in Asia. Several of its varieties have been used interchangeably as raw materials for commercial production. High resolution genetic markers are in urgent need to distinguish these varieties. Here, we sequenced and analyzed the chloroplast genome of A. membranaceus (Fisch.) Bunge var. mongholicus (Bunge) P.K. Hsiao using the next generation DNA sequencing technology. The genome was assembled using Abyss and then subjected to gene prediction using CPGAVAS and repeat analysis using MISA, Tandem Repeats Finder, and REPuter. Finally, the genome was subjected phylogenetic and comparative genomic analyses. The complete genome is 123,582 bp long, containing only one copy of the inverted repeat. Gene prediction revealed 110 genes encoding 76 proteins, 30 tRNAs, and four rRNAs. Five intra-specific hypermutation loci were identified, three of which are heteroplasmic. Furthermore, three gene losses and two large inversions were identified. Comparative genomic analyses demonstrated the dynamic nature of the Papilionoideae chloroplast genomes, which showed occurrence of numerous hypermutation loci, frequent gene losses, and fragment inversions. Results obtained herein elucidate the complex evolutionary history of chloroplast genomes and have laid the foundation for the identification of genetic markers to distinguish A. membranaceus varieties.
authors.affiliation: College of Life Science, Shanxi Agricultural University, Shanxi, P.R. China.
authors.forename: Wanjun
authors.initials: W
authors.lastname: Lei
authors.affiliation: Research Center of Medicinal Plants, Shandong Academy of Agricultural Sciences, Shandong, P.R. China.
authors.forename: Dapeng
authors.initials: D
authors.lastname: Ni
authors.affiliation: College of Life Science, Shanxi Agricultural University, Shanxi, P.R. China.
authors.forename: Yujun
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P.R. China.
authors.forename: Junjie
authors.initials: J
authors.lastname: Shao
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P.R. China.
authors.forename: Xincun
authors.initials: X
authors.lastname: Wang
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P.R. China.
authors.forename: Dan
authors.initials: D
authors.lastname: Yang
authors.affiliation: College of Life Science, Shanxi Agricultural University, Shanxi, P.R. China.
authors.forename: Jinsheng
authors.initials: J
authors.lastname: Wang
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P.R. China.
authors.forename: Haimei
authors.initials: H
authors.lastname: Chen
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P.R. China.
authors.forename: Chang
authors.initials: C
authors.lastname: Liu
mesh_terms: D027885:Astragalus propinquus / Q000145:classification / Q000235:genetics*; D001483:Base Sequence; D005075:Biological Evolution; D017353:Gene Deletion; D023061:Gene Order; D017343:Genes, Plant; D056426:Genetic Loci; D005819:Genetic Markers; D014644:Genetic Variation; D059646:Genome Size; D054628:Genome, Chloroplast; D055029:Inverted Repeat Sequences; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers; D010940:Plant Proteins; D012335:RNA, Ribosomal; D012343:RNA, Transfer