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.

Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species

“…With the rapid development of sequencing and bioinformation technology, an increasing number of plant chloroplast genomes, including medicinal plants, have been determined, such as Glyc i ne max 10 , Soughum b i color 11 , Magnol i a off i c i nal i s 12 , Taxus ch i nens i s var. ma i re i 13 and Astragalus membranaceus 14 .…”

Peer Review #1 of "A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional herbal medicinal genus (v0.1)"

“…The cp genome in angiosperms is a circular DNA molecule with a typically quadripartite structure, consisting of two copies of a large inverted repeat (IR) region that separates a largesingle-copy (LSC) region from a small-single-copy (SSC) region (Raubeson & Jansen, 2005;Yang et al, 2010;Gree, 2011;Wicke et al, 2011). Although highly conserved among plants, some differences in gene synteny, copy number and pseudogenes have been observed in cp genome structures (Shradha et al, 2010;Lei et al, 2016;Ivanova et al, 2017). A complete cp genome is valuable for plant taxonomical analyses, phylogenetic reconstructions, speciation processes, and biogeographical inferences at different taxonomic levels.…”

The complete chloroplast genome sequence of a threatened perennial herb species Taibai sweetvetch (Hedysarum taipeicum K.T. Fu)

“…After trimming, the high-quality paired-end reads were assembled with the program MITObim v1.7 (Hahn et al 2013) using the Astragalus mongholicus chloroplast genome sequence as a reference (GenBank accession number KU666554) (Lei et al 2016). Annotations were performed using the online program Dual Organellar Genome Annotator (DOGMA) (Wyman et al 2004).…”