A comparative analysis of complete plastid genomes from Prangos fedtschenkoi and Prangos lipskyi (Apiaceae)

摘要

Prangos fedtschenkoi (Regel & Schmalh.) Korovin and P. lipskyi Korovin (Apiaceae) are rare plant species endemic to mountainous regions of Middle Asia. Both are edificators of biotic communities and valuable resource plants. The results of recent phylogenetic analyses place them in Prangos subgen. Koelzella (M. Hiroe) Lyskov & Pimenov and suggest they may possibly represent sister species. To aid in development of molecular markers useful for intraspecific phylogeographic and population‐level genetic studies of these ecologically and economically important plants, we determined their complete plastid genome sequences and compared the results obtained to several previously published plastomes of Apiaceae. The plastomes of P.?fedtschenkoi and P.?lipskyi are typical of Apiaceae and most other higher plant plastid DNAs in their sizes (153,626 and 154,143?bp, respectively), structural organization, gene arrangement, and gene content (with 113 unique genes). A total of 49 and 48 short sequence repeat (SSR) loci of 10?bp or longer were detected in P.?fedtschenkoi and P.?lipskyi plastomes, respectively, representing 42–43 mononucleotides and 6 AT dinucleotides. Seven tandem repeats of 30?bp or longer with a sequence identity ≥90% were identified in each plastome. Further comparisons revealed 319 polymorphic sites between the plastomes (IR, 21; LSC, 234; SSC, 64), representing 43.8% transitions (Ts), 56.1% transversions (Tv), and a Ts/Tv ratio of 0.78. Within genic regions, two indel events were observed in rpo A (6 and 51?bp) and ycf 1 (3 and 12?bp), and one in ndh F (6?bp). The most variable intergenic spacer region was that of acc D/ psa I, with 21.1% nucleotide divergence. Each Prangos species possessed one of two separate inversions (either 5?bp in ndh B intron or 9?bp in pet B intron), and these were predicted to form hairpin structures with flanking repeat sequences of 18 and 19?bp, respectively. Both species have also incorporated novel DNA in the LSC region adjacent to the LSC/IRa junction, and BLAST searches revealed it had a 100?bp match (86% sequence identity) to noncoding mitochondrial DNA. Prangos ‐specific primers were developed for the variable acc D/ psa I intergenic spacer and preliminary PCR‐surveys suggest that this region will be useful for future phylogeographic and population‐level studies.