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

Feruza U. Mustafina, Dong Keun Yi, Kyung Choi, Chang Ho Shin, Komiljon Sh Tojibaev, Stephen R Downie

Research output: Contribution to journalArticle

Abstract

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 rpoA (6 and 51 bp) and ycf1 (3 and 12 bp), and one in ndhF (6 bp). The most variable intergenic spacer region was that of accD/psaI, with 21.1% nucleotide divergence. Each Prangos species possessed one of two separate inversions (either 5 bp in ndhB intron or 9 bp in petB 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 accD/psaI intergenic spacer and preliminary PCR-surveys suggest that this region will be useful for future phylogeographic and population-level studies.

Original languageEnglish (US)
Pages (from-to)364-377
Number of pages14
JournalEcology and Evolution
Volume9
Issue number1
DOIs
StatePublished - Jan 2019

Fingerprint

Prangos
Apiaceae
plastid
genome
intergenic DNA
gene
introns
DNA
development aid
biocenosis
tandem repeat sequences
genes
plastid DNA
mitochondrial DNA
aid
indigenous species
divergence
nucleotides
plastid genome
analysis

Keywords

  • Apiaceae
  • Umbelliferae
  • chloroplast genome
  • mitochondrial DNA
  • plastid DNA

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Ecology
  • Nature and Landscape Conservation

Cite this

A comparative analysis of complete plastid genomes from Prangos fedtschenkoi and Prangos lipskyi (Apiaceae). / Mustafina, Feruza U.; Yi, Dong Keun; Choi, Kyung; Shin, Chang Ho; Tojibaev, Komiljon Sh; Downie, Stephen R.

In: Ecology and Evolution, Vol. 9, No. 1, 01.2019, p. 364-377.

Research output: Contribution to journalArticle

Mustafina, Feruza U. ; Yi, Dong Keun ; Choi, Kyung ; Shin, Chang Ho ; Tojibaev, Komiljon Sh ; Downie, Stephen R. / A comparative analysis of complete plastid genomes from Prangos fedtschenkoi and Prangos lipskyi (Apiaceae). In: Ecology and Evolution. 2019 ; Vol. 9, No. 1. pp. 364-377.
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