A comparative analysis of complete plastid genomes fromPrangos fedtschenkoiandPrangos lipskyi(Apiaceae)

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.

Complete Plastid Genome Sequencing of Eight Species from Hansenia, Haplosphaera and Sinodielsia (Apiaceae): Comparative Analyses and Phylogenetic Implications

“…Not surprisingly, Hansenia is more closely related to Haplosphaera but distantly related to Sinodielsia, which has also been confirmed by nrITS sequences and transcriptome data [8,20]. A collective analysis of our results and previous studies [26][27][28][29] found that the lengths of rps19 and trnH genes entering IRs are usually stable in the same genus or phylogenetically related groups. For example, the length of rps19 gene entering IRs is 57-96 bp in Chamaesium species [27], and 49-84 bp in Bupleurum species [26], which are the phylogenetically basal groups in the Chamaesium clade and Bupleureae.…”

The chloroplast genomes of four Bupleurum (Apiaceae) species endemic to Southwestern China, a diversity center of the genus, as well as their evolutionary implications and phylogenetic inferences

“…However, the LSC/IR borders showed differences among Bupleurum species and some Apiaceae taxa. For instance, while the LSC/IRb junction was located within the rps 19 gene in Bupleurum species as well as some taxa in Apiaceae ( Anthriscus , Daucus , Tiedemannia , [ 48 ]), it resided within the rps 12 gene in Anethum [ 48 ], Foeniculum [ 48 ], Prangos [ 51 , 52 ], Petroselinum [ 48 , 52 ]. Our repetitive sequences analysis in addition to previous studies [ 32 – 40 ] showed that the tendency of SDRs and SSRs were similar among Bupleurum species, while the certain diversity in numbers varied.…”

Comparative Analysis of the Complete Plastid Genome of Five Bupleurum Species and New Insights into DNA Barcoding and Phylogenetic Relationship

“…It's worth noting that the gene ndhF traversed the IRb and SSC region, which indicated that there might also be a tendency of expansion in gene ndhF. Among Apiaceae species, the size variation of the plastid genome in the process of evolution mainly results from the expansion and contraction of the IR regions [71,72], and double-strand break (DSB) events may be the main reason of expansions [73]. Plants 2020, 9,…”