ИСТИНА

The development of less expensive, high-throughput DNA sequencing methods resulted in a rapid rise in the number of publicly available plastome sequences during the past decade. The increased availability of plastome sequences has provided a wealth of new comparative data for understanding patterns of genome organization, rates of sequence evolution, mechanisms of evolutionary change, and phylogenetic relationships among seed plants. Apiaceae is the important family economically and socially.The best known as medicinal and culinary herbs, such as parsley (Petroselinum crispum ), dill (Anethum graveolens), coriander (Coriandrum sativum), anice (Pimpinélla anísum), chevil (Foeniculum vulgare), caraway (Carum carvi) and cumin (Cuminum cyminum) which are extensively used in cuisines across the world. It contains approximately 3500 of species. Due to extensive phylogenetic research on Apiaceae, over one-third of its species have been sampled for nuclear ribosomal DNA internal transcribed spacer (nrDNA ITS) sequence variation. Phylogenetic classification of Apiaceae was based on taxonomic congruence among the results of phylogenetic analyses of different molecular data sets, including nr ITS DNA, chloroplast DNA (cpDNA) gene and intron sequences, cpDNA restriction sites. Despite numerous phylogenetic studies of this family, intertribal and, especially, deep level relationships within Apioideae remain poorly resolved, or conflicting depending upon the sampling and method of analysis. Comparative analysis of complete plastom genomes is one of the sources of additional phylogenetic information to address these problems. Only two complete plastid genomes of a large Apiaceae family are available from the GeneBank currently (September 2014). It has been shown previously by restriction endonuclease analysis, that some Apioideae cpDNAs have large LSC-IR junction shifts [1]. The goal of our research was to study general and specific patterns of plastome structure and expansions and contractions of the IR in Apioideae. We sequenced and annotated plastid genomes of Seseli montanum and Pastinaca pimpinellifolia. Both genomes possess a typical architecture with a large single copy, a small single copy regions and 2 inverted repeats. The plastomes contain the same set of genes and introns as in other Apioideae (Daucus carota and Anthriscus cerefolium). The length and number of direct repeats vary greatly among the compared genomes, while dispersed inverted repeats in Seseli and Pastinaca are longer than in Daucus or Anthriscus. The de novo sequenced genomes possess shorter IR compared to Daucus and Anthriscus, containing the full ycf2 gene. IR in Seseli contains a partial ycf2 sequence, and Pastinaca lacks ycf2 altogether. Moreover, the genome of P.pimpinellifolia differs from others by the presence of a psbA-pseudogene and the trnH-GUG gene within the inverted repeat B. Such IR may have derived from a Seseli-like genome by shortening of IRb that resulted in the elimination of ycf2 from IR, and the following expansion of IRa that led to the acquisition of the trnH-GUG and pseudo-psbA gene copies at the start of IRb. To determine presence of the psbA-pseudogene in plastid genomes of other Tordylieae species, the ycf2 3’-end region was sequenced. The psbA-pseudogene was found in several Tordyleae species belonging to closely related clades of Heracleum and Pastinaca in ITS trees. All members of “Pastinaca” clade (Leiotulus Pastinaca and Malabaila) are characterized by an insertion of GTA nucleotides in ITS1, which may serve as a synapomorphy of the Pastinaca clade. The genome of S.montanum is similar to typical genomes of eudicots, while the P.pimpinellifolia genome differs by the presence of a psbA-pseudogene and a duplication of trnH-GUG. PCR-based analyses of the Pastinaca relatives also detect presence of the psbA-pseudogene, making this rearrangement a likely clade-specific synapomorphy for the Apioideae tree.