Elena I. Terentieva

Tribes and clades within apiaceae subfamily apioideae: The contribution of molecular data

Phylogenetic analyses of chloroplast gene ( rbc L, mat K), intron ( rpl 16, rps 16, rpo C1) and nuclear ribosomal DNA internal transcribed spacer (ITS) sequences and chloroplast DNA restriction sites, with supplementary data from variation in size of the chloroplast genome inverted repeat, have been used to elucidate major clades within Apiaceae ( Umbelliferae ) subfamily Apioideae Drude. This paper summarizes the results of previously published molecular cladistic analyses and presents a provisional classification of the subfamily based on taxonomic congruence among the data sets. Ten tribes ( Aciphylleae M. F. Watson & S. R. Downie, Bupleureae Spreng., Careae Baill., Echinophoreae Benth., Heteromorpheae M. F. Watson & S. R. Downie, Oenantheae Dumort., Pleurospermeae M. F. Watson & S. R. Downie, Pyramidoptereae Boiss., Scandiceae Spreng. and Smyrnieae Spreng.) are erected or confirmed as monophyletic, with Scandiceae comprising subtribes Daucinae Dumort., Scandicinae Tausch and Torilidinae Dumort. Seven additional clades are also recognized but have yet to be treated formally, and at least 23 genera examined to date are of dubious tribal or clade placement. The utility of these different molecular markers for phylogenetic inference in Apioideae is compared based on maximum parsimony analyses of subsets of previously published molecular data sets. Of the six loci sequenced, the ITS region is seen to be evolving most rapidly and rbc L is the most conservative. Intermediate in rate of evolution are mat K and the three chloroplast introns; with rpl 16 and rps 16 evolving slightly faster than mat K or rpo C1. The analysis of restriction sites, however, provided 2–4 times more parsimony informative characters than any single DNA locus sequenced, with estimates of divergence just slightly lower than that of the ITS region. The trees obtained from separate analyses of these reduced data sets are consistent with regard to the major clades inferred and the relationships among them. Similar phylogenies are obtained by combining data or combining trees, representing the supermatrix and supertree approaches to phylogenetic analysis, respectively. The inferred relationship among the tribes and informally recognized major clades within Apioideae is presented.

Towards a molecular phylogeny of Apiaceae subfamily Apioideae: additional information from nuclear ribosomal DNA ITS sequences

Evolutionary relationships among 116 representatives (80 genera) ofApiaceae (Umbelliferae) subfam.Apioideae were investigated by comparative sequencing of the two internal transcribed spacers of the 18S–26S nuclear ribosomal DNA repeat. The resultant phylogenies, inferred using maximum parsimony and neighbor-joining methods, clarified the relationships of several genera whose phylogenetic placements have heretofore been problematic. Comparisons between the phylogenies inferred and the distribution of several phytochemical (coumarins, flavonoids, and phenylpropenes) and morphological (stomates, pollen, and cotyledonary shape) characters were also made, revealing that many of these characters (like those morphological and anatomical characters of the fruit) are highly homoplastic. It is not surprising then that systems of classification ofApioideae based on these characters, particularly with regard to tribal and subtribal designations and relationships, are unsatisfactory. The results of recent serological investigations of the subfamily support several relationships proposed herein using molecular data.

Relationships among genera in Saniculoideae and selected Apioideae (Umbelliferae) inferred from nrITS sequences

The internal transcribed spacers (ITS1 and ITS2) of 18S-26S nuclear ribosomal DNA were newly sequenced for eight species of Umbelliferae (six species from subfamily Saniculoideae: Actinolema macrolema, Astrantia minor, Eryngium giganteum, E. coeruleum, Hacquetia epipactis, and Lagoecia cum inoides, two species from subfamily Hydrocotyloideae: Dickinsia hydrocotyloides and Azorella trifurcata), as well as Hohenackeria exscapa, a species of uncertain position in the family. Phylogenetic analyses of new data, plus previously reported sequences of 52 other species using neighbor-joining, maximum parsimony, and maxim um likelihood methods yielded similar results: (1) Actinolema is sister to Astrantia corresponding to Drude’s treatments; (2) in Astrantia, molecular divergence is revealed between sects. Astrantiella (A. minor) and Astrantia (A. major, A. maxima); (3) Eryngium appears to be paraphyletic; (4) Hacquetia might be treated as a part of Sanicula; and (5) Lagoecia is very distant from all other Saniculoideae and close to some genera of Apioideae. Our results correspond to matK data previously published: (1) Hohenackeria forms a clade with Bupleurum, in a position near the base of the Apioideae tree; (2) Azorella is sister to a large cluster uniting all Saniculoideae and Apioideae, being slightly closer to them than to the Hydrocotyle-Araliaceae clade; (3) Dickinsia is very distant from phenetically similar Hydrocotyle, falling within a large cluster of Apioideae, but also including Lagoecia and Naufraga.

nrDNA ITS sequences and affinities of Sino-Himalayan Apioideae (Umbelliferae)

The internal transcribed spacers (ITS1 and ITS2) of 18S-26S nuclear ribosomal DNA were sequenced for 13 species of Apioideae from the Sino-Himalayan flora [Apium ventricosum (= Sium frigidum), Arcuatopterus thalictrioideus, Cyclorhiza peucedanifolia, Meeboldia achilleifolia, Notopterygium forbesii, N. weberbauerianum, Pternopetalum delavayi, P. vulgare, Pterocyclus rivulorum, Sinocarum cruciatum, Sinodielsia delavayi, Tongoloa elata, and Trachydium simplicifolium], relationships of which are controversial or obscure and unresolved on the basis of morphological data. Phylogenetic trees inferred by neighbor-joining, parsimony analysis, and Bayesian inference are topologically congruent, but not identical. The newly obtained data permit testing of several hypotheses regarding these taxa. Some of the early hypotheses treat local species under well-known European genera (e.g., Apium, Carum, Pimpinella, etc.), but these are not supported by phylogenetic analysis of nuclear rDNA spacer sequences. In particular, Sinodielsia, Meeboldia, Tongoloa, and Pternopetalum are distant from Pimpinella; Pternopetalum, Sinocarum and Tongoloa are remote from Carum; Arcuatopterus is separate from Peucedanum and Angelica; Pternopetalum is distinct from Cryptotaenia; and Notopterygium and Pterocyclus are separate from Pleurospermum. Chinese Notopterygium is shown to be closely related to Siberian and Mongolian Hansenia; this, plus similarity in fruit structure, suggests that they are congeneric. Apium ventricosum, more commonly known as Sium frigidum, appears a close relative of Sinocarum. Affinities of most Sino-Himalayan Apioideae, therefore, are found among taxa from the same and adjacent territories. Wide disjunction between presumptively related taxa has been revealed only in Cyclorhiza and Komarovia. Sinodielsia and Meeboldia are also revealed to be clearly distinct genera.

An attempt to clarify taxonomic relationships in ‘‘Verwandtschaftskreis der Gattung Ligusticum’’ (Umbelliferae-Apioideae) by molecular analysis

Relationships among the taxa of Umbelliferae, presumably close to Ligusticum and Selinum were investigated by two independent molecular taxonomic methods. 134 ITS 1-2 sequences were analyzed (29 new and 2 reinvestigated species) and immunochemical comparison of storage seed proteins for 38 species of Apioideae of Ligusticum affinity was performed, eight reference systems (antisera) were used. Both approaches yield similar results, showing the extremely polyphyletic nature of this group and some large genera (Ligusticum s.l., Selinum s.l., Pachypleurum) in the Umbelliferae. The independent status of the genera Magadania, Sphaenolobium, Arafoe, Lomatocarpa, Dimorphosciadium and some other segregates of Ligusticum, Cnidium and Selinum have been confirmed, but Cnidium proved to be unnatural even as currently circumscribed. In the group of East Asian taxa the genera Oreocome, Ligusticopsis, Cortia and Cortiella appeared to be closely related. Haplosphaera was shown to be a genus of Hansenia-Notopterygium group.

Organization of chloroplast psbA-trnH intergenic spacer in dicotyledonous angiosperms of the family umbelliferae

Chloroplast intergenic psbA-trnH spacer has recently become a popular tool in plant molecular phylogenetic studies at low taxonomic level and as suitable for DNA barcoding studies. In present work, we studied the organization of psbA-trnH in the large family Umbelliferae and its potential as a DNA barcode and phylogenetic marker in this family. Organization of the spacer in Umbelliferae is consistent with a general pattern evident for angiosperms. The 5′-region of the spacer situated directly after the psbA gene is more conserved in length compared to the 3′-region, which has greater sequence variation. This pattern can be attributed to the maintenance of the secondary structural elements in the 5′-region of the spacer needed for posttranscriptional regulation of psbA gene expression. In Umbelliferae only, the conserved region contains a duplication of the fragment corresponding to the loop of the stem-loop structure and an independent appearance of identical sequence complementarities (traits) necessary to stabilize the stem-loop structure in different lineages. The 3′-region of the spacer nearest to trnH ranges greatly in size, mainly due to deletions, and the decrease in spacer length is a general trend in the evolution psbA-trnH in Umbelliferae. The features revealed in spacer organization allow us to use it as phylogenetic marker, and indels seem to be more informative for analyses than nucleotide substitutions. However, high conservation among closely related taxa and occurrence of homoplastic inversions in the stem-loop structure limit its application as DNA barcode.

Broad polyphyly in Pleurospermum s.l. (Umbelliferae-Apioideae) as inferred from nrDNA ITS and chloroplast sequences

Abstract Traditionally the genus Pleurospermum and the related genera Aulacospermum, Hymenidium, Hymenolaena, Physospermopsis, Pseudotrachydium, Pterocyclus, and Trachydium, have been problematic taxa with regard to their circumscription and composition. Pleurospermum s. s. includes one or two closely related boreal species but more than 40 other species, distributed mainly in the Sino-Himalayan floristic area, have been attributed to it by different authors in various classifications. Relationships in this taxonomic group are unclear. A molecular phylogenetic analysis of nuclear (nrITS) and cpDNA (psbA-trnH and trnL-trnF) sequences of representative species of Pleurospermum s. l. and closely related Hymenidium, Aulacospermum, Trachydium, Physospermopsis, Pseudotrachydium, Sinolimprichtia, Pterocyclus, and Hymenolaena (55 species in all) was conducted and compared with an analysis of morphological characters. Only two traditional genera were supported as monophyletic groups in the molecular trees, namely Aulacospermum (including Pseudotrachydium) and Hymenolaena. Two stable groups were revealed within Hymenidium. One group included H. chloroleucum, H. heterosciadium, H. hookeri, and H. delavayi. The second included H. lindleyanum, H. stellatum, H. huzhihaoi, H. wilsonii, and Trachydium roylei. Various species of Hymenidium and Trachydium were scattered throughout the tree. The molecular data did not confirm an early divergence between northern and Sino-Himalayan species of Pleurospermum. This indicates that Pleurospermum s. l. and most of the other genera included in this study are polyphyletic.

Complete plastome sequence of Paeonia lactiflora Pall. (Paeoniaceae: Saxifragales)

Abstract Paeonia lactiflora has been listed as an Endangered species in Russian Federation. The complete plastome was assembled from Next-Generation Sequencing data. It is 152,747 bp in length. It consists of a pair of Inverted Repeat regions (25,651 bp), separated by a small single copy region of 17,033 bp and a large single copy region of 84,412 bp. The plastome encoded 128 genes, including 83 protein coding genes, 37 tRNA, eight rRNA genes, four pseudogenes, and is characterized by loss of the rpl32 and infA genes. Phylogenetic analysis of Paeoniaceae plastomes revealed that P. lactiflora clustered with Eurasian peonies (section Paeoniae).