Tahir H. Samigullin

Comparative chloroplast genomics and phylogenetics of Fagopyrum esculentum ssp. ancestrale– A wild ancestor of cultivated buckwheat

BackgroundChloroplast genome sequences are extremely informative about species-interrelationships owing to its non-meiotic and often uniparental inheritance over generations. The subject of our study, Fagopyrum esculentum, is a member of the family Polygonaceae belonging to the order Caryophyllales. An uncertainty remains regarding the affinity of Caryophyllales and the asterids that could be due to undersampling of the taxa. With that background, having access to the complete chloroplast genome sequence for Fagopyrum becomes quite pertinent.ResultsWe report the complete chloroplast genome sequence of a wild ancestor of cultivated buckwheat, Fagopyrum esculentum ssp. ancestrale. The sequence was rapidly determined using a previously described approach that utilized a PCR-based method and employed universal primers, designed on the scaffold of multiple sequence alignment of chloroplast genomes. The gene content and order in buckwheat chloroplast genome is similar to Spinacia oleracea. However, some unique structural differences exist: the presence of an intron in the rpl2 gene, a frameshift mutation in the rpl23 gene and extension of the inverted repeat region to include the ycf1 gene. Phylogenetic analysis of 61 protein-coding gene sequences from 44 complete plastid genomes provided strong support for the sister relationships of Caryophyllales (including Polygonaceae) to asterids. Further, our analysis also provided support for Amborella as sister to all other angiosperms, but interestingly, in the bayesian phylogeny inference based on first two codon positions Amborella united with Nymphaeales.ConclusionComparative genomics analyses revealed that the Fagopyrum chloroplast genome harbors the characteristic gene content and organization as has been described for several other chloroplast genomes. However, it has some unique structural features distinct from previously reported complete chloroplast genome sequences. Phylogenetic analysis of the dataset, including this new sequence from non-core Caryophyllales supports the sister relationship between Caryophyllales and asterids.

Inflorescence and Early Flower Development in Loteae (Leguminosae) in a Phylogenetic and Taxonomic Context

Molecular phylogeny shows that the temperate legume tribe Loteae is close to the mostly tropical Robinieae and monogeneric Sesbanieae, but comparative morphological studies of these groups are limited. Unusual patterns of inflorescence symmetry and calyx development have been described in some Loteae, but taxon sampling was low. We studied these features with scanning electron microscopy in 25 species of Loteae plus in three Robinia species. Phylogenetic trees of Loteae based on nuclear ribosomal ITS sequences and 77 morphological characters are constructed. Our data show that whorled flower arrangement is a synapomorphy of Loteae; joint initiation of the two adaxial sepals is a synapomorphy of a clade containing Hippocrepis, Scorpiurus, and Coronilla; floral buds bent backward early in development are a synapomorphy of Coronilla; bilateral umbel symmetry and the presence of a single whorl of flowers are probably primitive within Loteae. Inflorescences of Robinia show no special similarities with those of Loteae. Developmental data support homologies between sterile bracts in all Loteae. Even if the sterile bract is situated at the top of the peduncle, it is morphologically the first leaf on the peduncle. Monosymmetric umbels of Loteae (including the model legume Lotus japonicus) could be useful for investigating genetic control of symmetry in structures of hierarchic levels higher than flowers.

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.

Complete Plastid Genome of the Recent Holoparasite Lathraea squamaria Reveals Earliest Stages of Plastome Reduction in Orobanchaceae.

Plants from the family Orobanchaceae are widely used as a model to study different aspects of parasitic lifestyle including host–parasite interactions and physiological and genomic adaptations. Among the latter, the most prominent are those that occurred due to the loss of photosynthesis; they include the reduction of the photosynthesis-related gene set in both nuclear and plastid genomes. In Orobanchaceae, the transition to non-photosynthetic lifestyle occurred several times independently, but only one lineage has been in the focus of evolutionary studies. These studies included analysis of plastid genomes and transcriptomes and allowed the inference of patterns and mechanisms of genome reduction that are thought to be general for parasitic plants. Here we report the plastid genome of Lathraea squamaria, a holoparasitic plant from Orobanchaceae, clade Rhinantheae. We found that in this plant the degree of plastome reduction is the least among non-photosynthetic plants. Like other parasites, Lathraea possess a plastome with elevated absolute rate of nucleotide substitution. The only gene lost is petL, all other genes typical for the plastid genome are present, but some of them–those encoding photosystem components (22 genes), cytochrome b6/f complex proteins (4 genes), plastid-encoded RNA polymerase subunits (2 genes), ribosomal proteins (2 genes), ccsA and cemA–are pseudogenized. Genes for cytochrome b6/f complex and photosystems I and II that do not carry nonsense or frameshift mutations have an increased ratio of non-synonymous to synonymous substitution rates, indicating the relaxation of purifying selection. Our divergence time estimates showed that transition to holoparasitism in Lathraea lineage occurred relatively recently, whereas the holoparasitic lineage Orobancheae is about two times older.

Phylogeny of flowering plants by the chloroplast genome sequences: in search of a "lucky gene".

One of the most complicated remaining problems of molecular-phylogenetic analysis is choosing an appropriate genome region. In an ideal case, such a region should have two specific properties: (i) results of analysis using this region should be similar to the results of multigene analysis using the maximal number of regions; (ii) this region should be arranged compactly and be significantly shorter than the multigene set. The second condition is necessary to facilitate sequencing and extension of taxons under analysis, the number of which is also crucial for molecular phylogenetic analysis. Such regions have been revealed for some groups of animals and have been designated as “lucky genes”. We have carried out a computational experiment on analysis of 41 complete chloroplast genomes of flowering plants aimed at searching for a “lucky gene” for reconstruction of their phylogeny. It is shown that the phylogenetic tree inferred from a combination of translated nucleotide sequences of genes encoding subunits of plastid RNA polymerase is closest to the tree constructed using all protein coding sites of the chloroplast genome. The only node for which a contradiction is observed is unstable according to the different type analyses. For all the other genes or their combinations, the coincidence is significantly worse. The RNA polymerase genes are compactly arranged in the genome and are fourfold shorter than the total length of protein coding genes used for phylogenetic analysis. The combination of all necessary features makes this group of genes main candidates for the role of “lucky gene” in studying phylogeny of flowering plants.

Phylogenetics of Anthyllis (Leguminosae: Papilionoideae: Loteae): partial incongruence between nuclear and plastid markers, a long branch problem and implications for morphological evolution

Phylogenetic relationships in the genus Anthyllis (Leguminosae: Papilionoideae: Loteae) were investigated using data from the nuclear ribosomal internal transcribed spacer regions (ITS) and three plastid regions (psbA-trnH intergenic spacer, petB-petD region and rps16 intron). Bayesian and maximum parsimony (MP) analysis of a concatenated plastid dataset recovered well-resolved trees that are topologically similar, with many clades supported by unique indels. MP and Bayesian analyses of the ITS sequence data recovered trees that have several well-supported topological differences, both among analyses, and to trees inferred from the plastid data. The most substantial of these concerns A. vulneraria and A. lemanniana, whose placement in the parsimony analysis of the ITS data appears to be due to a strong long-branch effect. Analysis of the secondary structure of the ITS1 spacer showed a strong bias towards transitions in A. vulneraria and A. lemanniana, many of which were also characteristic of certain outgroup taxa. This may contribute to the conflicting placement of this clade in the MP tree for the ITS data. Additional conflicts between the plastid and ITS trees were more taxonomically focused. These differences may reflect the occurrence of reticulate evolution between closely related species, including a possible hybrid origin for A. hystrix. The patterns of incongruence between the plastid and the ITS data seem to correlate with taxon ranks. All of our phylogenetic analyses supported the monophyly of Anthyllis (incl. Hymenocarpos). Although they are often taxonomically associated with Anthyllis, the genera Dorycnopsis and Tripodion are shown here to be more closely related to other genera of Loteae. We infer up to six major clades in Anthyllis that are morphologically well-characterized, and which could be recognized as sections. Four of these agree with various morphology-based classifications, while the other two are novel. We reconstruct the evolution of several morphological characteristics found only in Anthyllis or tribe Loteae. Some of these characters support major clades, while others show evidence of homoplasy within Anthyllis.

Pollination of Vietnamese Aspidistra xuansonensis (Asparagaceae) by female Cecidomyiidi flies: Larvae of pollinator feed on fertile pollen in anthers of anthetic bisexual flowers

UNLABELLED • PREMISE OF THE STUDY Aspidistra is a species-rich, herbaceous monocot genus of tropical Southeast Asia. Most species are recently discovered and apparently endangered, though virtually nothing is known about their biology. Species of the genus are primarily distinguished using flower morphology, which is enormously diverse. However, the pollination process has not been directly observed in the center of diversity of the genus (N Vietnam and S China). Indirect and partly direct data on the only widely cultivated species of the genus (A. elatior) placed it among angiosperms with the most unusual pollination biology, though these data are highly controversial, suggesting pollen transfer by mollusks, crustaceans, flies, or possibly tiny soil invertebrates such as collembolans.• METHODS Pollination of Aspidistra xuansonensis in the center of diversity of the genus was studied using visual observations and videos and light and scanning electron microscopy investigation of flowers and their pollinators. Pollinators and their larvae were molecularly barcoded.• KEY RESULTS Aspidistra xuansonensis is pollinated by female cecidomyiid flies (gall midges). They oviposit on anthers, and larvae develop among the pollen mass. Molecular barcoding proved taxonomic identity of the larvae and the flies. The larvae neither damage floral parts nor cause gall formation, but feed on pollen grains by sucking out their content. The larvae move out of the flowers before decomposition starts. Carebara ants steal developing larvae from flowers but do not contribute to pollination.• CONCLUSIONS More than one kind of myiophily is present in Aspidistra. Brood site pollination was documented for the first time in Aspidistra. The pollination system of A. xuansonensis differs from other kinds of brood site pollination in the exit of the larvae prior to the decomposition of floral parts.

ITS phylogeny of Middle Asian geophilic Umbelliferae-Apioideae genera with comments on their morphology and utility of psbA-trnH sequences

Generic delimitation and relationships within the taxonomically controversial group of geophilic Umbelliferae from Middle Asia are problematic. Geophilic plants in arid regions have a short period of development during spring and early summer and survive unfavorable seasons due to the presence of tuber-like underground storage organs. To investigate the circumscription of recently recognized Middle Asian geophilic genera and their relationships, we conducted phylogenetic analyses using DNA sequence data from rapidly evolving nuclear (nrITS) and chloroplast (psbA-trnH intergenic spacer) regions as well as multivariate analyses of the morphological and ITS data. Our results show that Galagania and Mogoltavia are monophyletic, whereas Bunium, Hyalolaena and Oedibasis are polyphyletic. Elaeosticta, one of the larger genera of geophilic Middle Asian umbellifers, is rendered paraphyletic by the inclusion of the enigmatic Hyalolaenamelanorrhiza. The genus Scaligeria, in which most species of Elaeosticta were initially described, is not grouped with these genera and has other affinities. Our analyses also show that the morphological characters used for the delimitation of genera within this group of Umbelliferae (such as life form, cotyledon number, presence/absence of petiolules of basal leaflets, shape of mericarp ribs, width of mericarp commissure, number of secretory ducts in mericarp furrows) are rather homoplastic. The psbA-trnH sequences were not informative enough to reveal relationships among the genera studied, although some interesting features in the spacer evolution were revealed (maximum reduction in length among Umbelliferae, homoplasious directed substitutions to restore secondary structure).

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.