cpDNA Spacers Research Articles

The search for hybrids between Myriophyllum sibiricum and M. spicatum (Haloragaceae) in North Eurasia allowed to clarify their morphological differences and distribution

Myriophyllum sibiricum and M. spicatum are sympatric in large part of their vast ranges in Eurasia and North America and have different habitat preferences only in East Europe and Siberia. Such absence of both geographic and ecological isolation should trigger extensive hybridization between these species that is indeed observed in North America. The hybrid could be reliably documented only with genetic markers, and in Eurasia this was done only in China. Using genetic markers (ITS2 region of nuclear ribosomal DNA and trnL-trnF intergenic spacer of cpDNA) we documented hybrids between M. sibiricum and M. spicatum on the North Asian Pacific islands with dynamic geological history and climate (Commander and the southern Kuril islands). The hybrid also originated in East Europe (Ivanovo Region) as a result of ecological isolation break due to rapid artificial habitat change. Using genetically verified material throughout temperate Eurasia we clarified morphological characters discriminating M. sibiricum and M. spicatum and, basing on them, refined the species distribution. For the first time we provide a full morphological characteristic of the hybrid between M. sibiricum and M. spicatum and suggest a name for it, M. × hybridum.

Reassessment of generic boundaries in Neotropical Chrysophylloideae (Sapotaceae): Eleven reinstated genera and narrowed circumscriptions of Chrysophyllum and Pouteria

AbstractClassifications of the pantropical plant family Sapotaceae based solely on morphology have historically recognized between 125 and 53 genera. Phylogenetic analyses using molecular data have repeatedly demonstrated that broad concepts of two large genera belonging to subfamily Chrysophylloideae, Chrysophyllum and Pouteria, are untenable and their narrowed delimitations have restricted them to the Neotropics. A recent phylogenetic study proposed further amendments by resurrecting the genera Achrouteria, Cornuella, Lucuma, Martiusella, Nemaluma, Prieurella and Ragala, and questioned the status of three generally accepted genera, Chromolucuma, Pradosia and Sarcaulus. We test this suggested classification using expanded sampling that comprises 122 terminals, including material of 29 of the 34 name‐bringing species for generic names historically regarded as synonyms of Chrysophyllum and Pouteria. We used sequence data from ribosomal nrDNA (ETS, ITS), the nuclear gene RPB2, two cpDNA spacers (petN‐psbM, trnH‐psbA), and indel information to estimate phylogenetic relationships in a Bayesian framework using BEAST. All sequences were newly realigned to test reproducibility, and 26 morphological characters were mapped on the resulting tree. Our analyses recovered three African genera embedded within a large Neotropical clade of Chrysophylloideae. We found strong support for the reinstatement of the seven genera listed above as well as for four other genera, viz. Chloroluma, Englerella, Labatia, and Peteniodendron. This subsequently leads to further amendments of Chrysophyllum and Pouteria, which are now limited to include 25–30 and 7 species, respectively. However, one clade that includes many name‐bringing lineages largely corresponds to Pouteria s.l., a group that needs further phylogenetic research to unravel relationships and generic limits. The hypothesis that Chrysophyllum cuneifolium had an inter‐continental hybrid origin involving genomes from Africa and South America is rejected because it is shown to have been based on erroneous results obtained from a contaminated DNA aliquot. A total of 73 genera are currently recognised in Sapotaceae, 21 of which are Neotropical members of Chrysophylloideae. We update the nomenclature and synonymy of 75 species, make 36 new combinations, and designate lectotypes for 31 names.

Genetic Divergence of Closely Related Species <i>Oxytropis strobilacea</i>, <i>Oxytropis adamsiana </i>and<i> Oxytropis vassilczenkoi</i> (Series <i>Strobilacei</i> of the Section <i>Orobia</i> Fabaceae) from Asian Russia

The genetic diversity and divergence of closely related species Oxytropis strobilacea, O. adamsiana, and O. vassilczenkoi series Strobilacei of the section Orobia (Fabaceae) from Asian Russia were studied using the data of nucleotide polymorphism of the psbA–trnH, trnL–trnF, and trnS–trnG intergenic spacers of cpDNA, as well as the ITS nrDNA. Most populations are characterized by an average and high level of chloroplast genetic diversity (h varies from 0.600 to 1.000). 65 chlorotypes were identified, no shared chlorotypes were found in taxa, and that confirms the status of O. vassilczenkoi as a separate species. Two phyletic lineages were found for O. strobilacea that indicates an intensively proceeding diversification process. Among the seven identified ITS ribotypes, one ribotype was shared for all three species, probably, due to their common origin and relatively recent divergence.

Comparative evolutionary history of two closely related desert plant, Convolvulus tragacanthoide and Convolvulus gortschakovii (Convolvulaceae) from northwest China.

Desert ecosystems are one of the most fragile ecosystems on Earth. The study of the effects of paleoclimatic and geological changes on genetic diversity, genetic structure, and species differentiation of desert plants is not only helpful in understanding the strategies of adaptation of plants to arid habitats, but can also provide reference for the protection and restoration of vegetation in desert ecosystem. Northwest China is an important part of arid regions in the northern hemisphere. Convolvulus tragacanthoides and Convolvulus gortschakovii are closely related and have similar morphology. Through our field investigation, we found that the annual precipitation of the two species distribution areas is significantly different. Thus, C. tragacanthoides and C. gortschakovii provide an ideal comparative template to investigate the evolutionary processes of closely related species, which have adapted to different niches in response to changes in paleogeography and paleoclimate in northwest China. In this study, we employed phylogeographical approaches (two cpDNA spacers: rpl14–rpl36 and trnT–trnY) and species distribution models to trace the demographic history of C. tragacanthoides and C. gortschakovii, two common subshrubs and small shrubs in northwest China. The results showed the following: (1) Populations of C. tragacanthoides in northwest China were divided into three groups: Tianshan Mountains—Ili Valley, west Yin Mountains—Helan Mountains‐Qinglian Mountains, and Qinling Mountains—east Yin Mountains. There was a strong correlation between the distribution of haplotypes and the floristic subkingdom. The three groups corresponded to the Eurasian forest subkingdom, Asian desert flora subkingdom, and Sino‐Japanese floristic regions, respectively. Thus, environmental differences among different flora may lead to the genetic differentiation of C. tragacanthoides in China. (2) The west Yin Mountains—Helan Mountains‐Qinglian Mountains, and Qinling Mountains—east Yin Mountains were thought to form the ancestral distribution range of C. tragacanthoides. (3) C. tragacanthoides and C. gortschakovii adopted different strategies to cope with the Pleistocene glacial cycle. Convolvulus tragacanthoides contracted to the south during the glacial period and expanded to the north during the interglacial period; and there was no obvious north–south expansion or contraction of C. gortschakovii during the glacial cycle. (4) The interspecific variation of C. tragacanthoides and C. gortschakovii was related to the orogeny in northwest China caused by the uplift of the Tibetan Plateau during Miocene. (5) The 200 mm precipitation line formed the dividing line between the niches occupied by C. tragacanthoides and C. gortschakovii, respectively. In this study, from the perspective of precipitation, the impact of the formation of the summer monsoon limit line on species divergence and speciation is reported, which provides a new perspective for studying the response mechanism of species to the formation of the summer monsoon line, and also provides a clue for predicting how desert plants respond to future environmental changes.

The species of Oxytropis DC. of section Gloeocephala Bunge (Fabaceae) from Northeast Asia: genetic diversity and relationships based on sequencing of the intergenic spacers of cpDNA and ITS nrDNA.

Phylogenetic relationships within Oxytropis DC. sect. Gloeocephala Bunge from Northeast Asia were studied using plastid intergenic spacers (psbA-trnH + trnL-trnF + trnS-trnG) and ITS nrDNA. Populations of O. anadyrensis Vass., O. borealis DC., O. middendorffii Trautv., O. trautvetteri Meinsh., and O. vasskovskyi Jurtz. were monomorphic or characterised by a low level of chloroplast genetic diversity (h varied from 0.143 to 0.692, and π from 0.0001 to 0.0005). Presumably, the low genetic diversity was a result of the severe bottlenecks during Pleistocene glaciation-interglacial cycles. Twenty chlorotypes were identified; species studied had no shared chlorotypes. Chlorotypes of O. anadyrensis, O. borealis, and O. middendorffii formed two lineages each, while the chlorotypes of O. trautvetteri and O. vasskovskyi formed one separate lineage each in the phylogenetic network. There were specific diagnostic markers of cpDNA in each lineage, excluding O. vasskovskyi. The presence of a species-specific diagnostic marker in O. trautvetteri and specific markers in two lineages of O. anadyrensis support circumscribing these taxa as independent species. Regarding ITS nrDNA polymorphism, five ribotypes were detected. The differences revealed in plastid and nuclear genomes of Oxytropis sect. Gloeocephala confirmed that the Asian sector of Megaberingia was the main centre of diversification of arctic legumes.

Relative DNA content differences reliably identify Solidago ×niederederi, a hybrid between native and invasive alien species

Hybridization between native and alien congeners may pose a serious threat to biodiversity and negatively affect native flora. Here we study Solidago ×niederederi, which originated and became established in Europe as a result of a cross between the alien S. canadensis and native S. virgaurea. The recent increase in the number of records of S. ×niederederi in Europe has highlighted the need to monitor its occurrence, spread and behaviour. In the present study, we tested the effectiveness of flow cytometry for detecting hybrid plants of S. ×niederederi. Sequences of the ITS region of nrDNA and the rpS15-ycf1 spacer of cpDNA were used to confirm the hybrid origin of analysed plants and to identify the maternal species. Our study included 60 single-species populations of S. canadensis, S. gigantea and S. virgaurea, and 16 mixed populations with the presence of hybrid S. ×niederederi sampled from six countries in central Europe and adjacent areas. All individuals of S. canadensis, S. ×niederederi and S. virgaurea investigated were diploid (2n~2x~18) but differed in their relative DNA content values. The DNA content of S. ×niederederi was intermediate between S. canadensis and S. virgaurea with no overlaps, with the differences between the species being statistically significant. Therefore, we conclude that flow cytometry is a reliable and efficient method for detailed screening for hybrids within mixed Solidago populations and for identifying non-flowering or morphologically ambiguous Solidago plants. Since both parental species varied only negligibly in their DNA content, it may also be applicable across a broader geographic scale. Genetic, flow cytometric and distributional data suggest that the hybrids are to a large extent early generation (likely F1) hybrids as very few cases of supposed introgressants were also inferred. The results from chloroplast rpS15-ycf1 spacer showed that hybridization has occurred in both directions.

Genetic diversity of Oxytropis section Xerobia (Fabaceae) in one of the centres of speciation.

The genetic diversity and phylogenetic relationships of Oxytropiscaespitosa, O.grandiflora, O.eriocarpa, O.mixotriche, O.nitens, O.peschkovae and O.triphylla, section Xerobia subgenus Oxytropis, in one of the main speciation centres of the genus Oxytropis (Baikal Siberia and adjacent territories of Northeastern Mongolia) were studied based on sequence analysis of the psbA-trnH, trnL-trnF and trnS-trnG intergenic spacers of cpDNA, as well as the ITS nrDNA. Most populations are characterized by a high level of chloroplast genetic diversity (h varied from 0.327 to 1.000 and π from 0.0001 to 0.0090) due to the ancient origin for some species and to hybridization and polyploidy for others. 67 haplotypes were identified, of which six were shared. Phylogenetic relationships among species could not be satisfactorily resolved. Only the haplotypes of O.triphylla formed a group with rather high support. Probably, O.caespitosa, O.grandiflora, O.mixotriche and O.nitens constitute a single genetic complex. As regards the ITS nrDNA polymorphism, we detected only two ribotypes (RX1, RX2). Both were found in O.caespitosa, O.eriocarpa, O.mixotriche and O.peschkovae, while RX1 was present in O.nitens and O.triphylla, RX2 in O.grandiflora. The absence of diagnostic species-specific variants for the markers studied, together with the sharing of cpDNA haplotypes and nrDNA ribotypes between species, and the resulting polytomies on the phylogenetic trees, confirm the hypothesis on the hybrid origin of some of them. Obviously, the reproductive barriers within the sect. Xerobia are weak. However, morphological differences between the species of the sect. Xerobia are clearly pronounced, even when they grow in sympatry.

Characterization of variability of the intergenic spacers cpDNA trnH–psbA, trnY–trnT AND rpoB–trnC in representatives of Pisum L. (Tribe Fabeae)

Background. Plant chloroplast genome have conservative structure, but its nucleotide sequence is polymorphous due to which cpDNA fragments are often used in taxonomic and phylogenetic studies. Despite the widespread distribution and use of Fabeae species, mainly peas (Pisum), data on the intraspecific diversity of cpDNA fragments are almost absent. The aim of the work was to analyze the intraspecific variability of three cpDNA spacers in Pisum.
 Materials and methods. As a result of the work, intergenic spacers trnYtrnT, trnHpsbA and rpoBtrnC in 38 accessions of the Pisum and related Fabeae species were sequenced. Despite the fact that the selected chloroplast fragments are generally considered to be sufficiently variable in plants and are often used for phylogenetic studies, Pisum accessions have been found to have no intraspecific differences in two of the three spacers sequences analyzed.
 Results and conclusion. A total 97 SNPs were detected in Pisum accessions, seven of them distinguished P. sativum from P. fulvum. The most variable of the analyzed fragments was the intergenic spacer rpoBtrnC. Based on rpoBtrnC sequence 17 haplotypes in P. sativum and four haplotypes in P. fulvum were revealed. The cpDNA sequencing data were used for a phylogenetic analysis. On the obtained tree Vavilovia formosa accession formed a separate branch from pea accessions. All Pisum accessions fall in one cluster, split into distinct P. sativum and P. fulvum subclusters (BI = 99%).

Development of Novel Low-Copy Nuclear Gene Primers by Transcriptomes in an Endemic Genus Orinus Hitchc. (Poaceae) from the Qinghai-Tibet Plateau

In the present study, a total of eleven low-copy nuclear gene markers were developed using transcriptomes for the plant genus Orinus Hitchc. (Poaceae), which comprises three species of grasses widely distributed in the Qinghai-Tibet Plateau. These developed markers were successfully amplified and sequenced for 90 individuals from nine populations of three Orinus species. The DNA sequences for the eleven loci ranged from 606 to 1152 aligned based pairs. Compared with four candidate DNA barcoding markers in our previous studies, the newly developed markers had a relatively higher number of parsimony informative sites than three cpDNA spacers (7–20 vs. 1–8), but slightly lower than those of the internal transcribed spacers (ITS). Hence, these novel low-copy nuclear gene primer pairs were validly useful for the study of phylogeography, phylogenetic analysis and population genetics. Moreover, they could be used in phylogeny reconstruction and speciation for a broad range of Orinus and even the entire subtribe Tridentinae.

Reinterpretation of an endangered taxon based on integrative taxonomy: The case of Cynara baetica (Compositae).

The Strait of Gibraltar, the gateway between the Atlantic Ocean and the Mediterranean Sea, has a convulsive geological history, with recurring closing and opening events since the late Miocene. As a consequence, this region has played a major role in the evolutionary history of many species. Cynara baetica (Compositae) is a diploid perennial herb distributed in both sides of this strait. It is currently subdivided into two subspecies: C. baetica subsp. baetica for the Spanish populations, and C. baetica subsp. maroccana for the Moroccan ones. Following three different approximations of species delimitation, including phylogenetic and population genetic analyses (based on three AFLP primer combinations and two intergenic spacers of cpDNA), ecological niche modeling (ENM) and morphological studies, this taxon is investigated and reinterpreted. The results obtained showed a clear genetic, morphological and ecological differentiation between the two taxa and the important role played by the Strait of Gibraltar as a geographical barrier. Based on this evidence, the current taxonomic treatment is modified (both taxa should recover their specific rank) and specific conservation guidelines are proposed for the newly delimited taxa.

Pleistocene radiation of coastal species of Pilosocereus (Cactaceae) in eastern Brazil

The semiarid region in Northeast Brazil (Caatinga) suffered several high moisture periods during the Pleistocene, while neighbouring regions experienced drying events. Effects of this climatic history on the evolution of Caatinga xeric flora are poorly understood. Demography and evolutionary relationships between Pilosocereus arrabidae and Pilosocereus catingicola (Cactaceae) were investigated using two non-coding intergenic spacers of cpDNA (1424 bp) employing distinct statistical methods, such as Bayesian Inference analysis, haplotype network, AMOVA, neutrality tests and Bayesian Skyline Plot. Our data suggests that species formerly arranged as the informal Pilosocereus arrabidae group do not form a monophyletic clade. P. arrabidae and P. catingicola are not reciprocally monophyletic and present very low genetic diversity. The Tajima's D and Fu's Fs statistics provided no significant results. Results suggest a very recent origin for P. arrabidae and P. catingicola. The beginning of P. arrabidae and P. catingicola diversification dates back to the Pleistocene. Genetic diversity of P. catingicola subsp. salvadorensis is geographically structured between major rivers of the region, suggesting a history of isolation in interfluves during Pleistocene climatic cycles.

Allopolyploid Origin of Chenopodium album s. str. (Chenopodiaceae): A Molecular and Cytogenetic Insight.

Reticulate evolution is characterized by occasional hybridization between two species, creating a network of closely related taxa below and at the species level. In the present research, we aimed to verify the hypothesis of the allopolyploid origin of hexaploid C. album s. str., identify its putative parents and estimate the frequency of allopolyploidization events. We sampled 122 individuals of the C. album aggregate, covering most of its distribution range in Eurasia. Our samples included putative progenitors of C. album s. str. of both ploidy levels, i.e. diploids (C. ficifolium, C. suecicum) and tetraploids (C. striatiforme, C. strictum). To fulfil these objectives, we analysed sequence variation in the nrDNA ITS region and the rpl32-trnL intergenic spacer of cpDNA and performed genomic in-situ hybridization (GISH). Our study confirms the allohexaploid origin of C. album s. str. Analysis of cpDNA revealed tetraploids as the maternal species. In most accessions of hexaploid C. album s. str., ITS sequences were completely or nearly completely homogenized towards the tetraploid maternal ribotype; a tetraploid species therefore served as one genome donor. GISH revealed a strong hybridization signal on the same eighteen chromosomes of C. album s. str. with both diploid species C. ficifolium and C. suecicum. The second genome donor was therefore a diploid species. Moreover, some individuals with completely unhomogenized ITS sequences were found. Thus, hexaploid individuals of C. album s. str. with ITS sequences homogenized to different degrees may represent hybrids of different ages. This proves the existence of at least two different allopolyploid lineages, indicating a polyphyletic origin of C. album s. str.

Genetic structure of Salsola junatovii (Chenopodiaceae) in the northern edge of the Taklimakan desert and conservational implications

Salsola junatovii Botsch. (Chenopodiaceae), a desert shrub endemic to the northern edge of the Taklimakan desert in China, is listed as an endangered species because of its narrow habitat requirements and a decline in numbers of individuals. In order to provide information on conservation strategies, we investigated the genetic patterns and evolutionary history of this species. Two cpDNA spacers, (psbA-trnH and psbK-psbI), and the nrITS sequence were employed in 116 individuals from 15 populations across the whole range of the species. A total of 7 haplotypes and 12 ribotypes were detected. Based on separate BEAST analyses, we suggest that intraspecific differentiation of S. junatovii occurred at 2.284–0.264 Ma for cpDNA haplotypes, and 1.304–0.1 Ma for nrITS ribotypes, both in the Pleistocene. Only mismatch analysis and neutrality tests for nrITS sequences over all populations were indicative of demographic expansion. Inconsistency between results from chloroplast and nuclear sequences was detected, apparently due to a stronger seed-mediated gene flow among populations than pollen-mediated flow under the severe desert conditions. Based on genetic structure results, one population, KMS, with the highest number of unique genotypes, should be a conservation priority; another nine populations containing unique genotypes were suggested for ex situ conservation.

Genetic diversity and ecological niche modelling of the restrictedRecordia reitzii(Verbenaceae) from southern Brazilian Atlantic forest

Genetic diversity analyses, coupled with ecological niche modelling (ENM) of species with a restricted distribution, may provide valuable information for understanding diversification patterns in endangered areas. We analyzed the genetic diversity of Recordia reitzii, a tree restricted to the threatened and highly fragmented Brazilian Atlantic forest, using three intergenic cpDNA spacers and ten microsatellite (SSR) loci. To assess the historical processes that may have influenced the distribution of extant R. reitzii populations, the current potential distributions of R. reitzii and Recordia boliviana, a closely related species, were modelled and projected onto the Last Glacial Maximum (LGM) and Last Interglacial (LIG) periods. Niche divergence was quantified between these two. The cpDNA and SSR data showed a north–south pattern of the diversity distribution and structured populations, suggesting that gene flow is probably limited. According to our data, R. reitzii exhibits low genetic diversity, which may be a result of a founder or distribution-reduction effect, narrow distribution or small population size. The ecological niche models showed a wider palaeodistribution during the LIG and a retraction during the LGM for both species. Tests of niche divergence and conservatism indicated that bioclimatic factors might have influenced the diversification of these Recordia species. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176, 332–348.

Evaluation of DNA barcode candidates for the discrimination of the large plant family Apocynaceae

The chloroplast loci matK, rbcL, atpB, rpoC1, plastid spacer region psbA-trnH and nuclear internal transcribed spacer loci ITS sequences were evaluated for its discriminating ability among the closely related medicinal plant species of Apocynaceae. Our main criteria for ranking these barcodes were based on levels of inter and intra-specific divergence. Twenty-one medicinal plants were sequenced for matK, rbcL, atpB, rpoC1, psbA-trnH and ITS. Additionally sequences collected from GenBank were also included in this study. Altogether, 1,876 DNA sequences were used that included 525 sequences belonging to 110 genera of matK, 390 sequences belonging to 68 genera of rbcL, 90 sequences belonging to 13 genera of atpB, 38 sequences belonging to 16 genera of rpoC1, 32 sequences belonging to 27 genera of psbA-trnH and 780 sequences belonging to 70 genera of ITS region. The analyses of inter-specific and intra-specific divergence using the cpDNA spacer region psbA-trnH showed 0.3–0.5 and 0.04–0.2 %, whereas matK showed 0.8–1 and 0.07–0.1 % inter-specific and intra-specific divergence, respectively. Likewise rbcL showed 0.4–0.5 % inter-specific divergence and 0.2–0.1 % intra-specific divergence. The gene rpoC1 showed 0.2–0.3 % inter-specific divergence and 0.02–0.01 % intra-specific divergence, respectively. Similarly atpB showed 0.1–0.4 % inter-specific divergence and 0.09–0.04 % of intra-specific divergence. The nrDNA ITS (ITS1 and ITS2) were analyzed and the results indicated that ITS2 showed better discriminating ability, as it resulted in considerable variation at the generic and species level. The inter-specific divergence in ITS2 ranged from 1 to 9 % with an average of 8 % and the intra-specific divergence ranged from 0.4 to 6 % with an average of 4 %. Thus, ITS2 successfully identified the species and genera at the rate of 91 and 98 %, respectively. The cpDNA spacer psbA-trnH exhibited an identification percentage of 40 and 36 % at the genus and species level, respectively. Additionally ITS2 was also used to authenticate the herbal medicinal species of the genus Caralluma, Rauwolfia and Hoodia. Overall, our data suggest that nuclear ITS2 is the ideal barcode loci to identify/discriminate the large plant family Apocynaceae.

Tertiary montane origin of the Central Asian flora, evidence inferred from cpDNA sequences of Atraphaxis (Polygonaceae).

Atraphaxis has approximately 25 species and a distribution center in Central Asia. It has been previously used to hypothesize an origin from montane forest. We sampled 18 species covering three sections within the genus and sequenced five cpDNA spacers, atpB-rbcL, psbK-psbI, psbA-trnH, rbcL, and trnL-trnF. BEAST was used to reconstruct phylogenetic relationship and time divergences, and S-DIVA and Lagrange were used, based on distribution area and ecotype data, for reconstruction of ancestral areas and events. Our results appear compatible with designation of three taxonomic sections within the genus. The generic stem and crown ages were Eocene, approximately 47 Ma, and Oligocene 27 Ma, respectively. The origin of Atraphaxis is confirmed as montane, with an ancestral area consisting of the Junggar Basin and uplands of the Pamir-Tianshan-Alatau-Altai mountain chains, and ancestral ecotype of montane forest. Two remarkable paleogeographic events, shrinkage of the inland Paratethys Sea at the boundary of the late Oligocene and early Miocene, and the time intervals of cooling and drying of global climate from 24 (22) Ma onward likely facilitated early diversification of Atraphaxis, while rapid uplift of the Tianshan Mountains during the late Miocene may have promoted later diversification.

Diversification and vicariance of desert plants: Evidence inferred from chloroplast DNA sequence variation of Lagochilus ilicifolius (Lamiaceae)

To document arid Northern China as a diversification center for desert plants, and to better understand the mechanisms of desert taxa diversification, we used five cpDNA spacers (trnL-trnF, rps16, psbA-trnH, psbK-psbI and trnS-trnG) to investigate Lagochilus ilicifolius in all distribution areas, including Northern China, Mongolia and Russia. Phylogenetic analyses showed that L. ilicifolius comprises two distinctive lineages, one distributed in China, and another in Mongolia–Russia. Our data confirmed that arid Northern China, is a distinctive area with many endemic genera. Biogeographic inferences, based on a Bayesian uncorrelated lognormal model together with molecular dating, suggested that the main diversification within the species occurred in the Pleistocene (ca. 1.38–0.3 Ma), resulting from the transition of the climate of Eurasia to a dry-cold pattern as well as the desertification caused the vicariance of desert plants.

Evaluation of the taxonomic status of the genus Aliella (Compositae, Gnaphalieae): a recircumscription of the genus Phagnalon

A taxonomic evaluation of the genus Aliella, endemic to the Moroccan Atlas Mountains, is presented. We evaluate the taxonomic status of Aliella using a morphologic and molecular approach. Firstly, we discuss the variability and usefulness of its morphological diagnostic characters. Secondly, we analyse nuclear ETS and ITS, and chloroplast ycf3-trnS and trnT-trnL spacers. Phylogenetic analyses of the nrDNA and cpDNA spacers suggest the paraphyly of Aliella and Phagnalon. Two species of Aliella, A. ballii and A. embergeri, form a strongly supported clade. In contrast, relationships of A. platyphylla to A. ballii and A. embergeri are only weakly supported, and A. iminouakensis do not form a group with the other species and shows two different haplotypes. The morphological and diagnostic characters of Aliella are described and compared with an extensive sampling of the closely related genus Phagnalon. Our results strongly suggest that Aliella should be merged into Phagnalon. For each accepted taxon, taxonomical, chorological, and ecological data are provided. Six taxa are recognized, three species and three subspecies. Three lectotypifications of specific names and three new combinations are proposed. New descriptions and distribution maps of the recognized taxa are given.

Identification of ethnomedicinal plants (Rauvolfioideae: Apocynaceae) through DNA barcoding from northeast India.

Background:DNA barcode-based molecular characterization is in practice for plants, but yet lacks total agreement considering the selection of marker. Plant species of subfamily Rauvolfioideae have long been used as herbal medicine by the majority of tribal people in Northeast (NE) India and at present holds mass effect on the society. Hence, there is an urgent need of correct taxonomic inventorization vis-à-vis species level molecular characterization of important medicinal plants.Objective:To test the efficiency of matK in species delineation like DNA barcoding in Rauvolfiadae (Apocynaceae).Materials and Methods:In this study, the core DNA barcode matK and trnH-psbA sequences are examined for differentiation of selected ethnomedicinal plants of Apocynaceae. DNA from young leaves of selected species was isolated, and matK gene (~800 bp) and trnH-psbA spacer (~450 bp) of Chloroplast DNA was amplified for species level identification.Results:The ~758 bp matK sequence in comparison to the trnH-psbA showed easy amplification, alignment, and high level of discrimination value among the medicinal Rauvolfioidae species. Intergenic spacer trnH-psbA is also exhibited persistent problem in obtaining constant bidirectional sequences. Partial matK sequences exhibited 3 indels in multiple of 3 at 5 end. Evidently, generated matK sequences are clustered cohesively, with their conspecific Genbank sequences. However, repeat structures with AT-rich regions, possessing indels in multiple of 3, could be utilized as qualitative molecular markers in further studies both at the intra-specific and shallow inter-specific levels like the intergenic spacers of CpDNA.Conclusion:matK sequence information could help in correct species identification for medicinal plants of Rauvolfioideae.

Analysis of Liriope spicata and Its Related Species Based on DNA Barcoding Technique

To discuss the potential of cpDNA trnL-F and psbA-trnH as DNA barcode of Liriope spicata(Thunberg) Loureiro and its related species,cpDNA trnL-F and psbA-trnH sequences were analysed.These two regions were respectively amplified by PCR and then purified and sequenced successfully.The results showed that the lengths of trnL-F sequences in 18 plant samples belonging to 9 species of liriopogons varied from 355 to 356 bp.There was no difference in the trnL-F of various species of liriope,but some specifically variable sites were found in this fragment,which led to the identification between Ophiopogon japonicus(Thunb.) Ker-Gawl and Ophiopogon bodinieri Levl.The length of psbA-trnH region was 543-544 bp,there were only some identification sites in O.japonicus(Thunb.) Ker-Gawl.Because of the low rate of evolution and the high conservation,these two cpDNA spacer regions could be only appropriate as a DNA barcode to identify liriopogons at generic level,but there is a degree of limit at lower taxonomic level.