Filtrates from cultures of endophytic fungi isolated from leaves of Copaifera oblongifolia (Fabaceae) affect germination and seedling development differently

Interactions between endophytic fungi (EFs) and their host plants range from positive to neutral to negative. The results of such interactions can vary depending on the organ of the infected host plant. EFs isolated from the leaves of some species of plants have potential for use as agents to inhibit seed germination and control invasive plants. The objectives of this study were to identify EFs present in the leaves of Copaifera oblongifolia and to evaluate the role of these fungi in seed germination and seedling development. A total of 11 species of EFs were isolated, which were identified using the internal transcribed spacers (ITS) sequence of the nuclear ribosomal DNA. The isolated species of EFs are generalists and probably are transmitted horizontally. Laboratory tests revealed that filtrates of these fungal isolates differently affect seed germination and seedling development of C. oblongifolia. The species Curvularia intermedia, Neofusicoccum parvum, Pseudofusicoccum stromaticum and Phomopsis sp. negatively affected seed germination, with N. parvum standing out for its negative effects, inhibiting seedling germination and survival in 89 and 222%, respectively. In addition, Cochliobolus intermedius negatively affected seedling development. Thus, the combined use of N. parvum and C. intermedius, or products from the metabolism of these microorganisms, in the control of invasive plants deserves attention from future studies.

Weak population spatial genetic structure and low infraspecific specificity for fungal partners in the rare mycoheterotrophic orchid Epipogium aphyllum

Some plants abandoned photosynthesis and developed full dependency on fungi for nutrition. Most of the so-called mycoheterotrophic plants exhibit high specificity towards their fungal partners. We tested whether natural rarity of mycoheterotrophic plants and usual small and fluctuating population size make their populations more prone to genetic differentiation caused by restricted gene flow and/or genetic drift. We also tested whether these genetic characteristics might in turn shape divergent fungal preferences. We studied the mycoheterotrophic orchid Epipogium aphyllum, addressing the joint issues of genetic structure of its populations over Europe and possible consequences for mycorrhizal specificity within the associated fungal taxa. Out of 27 sampled E. aphyllum populations, nine were included for genetic diversity assessment using nine nuclear microsatellites and plastid DNA. Population genetic structure was inferred based on the total number of populations. Individuals from 17 locations were included into analysis of genetic identity of mycorrhizal fungi of E. aphyllum based on barcoding by nuclear ribosomal DNA. Epipogium aphyllum populations revealed high genetic diversity (uHe = 0.562) and low genetic differentiation over vast distances (FST = 0.106 for nuclear microsatellites and FST = 0.156 for plastid DNA). Bayesian clustering analyses identified only two genetic clusters, with a high degree of admixture. Epipogium aphyllum genets arise from panmixia and display locally variable, but relatively high production of ramets, as shown by a low value of rarefied genotypic richness (Rr = 0.265). Epipogium aphyllum genotype control over partner selection was negligible as (1) we found ramets from a single genetic individual associated with up to 68% of the known Inocybe spp. associating with the plant species, (2) and partner identity did not show any geographic structure. The absence of mosaicism in the mycorrhizal specificity over Europe may be linked to preferential allogamous habit of E. aphyllum and significant gene flow, which tend to promote host generalism.

Mahonia vs. Berberis Unloaded: Generic Delimitation and Infrafamilial Classification of Berberidaceae Based on Plastid Phylogenomics

The early-diverging eudicot family Berberidaceae is composed of a morphologically diverse assemblage of disjunctly distributed genera long praised for their great horticultural and medicinal values. However, despite century-long studies, generic delimitation of Berberidaceae remains controversial and its tribal classification has never been formally proposed under a rigorous phylogenetic context. Currently, the number of accepted genera in Berberidaceae ranges consecutively from 13 to 19, depending on whether to define Berberis, Jeffersonia, and Podophyllum broadly, or to segregate these three genera further and recognize Alloberberis, Mahonia, and Moranothamnus, Plagiorhegma, and Dysosma, Diphylleia, and Sinopodophyllum, respectively. To resolve Berberidaceae’s taxonomic disputes, we newly assembled 23 plastomes and, together with 85 plastomes from the GenBank, completed the generic sampling of the family. With 4 problematic and 14 redundant plastome sequences excluded, robust phylogenomic relationships were reconstructed based on 93 plastomes representing all 19 genera of Berberidaceae and three outgroups. Maximum likelihood phylogenomic relationships corroborated with divergence time estimation support the recognition of three subfamilies Berberidoideae, Nandinoideae, and Podophylloideae, with tribes Berberideae and Ranzanieae, Leonticeae and Nandineae, and Podophylleae, Achlydeae, Bongardieae tr. nov., Epimedieae, and Jeffersonieae tr. nov. in the former three subfamilies, respectively. By applying specifically stated criteria, our phylogenomic data also support the classification of 19 genera, recognizing Alloberberis, Mahonia, and Moranothamnus, Plagiorhegma, and Diphylleia, Dysosma, and Sinopodophyllum that are morphologically and evolutionarily distinct from Berberis, Jeffersonia, and Podophyllum, respectively. Comparison of plastome structures across Berberidaceae confirms inverted repeat expansion in the tribe Berberideae and reveals substantial length variation in accD gene caused by repeated sequences in Berberidoideae. Comparison of plastome tree with previous studies and nuclear ribosomal DNA (nrDNA) phylogeny also reveals considerable conflicts at different phylogenetic levels, suggesting that incomplete lineage sorting and/or hybridization had occurred throughout the evolutionary history of Berberidaceae and that Alloberberis and Moranothamnus could have resulted from reciprocal hybridization between Berberis and Mahonia in ancient times prior to the radiations of the latter two genera.

Genome structure and diversity among Cynanchum wilfordii accessions

Background Cynanchum wilfordii (Cw) and Cynanchum auriculatum (Ca) have long been used in traditional medicine and as functional food in Korea and China, respectively. They have diverse medicinal functions, and many studies have been conducted, including pharmaceutical efficiency and metabolites. Especially, Cw is regarded as the most famous medicinal herb in Korea due to its menopausal symptoms relieving effect. Despite the high demand for Cw in the market, both species are cultivated using wild resources with rare genomic information. Results We collected 160 Cw germplasm from local areas of Korea and analyzed their morphological diversity. Five Cw and one Ca of them, which were morphologically diverse, were sequenced, and nuclear ribosomal DNA (nrDNA) and complete plastid genome (plastome) sequences were assembled and annotated. We investigated the genomic characteristics of Cw as well as the genetic diversity of plastomes and nrDNA of Cw and Ca. The Cw haploid nuclear genome was approximately 178 Mbp. Karyotyping revealed the juxtaposition of 45S and 5S nrDNA on one of 11 chromosomes. Plastome sequences revealed 1226 interspecies polymorphisms and 11 Cw intraspecies polymorphisms. The 160 Cw accessions were grouped into 21 haplotypes based on seven plastome markers and into 108 haplotypes based on seven nuclear markers. Nuclear genotypes did not coincide with plastome haplotypes that reflect the frequent natural outcrossing events. Conclusions Cw germplasm had a huge morphological diversity, and their wide range of genetic diversity was revealed through the investigation with 14 molecular markers. The morphological and genomic diversity, chromosome structure, and genome size provide fundamental genomic information for breeding of undomesticated Cw plants.

Bulbophyllum versicolor (Orchidaceae, Malaxideae), a new species from Yunnan, China: evidence from morphology and molecular analyses

A new orchid species, Bulbophyllum versicolor (Malaxideae, Epidendroideae, Orchidaceae), from Malipo, Yunnan, China, is described and illustrated here. Detailed morphological study indicates that B. versicolor is similar to B. japonicum, but it differs in the shape and size of leaf and flower and flower colour. Molecular analyses based on the nuclear ribosomal DNA (nrITS) and plastid DNA (matK, atpI-atpH and trnL-F) reveal that B. versicolor is a new species and genetically similar to B. japonicum.

The Madeiran laurel forest endemic Goodyera macrophylla (Orchidaceae) is related to American orchids

Macaronesian laurel forests harbour many herbs and laurophyllous trees with Mediterranean/European or Macaronesian affinities. Traditionally, the origin of these taxa has been explained by the relict hypothesis interpreting these taxa as relics of formerly widespread laurel forests in the European continent and the Mediterranean. We analysed the phylogenetic relationships of the Madeiran laurel forest endemic Goodyera macrophylla (Orchidaceae) using sequences from the nuclear ribosomal DNA Internal Transcribed Spacers (ITS) and plastid DNA regions. The results were incongruent, either the two Central American G. brachyceras and G. striata (ITS) or the North American G. oblongifolia (plastid DNA) were sister group to G. macrophylla. Nonetheless, biogeographic analyses indicated an American origin of this nemoral laurel forest plant in the two data sets. Molecular clock analyses suggest a colonisation of Madeira in the span of the upper Miocene/lower Pliocene to the Pleistocene. Although the relict hypothesis cannot be ruled out by our data when assuming extinction events on the European and northern African mainland, dispersal from Central or North America to the archipelago of Madeira is a much more likely explanation of the data.

Mitochondrial Genome Recombination in Somatic Hybrids of Solanum Commersonii and S. Tuberosum

Interspecific somatic hybridization has been performed in potato breeding experiments to increase plant resistance against biotic and abiotic stress conditions. We analyzed the mitochondrial and plastid genomes and 45S nuclear ribosomal DNA (45S rDNA) for the cultivated potato (S. tuberosum, St), wild potato (S. commersonii, Sc), and their somatic hybrid (StSc). Complex genome components and structure, such as the hybrid form of 45S rDNA in StSc, unique plastome in Sc, and recombinant mitogenome were identified. However, the mitogenome exhibited dynamic multipartite structures in both species as well as in the somatic hybrid. In St, the mitogenome is 756,058 bp and is composed of five subgenomes ranging from 297,014 to 49,171 bp in St. In Sc, it is 552,103 bp long and is composed of two sub-genomes of 338,427 and 213,676 bp length. StSc has 447,645 bp long mitogenome with two subgenomes of length 398,439 and 49,206 bp. The mitogenome structure exhibited dynamic recombination mediated by tandem repeats; however, it contained highly conserved genes in the three species. Among the 35 protein-coding genes of the StSc mitogenome, 21 were identical for all the three species, and 12 and 2 were unique in Sc and St, respectively. The recombinant mitogenome might be derived from homologous recombination between both species during somatic hybrid development.

Phylogeography of Myrica nana: the Wumeng Mountains as a natural geographical isolation boundary on the Yunnan-Guizhou Plateau

The Yunnan-Guizhou Plateau (YGP) is characterized by the distinctive isolated habitat of limestone Karst Islands and features the Wumeng Mountains (Mts), which divide the YGP into the two Plateaus of Yunnan and Guizhou. This study aims to assess the effects of past geographic and environmental isolation and climate fluctuation on the flora distribution in the YGP. To this effect, we analyzed the phylogeographical pattern and genetic structure for Myrica nana, a vulnerable species endemic to the YGP, based on chloroplast and nuclear ribosomal DNA sequence. The results suggest that the genetic and haplotype network structures are divided into at least two groups—cpDNA haplotype H2 (or nrDNA haplotypes h1, h2, and the native haplotype) mainly distributed to the east of the Wumeng Mts, and cpDNA haplotype H1 and haplotypes H3–H10 (or nrDNA haplotype h3) distributed to the west of the Wumeng Mts. A deep genetic split was noted within the two groups to reach 25 steps, especially for the cpDNA fragment variation. The east–west divergence reveals the existence of a natural geographical isolation boundary in the form of the Wumeng Mts, which divides the YGP into the Yunnan and Guizhou Plateaus. Therefore, there existed at least two glacial refugia during the Quaternary glacial period, along with a genetic diversity center, and at least two large geographic protection units for the vulnerable species of M. nana, distributed throughout the eastern and western sides of the Wumeng Mts. This study not only clarifies that the phylogeographical pattern and genetic structure for M. nana can be attributed to geographic and environmental isolation and climate fluctuation, but it also proposes an effective strategy to protect vulnerable species and the important wild flora of the YGP.

Sequence Analysis of the Internal Transcribed Spacer (ITS) Region of the Nuclear Ribosomal DNA (nrDNA), and trnL Intron of Chloroplast DNA (cpDNA) of the Chrysochamela (Fenzl) Boiss. (Brassicaceae) In Turkey

Brassicaceae family is an important one since it includes many economic and significant industrial oilseeds, spices, vegetables and some forage plants. In this study, sequences analysis among Chrysochamela (Brassicaceae) species distributed in Turkey were conducted nrDNA ITS and cpDNA trnL intron sequences. Chrysochamela species were collected and brought to the laboratory. ITS and trnL intron sequences were corrected with BioEdit and FinchTV programs. As a result of the study, ITS nucleotide compound compositions were determined as 22.7% T, 29.1 C, 21.5% A and 26.7% G. The lowest distance was 0.000 and the highest distance was 0.037. The phylogenetic tree obtained using the MEGA 6.0 program consists of two large groups. According to trnL intron sequences 37.9% T, 18.4 C, 28.3% A and 15.5% G. Nucleotide compound compositions were determined. The genetic distance between species was determined between 0.000 and 0.022. Maximum likelihood phylogenetic tree consists of two large groups. As a result, phylogenetic analyzes using ITS and trnL intron sequences were compatible with each other. It was also in past studies found to be supported by morphological, anatomical and RAPD data.

Molecular characterization of Fasciola isolates collected from sheep, goats and cattle in Kisumu, Baringo and Narok Counties, Kenya

Fasciolosis is a neglected trematode infection of public health and veterinary importance caused by Fasciola gigantica and Fasciola hepatica. Molecular analysis using the internal transcribed spacers’ ITS-1 and ITS-2 of nuclear ribosomal DNA is useful in distinguishing Fasciola species. This study aimed to characterize liver flukes from sheep, goats and cattle using these genetic markers. Fifty nine adult Fasciola specimens were collected from livers of naturally infected sheep, goats and cattle at selected abattoirs in Kisumu, Baringo and Narok Counties. Sequence comparison of ITS-1 and ITS-2 sequences of Fasciola isolates from this study and sequences in Genbank was carried out. A maximum likelihood tree was constructed for phylogenetic analysis. Analysis of ITS-1 and ITS-2 rDNA sequences revealed that F. hepatica and F. gigantica caused infection in both cattle and sheep and in goats only F. gigantica caused infection. The sequenced PCR amplicons showed a close relationship between Fasciola species in this study with Fasciola isolates from other regions in the world. Phylogenetic analysis showed that sequences of F. hepatica are similar to the sequence from Spain, China and Tunisia obtained from GenBank. The sequences of F. gigantica in this study have similarity to the sequence from Iran and Burkina Faso. Data from this study provides information that serves as basis for further studies on the distribution of F. gigantica and F. hepatica in other localities in Kenya, and is also important in designing epidemiological and control programmes for zoonotic fascioliasis.