High quality reference genome of drumstick tree (<Emphasis Type="Italic">Moringa oleifera</Emphasis> Lam.), a potential perennial crop

The drumstick tree (Moringa oleifera Lam.) is a perennial crop that has gained popularity in certain developing countries for its high-nutrition content and adaptability to arid and semi-arid environments. Here we report a high-quality draft genome sequence of M. oleifera. This assembly represents 91.78% of the estimated genome size and contains 19,465 protein-coding genes. Comparative genomic analysis between M. oleifera and related woody plant genomes helps clarify the general evolution of this species, while the identification of several species-specific gene families and positively selected genes in M. oleifera may help identify genes related to M. oleifera’s high protein content, fast-growth, heat and stress tolerance. This reference genome greatly extends the basic research on M. oleifera, and may further promote applying genomics to enhanced breeding and improvement of M. oleifera.     

Factors Determining the Use and Cultivation of <Emphasis Type="Italic">Moringa oleifera</Emphasis> Lam. in the Republic of Benin

Factors Determining the Use and Cultivation of Moringa oleifera Lam. in the Republic of Benin. Despite its nutritious leaves and considerable economic importance, the agroforestry species Moringa oleifera Lam. is still considered a neglected and underutilized species. To contribute to the development of an effective valorization strategy for M. oleifera, this study identified factors driving its use and cultivation in Benin. To this end, an ethnobotanical survey through individual interviews (n?=?801) was performed in 46 localities across biogeographical zones in Benin. Conditional inference tree–based classification models allowed us to identify factors that mostly influence the use, cultivation, and cultivation system of M. oleifera. Awareness, knowledge of the plant biology, gender, cultivation system, and age are factors influencing the use of M. oleifera. Cultivation systems are driven by ethnicity, knowledge of the plant’s biology, and the main socioprofessional activity. Effective valorization of M. oleifera requires awareness rising on its usefulness while providing knowledge on the plant biology.     

Taxonomic revisions in the Microstromatales: two new yeast species,two new genera,and validation of <Emphasis Type="Italic">Jaminaea</Emphasis> and two <Emphasis Type="Italic">Sympodiomycopsis</Emphasis> species

Environmental sampling yielded two yeast species belonging to Microstromatales (Exobasidiomycetes, Ustilaginomycotina). The first species was collected from a leaf phylloplane infected by the rust fungus Coleosporium plumeriae, and represents a new species in the genus Jaminaea, for which the name Jaminaea rosea sp. nov. is proposed. The second species was isolated from air on 50% glucose media and is most similar to Microstroma phylloplanum. However, our phylogenetic analyses reveal that species currently placed in Microstroma are not monophyletic, and M. phylloplanum, M. juglandis and M. albiziae are not related to the type species of this genus, M. album. Thus, Pseudomicrostroma gen. nov. is proposed to accommodate the following species: P. glucosiphilum sp. nov., P. phylloplanum comb. nov. and P. juglandis comb. nov. We also propose Parajaminaea gen. nov. to accommodate P. albizii comb. nov. and P. phylloscopi sp. nov. based on phylogenetic analyses that show these are not congeneric with Jaminaea or Microstroma. In addition, we validate the genus Jaminaea, its respective species and two species of Sympodiomycopsis and provide a new combination, Microstroma bacarum comb. nov., for the anamorphic yeast Rhodotorula bacarum. Our results illustrate non-monophyly of Quambalariaceae and Microstromataceae as currently circumscribed. Taxonomy of Microstroma and the Microstromataceae is reviewed and discussed. Finally, analyses of all available small subunit rDNA sequences for Jaminaea species show that J. angkorensis is the only known species that possess a group I intron in this locus, once considered a potential feature indicating the basal placement of this genus in Microstromatales.     

Morphological variation in pollen grains of <Emphasis Type="Italic">Mucuna</Emphasis> (Leguminosae): new biogeographic and evolutionary patterns

Mucuna comprises 105 species with an overall pantropical distribution and is divided into three subgenera: M. subg. Mucuna, M. subg. Stizolobium and M. subg. Macrocarpa. Although phylogenetic studies have supported the occurrence of three main clades, evolutionary relationships among them are not fully resolved. The objective of this study was to examine pollen grain morphology from representatives of all three subgenera and map these onto the phylogenetic trees generated by analysis of other characters. Pollen grain surface, form, size, and aperture number were compared. A Bayesian inference tree using matK sequences was constructed. The results indicate that the representatives of M. subg. Macrocarpa have the smallest pollen grains in the genus (a synapomorphic character here identified for this subgenus) and that species of subgenus Mucuna (those with umbelliform inflorescences) have the largest pollen grains. Additional morphological diversity of the pollen grain surface was noted: reticulate and/or micro-reticulate (in all three subgenera), perforate, gemmate or verrucose (only in M. subg. Mucuna). For all studied taxa, the pollen grains are triaperturate, except for two species of M. subg. Mucuna, which have tetraperturate pollen. The phylogenetic tree obtained using the matK marker resolved M. subg. Stizolobium as the earliest diverging lineage in Mucuna. Based on this phylogeny, a reticulate ornamentation pattern of the pollen surface may represent the ancestral state for the genus, while the larger pollen size and the foraminate, gemmate, and verrucose ornamentations are derived characteristics within the genus. These putative derived ornamentations have been observed only in neotropical species.     

Revision of the carabid genus <Emphasis Type="Italic">Meroctenus</Emphasis> Gemminger et Harold,with a new status of <Emphasis Type="Italic">Xenodochus</Emphasis> Andrewes (Coleoptera,Carabidae: Harpalini)

Originally described as a monotypical genus with unclear taxonomic position from Sudan, Meroctenus Gemminger et Harold, 1868 is treated as a polytypical genus of the Selenophori genus group with two subgenera: Meroctenus s. str. and Xenodochus Andrewes, 1941, stat. n. (the latter was previously considered a distinct genus). Within Meroctenus, two species are recognized: M. (Meroctenus) crenulatus Chaudoir, 1843 (type species) and M. (M.) mediocris (Andrewes, 1936), comb, n., transferred to Meroctenus s. str. from Xenodochus. A new subspecies M. (M.) crenulatus orientalis subsp. n. is described from Pakistan. Diagnoses of the genus Meroctenus in new interpretation as well as of its two subgenera are discussed, and a taxonomic review of the subgenus Meroctenus s. str. with a key to the species and subspecies is provided. The following synonymy is proposed: Meroctenus Gemminger et Harold, 1868 = Paregaploa Müller, 1947, syn. n.; Meroctenus crenulatus (Chaudoir, 1843) = Egaploa (Paregaploa) conviva Müller, 1947, syn. n. Lectotypes are designated for Ctenomerus crenulatus Chaudoir, 1843 and Xenodus mediocris Andrewes, 1936.     

Contribution to the phylogeny and a new species of <Emphasis Type="Italic">Coccodiella</Emphasis> (Phyllachorales)

Coccodiella is a genus of plant-parasitic species in the family Phyllachoraceae (Phyllachorales, Ascomycota), i.e., tropical tar spot fungi. Members of the genus Coccodiella are tropical in distribution and are host-specific, growing on plant species belonging to nine host plant families. Most of the known species occur on various genera and species of the Melastomataceae in tropical America. In this study, we describe the new species C. calatheae from Panama, growing on Calathea crotalifera (Marantaceae). We obtained ITS, nrLSU, and nrSSU sequence data from this new species and from other freshly collected specimens of five species of Coccodiella on members of Melastomataceae from Ecuador and Panama. Phylogenetic analyses allowed us to confirm the placement of Coccodiella within Phyllachoraceae, as well as the monophyly of the genus. The phylogeny of representative species within the family Phyllachoraceae, including Coccodiella spp., graminicolous species of Phyllachora and taxa with erumpent to superficial stroma from several host families, suggests that the genus Phyllachora might be polyphyletic. Furthermore, tar spot fungi with superficial or erumpent perithecia seem to be restricted to the family Phyllachoraceae, independently of the host plant. We also discuss the biodiversity and host-plant patterns of species of Coccodiella worldwide.     

Prolonged culture of <Emphasis Type="Italic">Boesenbergia rotunda</Emphasis> cells reveals decreased growth and shoot regeneration capacity

We evaluated the ploidy levels and tissue culture responses of 16 Japanese Miscanthus accessions, which are registered and vegetatively maintained in the National Agriculture and Food Research Organization GeneBank, Japan, to screen suitable genotypes for the molecular breeding of Miscanthus species. A ploidy analysis showed that most M. sinensis and M. sinensis var. condensatus (var. condensatus) were putative diploids, but one accession identified as M. sinensis was unexpectedly a putative tetraploid. Additionally, M. sacchariflorus and its hybrid accessions were putative tetraploids. The deoxyribonucleic acid levels in var. condensatus were significantly higher than those in the diploid M. sinensis. Of the accessions, 10, including M. sinensis and var. condensatus, could induce plant regenerable embryogenic calli from apical meristems. We selected three of these M. sinensis accessions for further experiments because their calli growth rates were faster than those of the var. condensatus accessions. Tissue culture experiments with the selected accessions indicated that the frequencies of callus and green shoot formation strongly correlated with genotype. The broad-sense heritabilities of the embryogenic callus and green shoot formation frequencies in the selected accessions were 0.75 and 0.65, respectively, indicating that the cultures’ responses were mainly controlled by genetic factors. Thus, we further selected one accession that had the highest efficiencies in callus and green shoot formation, and we observed that light during callus culturing significantly inhibited calli growth, but promoted plant regeneration from calli in the selected accession.     

Reduced ant defenses in <Emphasis Type="Italic">Macaranga</Emphasis> myrmecophytes (Euphorbiaceae) infested with a winged phasmid <Emphasis Type="Italic">Orthomeria cuprinus</Emphasis>

Macaranga is a tree genus that includes many species of myrmecophytes, which are plants that harbor ant colonies within hollow structures known as domatia. The symbiotic ants (plant–ants) protect their host plants against herbivores; this defense mechanism is called ‘ant defense’. A Bornean phasmid species Orthomeria cuprinus feeds on two myrmecophytic Macaranga species, Macaranga beccariana and Macaranga hypoleuca, which are obligately associated with Crematogaster ant species. The phasmids elude the ant defense using specialized behavior. However, the mechanisms used by the phasmid to overcome ant defenses have been insufficiently elucidated. We hypothesized that O. cuprinus only feeds on individual plants with weakened ant defenses. To test the hypothesis, we compared the ant defense intensity in phasmid-infested and non-infested M. beccariana trees. The number of plant–ants on the plant surface, the ratio of plant–ant biomass to tree biomass, and the aggressiveness of plant–ants towards experimentally introduced herbivores were significantly lower on the phasmid-infested trees than on the non-infested trees. The phasmid nymphs experimentally introduced into non-infested trees, compared with those experimentally introduced into phasmid-infested trees, were more active on the plant surface, avoiding the plant–ants. These results support the hypothesis and suggest that ant defenses on non-infested trees effectively prevent the phasmids from remaining on the plants. Thus, we suggest that O. cuprinus feeds only on the individual M. beccariana trees having decreased ant defenses, although the factors that reduce the intensity of the ant defenses remain unclear.     

Clavicipitaceous entomopathogens: new species in <Emphasis Type="Italic">Metarhizium</Emphasis> and a new genus <Emphasis Type="Italic">Nigelia</Emphasis>

In several surveys in the tropical forests in Thailand, specimens that looked morphologically similar to Metarhizium martiale and Cordyceps variegata, as well as other Metarhizium species were collected and cultured in vitro. A combined phylogeny of several genes including the small (18S) and large (28S) subunits of the ribosomal DNA, elongation factor 1-α (TEF), RNA polymerase II subunits 1 and 2 (RPB1, RPB2) genes has shown these to be new taxa in the Clavicipitaceae. Nigelia is described as a new genus closely related to Metarhizium, to the scale insect pathogens Aschersonia (Hypocrella), Samuelsia and Moelleriella, and to plant pathogens in Claviceps and Balansia, and other relatives. Nigelia comprises M. martiale and a new species Nigelia aurantiaca, which has been found infecting lepidopteran larvae and which produces pseudoimmersed, obliquely arranged, obpyriform perithecia with curved or bent ostioles and with whole (non-separating) cylindric ascospores. Metarhizium chaiyaphumense, M. kalasinense, M. prachinense, M. samlanense, and M. takense are described as new species of Metarhizium. Metarhizium martiale is transferred to Nigelia, and Paecilomyces reniformis is transferred to Metarhizium.     

The genus <Emphasis Type="Italic">Diaporthe</Emphasis>: a rich source of diverse and bioactive metabolites

The genus Diaporthe (asexual state: Phomopsis) comprises pathogenic, endophytic and saprobic species with both temperate and tropical distributions. Although species of Diaporthe have in the past chiefly been distinguished based on host association, studies have confirmed several taxa to have wide host ranges, suggesting that they move freely between hosts, frequently co-colonizing diseased or dead tissue, while some species are known to be host-specific. They are also very frequently isolated as endophytes of seed plants. Due to their importance as plant pathogens, the genus has been thoroughly investigated for secondary metabolites, including during screening programs aimed at the discovery of novel bioactive natural products, but the respective information has never been compiled. Therefore, we have examined the relevant literature to explore and highlight the major classes of metabolites of Diaporthe and their Phomopsis conidial states. These fungi predominantly produce a large number of polyketides, but cytochalasins and other types of commonly encountered fungal secondary metabolites are also predominant in some species. Interestingly, not a single metabolite which is also known from the host plant has ever been isolated as a major component from an endophytic Diaporthe strain, despite the fact that many of the recent studies were targeting endophytic fungi of medicinal plants.     

Distribution and stress tolerance of <Emphasis Type="Italic">Fimbristylis dichotoma</Emphasis> subsp. <Emphasis Type="Italic">podocarpa</Emphasis> (Cyperaceae) growing in highly acidic solfatara fields

Solfatara fields, areas surrounding fumaroles (volcanic vents) near the hot springs or volcanoes, are characterized by severe environmental conditions such as low soil pH and high aluminum contents. Fimbristylis dichotoma subsp. podocarpa is an endangered plant distributed in solfatara fields of Kyushu, western Japan. This species is known to form stands in sites closed to fumaroles where another solfatara plant Miscanthus sinensis do not colonize. We conducted field survey and culture experiments to test the hypothesis that F. dichotoma has higher tolerance to low pH and high aluminum conditions than M. sinensis, which corresponds to the distribution pattern of the two species. In the study site of Myoban Hot Spring, Oita Prefecture, rhizosphere soils of F. dichotoma showed lower pH and higher aluminum contents than those of M. sinensis. The culture experiment showed that germination of F. dichotoma was not inhibited even at pH 2, whereas significant decline in germination (%) was observed in M. sinensis. However, because of the low germination (%) of F. dichotoma, the values of the two species were similar at pH 2. In the pot culture, seedling growth of M. sinensis was suppressed at the aluminum concentrations tested (400 mg AlCl₃ L^?1). Conversely, no significant decline in the seedling growth was observed in F. dichotoma at the same aluminum levels. Considering soil conditions in the field, we concluded that that the difference in the tolerance to aluminum between the two species played a significant role in determining their distribution pattern.     

Chromosome counts in <Emphasis Type="Italic">Chaetogastra</Emphasis> (Melastomataceae,Melastomateae)

Chaetogastra is the largest genus in Melastomateae, with about 165–190 species. The genus was only recently resurrected, based on species that have been traditionally treated in Tibouchina sects. Diotanthera, Pseudopterolepis, Purpurella and Simplicicaules. This article presents 15 chromosome counts for the genus, a review of the available counts and also a discussion of these counts in a systematic context. Although the sampling in the genus is still poor, the data found in the literature and in our research indicate x=9 as the base chromosome number for the genus. We also found that euploidy may be common in Chaetogastra, with diploid, tetraploid and hexaploid species. Basic chromosome numbers also seem to be a taxonomic character that distinguishes Chaetogastra (x=9) from Brachyotum (x=10).     

A conserved repetitive DNA element located in the centromeres of chromosomes in <Emphasis Type="Italic">Medicago</Emphasis> genus

In most eukaryotic species, centromeres harbor large arrays of tandem repeated satellite DNA sequences. In this study, we report on the genomic distribution of a centromere satellite repeat “MtR3” in Medicago genus and three distantly related genera. Fluorescence in situ hybridization (FISH) results showed MtR3 repeats were detected in the centromere regions in M. truncatula, M. minima, M. edgeworthii, M. ruthenica, M. caerulea, M. sativa, and M. falcata (4×), but no signals were discovered in M. lupulina, M. polymorpha, and M. falcata (2×), Melilotus officinalis, Crotalaria medicaginea, and Trifolium repens. However, sequence analysis showed this MtR3 DNA had genomic distribution in all species and was highly conserved across the entire Medicago genus and three other genera. The conservation and widespread presence suggested MtR3 repeats may play important roles in centromeric function.     

Low genetic differentiation among altitudes in wild <Emphasis Type="Italic">Camellia oleifera</Emphasis>, a subtropical evergreen hexaploid plant

Camellia oleifera is a subtropical evergreen plant. Cultivated C. oleifera is the most important woody oil crop in China. Wild C. oleifera is an essential genetic resource for breeding. The patterns of genetic differentiation among altitudes/latitudes in wild C. oleifera are still unknown. Camellia oleifera may be predominantly hexaploid. The characteristics of polyploidy may lead to considerable biases in estimates of genetic diversity and differentiation. Our study used C. oleifera as a case study for analysing genetic diversity, structure and differentiation in polyploid plants using simple sequence repeats (SSRs). Wild C. oleifera samples were collected at different altitudes on the Jinggang and Lu mountains of China. The ploidy levels were determined with flow cytometry analysis. Eight highly polymorphic SSRs were used to genotype the samples. Genetic diversity and structure were analysed. Various estimates of genetic differentiation were compared. The flow cytometry results indicated that wild C. oleifera samples were all hexaploid at various altitudes of the Jinggang and Lu mountains. High levels of genetic diversity were found on both the Jinggang and Lu mountains. Genetic structure analyses indicated clear genetic differentiation between the Jinggang and Lu mountains and lower genetic differentiation among altitudes within each mountain. Classical genetic differentiation estimates of F_st failed to discriminate genetic differentiation between and within mountains. The Rho statistic showed a moderate level of genetic differentiation between mountains and lower levels of genetic differentiation within each mountain. Our study demonstrates that Rho is the statistic of choice for estimating genetic differentiation in polyploids.     

Species Discrimination of Co-Occurring Small Fossil Mammals: A Case Study of the Cretaceous-Paleogene Multituberculate Genus <Emphasis Type="Italic">Mesodma</Emphasis>

The mammalian fossil record is largely composed of isolated teeth and tooth-bearing elements. In vertebrate microfossil assemblages with closely related, co-occurring species of mammals, it can be difficult to identify isolated teeth to species level because morphological differences among species may be slight and based on a single tooth position. Here we investigate the utility of the allegedly diagnostic lower fourth premolar (p4) for species-level identification in the genus Mesodma (Multituberculata, Neoplagiaulacidae). We conducted linear and geometric morphometrics on 86 p4s representing four Cretaceous-Paleogene (K-Pg) species of Mesodma that are common in deposits of the western interior of North America. Although Mesodma has been extensively discussed in the literature, these four species overlap considerably in p4 size and shape, making species-level identifications challenging. Using linear measurements, landmarks, and semilandmarks, we quantified p4 size and shape to understand morphological variation across the genus and uncover practical sources of morphological differentiation among the species represented here. Our results indicate (1) size is more important than shape for identifying p4s of Mesodma species; p4 shape varies across the genus, but cannot be used alone to identify isolated p4s to species; (2) M. garfieldensis and M. thompsoni cannot be distinguished from each other using p4 size or shape; we therefore subsume M. garfieldensis within M. thompsoni; and (3) M. formosa increased in size across the K-Pg boundary. In light of these results, we recommend that taxonomic diagnoses relying on isolated teeth incorporate quantitative analyses of morphology whenever possible to increase the accuracy of species-level identifications and paleofaunal studies that employ them.     

The high diversity of <Emphasis Type="Italic">Lotus corniculatus</Emphasis> endosymbionts in soils of northwest Spain

The diversity of rhizobia that establish symbiosis with Lotus corniculatus has scarcely been studied. Several species of Mesorhizobium are endosymbionts of this legume, including Mesorhizobium loti, the type species of this genus. We analysed the genetic diversity of strains nodulating Lotus corniculatus in Northwest Spain and ten different RAPD patterns were identified among 22 isolates. The phylogenetic analysis of the 16S rRNA gene showed that the isolated strains belong to four divergent phylogenetic groups within the genus Mesorhizobium. These phylogenetic groups are widely distributed worldwide and the strains nodulate L. corniculatus in several countries of Europe, America and Asia. Three of the groups include the currently described Mesorhizobium species M. loti, M. erdmanii and M. jarvisii which are L. corniculatus endosymbionts. An analysis of the recA and atpD genes showed that our strains belong to several clusters, one of them very closely related to M. jarvisii and the remanining ones phylogenetically divergent from all currently described Mesorhizobium species. Some of these clusters include L. corniculatus nodulating strains isolated in Europe, America and Asia, although the recA and atpD genes have been sequenced in only a few L. corniculatus endosymbionts. The results of this study revealed great phylogenetic diversity of strains nodulating L. corniculatus, allowing us to predict that even more diversity will be discovered as further ecosystems are investigated.     

Relationships between the gall-midge genera <Emphasis Type="Italic">Trotteria</Emphasis> and <Emphasis Type="Italic">Verbasciola</Emphasis> (Diptera,Cecidomyiidae), with description of new species from the Middle Volga River Area

Gall midges of the genera Trotteria and Verbasciola of the supertribe Lasiopteridi are inquilines. The widespread genus Trotteria includes 28 species developing in galls of 30 species of gall midges; 24 species develop in galls of Asphondyliidi. Gall midges-hosts and inquilines were found on 57 plant species of 17 families. The Palaearctic genus Verbasciola comprises three species that have been recorded in galls of three gall-midge species damaging three plant species. Seven new species are described, Trotteria coronillacola, T. perkovskii, T. cytisiphila, T. kalininae, T. jigulensis, Schizomyia samaralukensis, and Verbasciola volgensis. The diagnoses of the genera were corrected. Trotteria spinosa Kovalev is restored from the synonyms of T. umbelliferarum Kieffer. Data on the distribution of all the species examined and their associations with host gall midges and taxonomic groups of plants are given.