Complex Genus Research Articles

Antifungal Activity of Bacillus Species Against Fusarium and Analysis of the Potential Mechanisms Used in Biocontrol.

Fusarium is a complex genus of ascomycete fungi that consists of plant pathogens of agricultural relevance. Controlling Fusarium infection in crops that leads to substantial yield losses is challenging. These economic losses along with environmental and human health concerns over the usage of chemicals in attaining disease control are shifting focus toward the use of biocontrol agents for effective control of phytopathogenic Fusarium spp. In the present study, an analysis of the plant-growth promoting (PGP) and biocontrol attributes of four bacilli (Bacillus simplex 30N-5, B. simplex 11, B. simplex 237, and B. subtilis 30VD-1) has been conducted. The production of cellulase, xylanase, pectinase, and chitinase in functional assays was studied, followed by in silico gene analysis of the PGP-related and biocontrol-associated genes. Of all the bacilli included in this study, B. subtilis 30VD-1 (30VD-1) demonstrated the most effective antagonism against Fusarium spp. under in vitro conditions. Additionally, 100 μg/ml of the crude 1-butanol extract of 30VD-1’s cell-free culture filtrate caused about 40% inhibition in radial growth of Fusarium spp. Pea seed bacterization with 30VD-1 led to considerable reduction in wilt severity in plants with about 35% increase in dry plant biomass over uninoculated plants growing in Fusarium-infested soil. Phase contrast microscopy demonstrated distortions and abnormal swellings in F. oxysporum hyphae on co-culturing with 30VD-1. The results suggest a multivariate mode of antagonism of 30VD-1 against phytopathogenic Fusarium spp., by producing chitinase, volatiles, and other antifungal molecules, the characterization of which is underway.

Typification of species names in Dichondra (Convolvulaceae)

AbstractDichondra is a genus of creeping and sprawling herbs with reniform leaves, entire leaf margins and inconspicuous flowers. It is included in the tribe Dichondreae (Convolvulaceae). Dichondra is a taxonomically complex genus with multiple unsolved nomenclatural problems. We propose lectotypes for Dichondra argentea, D. parvifolia, D. macrocalyx and D. sericea and a neotype for Demidofia repens, the basionym of Dichondra carolinensis.

Narcissus × munozii-alvarezii (Amaryllidaceae): a new hybrid from southern Spain

Daffodils are an attractive group by their striking flowers and scents, therefore very appreciated as ornamental plants. Cultivars are very numerous, leading to more than 27,000 names considering them (Kington 2008). In the wild, the Iberian Peninsula can be recognized as the centre of speciation of Narcissus Linnaeus (1753: 289) (Barra et al. 2011). Consequently, the richest global diversity is found there (Hanks 2002). It is a complex genus that according to diverse authors varies from 25 to 87 species (cf. Webb 1980, Blanchard 1990, Mathew 2002, Zonneveld 2008, Aedo 2013, RHS 2016). Moreover, new species are still described (Escobar García 2018). Some daffodils have been described considering only herbarium vouchers. Nonetheless, it is encouraged to study populations from living specimens by two main reasons: (i) some features such as corona or perigone size—and ratios that include them—cannot be retrieved from exsiccata; and (ii) to study daffodils in the wild allow better understanding of their ecology and phenology (Barra Lázaro et al. 2016). The latter is important to clarify species spatial distribution and their hybrids.

Biosystematic revision of the native and naturalised species of Rubus L. (Rosaceae) in the Cape Floristic Region, South Africa

Rubus L. is a highly diverse and taxonomically complex genus with a worldwide distribution. Although southern Africa is not a major centre of Rubus diversity, a number of indigenous and naturalised taxa have been recorded from the region, although their taxonomy, nomenclature and evolution are either confused or poorly studied at best. This paper represents the first results of a wider project focusing on the biosystematics of the southern African Rubus flora, and presents a taxonomic revision of the brambles of the Cape Floristic Region, including an estimation of ploidy levels. A total of eight taxa are recognised, including the two indigenous taxa R. pinnatus and R. rigidus agg., the four introduced species R. armeniacus, R. bergii, R. rosifolius and R. titanus, and two hybrids between indigenous and introduced taxa. Rubus rigidus agg. is an unresolved and variable species complex with at least two ploidy levels (5x, 6x). The hybrid taxon R. bergii × R. rigidus appears to be widespread and behaves as an independent apomictic complex. In addition, hybridization between R. bergii and R. pinnatus is relatively common in the contact zones between the two species. The two introductions Rubus armeniacus and R. titanus are recorded from South Africa for the first time. The invasive potential of the introduced species is regarded as low but the potential for hybridization by R. bergii seems to be high. An identification key, morphological descriptions, and notes on nomenclature, distribution and ecology are provided, and all taxa are illustrated.

Utility of molecular-assisted alpha taxonomy of the genus Cystophora (Fucales, Phaeophyceae) from New Zealand and Australia

:Many brown macroalgal species are difficult to identify because of limited morphological differentiation and/or high levels of plasticity. Molecular methods for distinguishing species coupled with morphological examination have been useful in clarifying species status in many groups. Cystophora is a species-rich, morphologically complex brown algal genus that has been carefully monographed, and it is ideal for testing the utility of molecular markers for genetic species delimitation. We evaluated the utility of the cytochrome oxidase subunit 1 (COI) DNA-barcode marker, alone and in combination with nuclear-encoded internal transcribed spacer (ITS) rDNA, in delimiting species. We also used several methods to delimit putative genetic species. Our results showed that for consistent species delimitation and species delimitation that approximates morphological species, both markers in combination are necessary. Most species in the genus are morphologically recognizable and genetically distinct but neither COI nor combined COI-ITS data separate Cystophora congesta from Cystophora retroflexa or Cystophora distenta from Cystophora scalaris. We showed that morphological characters used to separate these two species pairs are highly variable among samples, with many intermediates. Thus, we concluded that these are not independent species and synonymize these species. Our data showed that this genus, while widespread, mostly conforms to a morphospecies concept.

Insights into the phylogeny of false-branching heterocytous cyanobacteria with the description of Scytonema pachmarhiense sp. nov. isolated from Pachmarhi Biosphere Reserve, India.

A false branching cyanobacterium (strain 10A1_PS) was isolated from a freshwater body of the Pachmarhi Biosphere Reserve, India and was characterised using the polyphasic approach. The detailed morphological examination indicated that the strain belonged to the complex genus Scytonema as it exhibited typical false branching character whose frequency increased with age of the culture. As the family Scytonemataceae and the genus Scytonema has been shown to be polyphyletic in many studies, we provide deep insights into the phylogenetic complexities within the family Scytonemataceae based on 16S rRNA gene phylogeny along with complete morphological, molecular and phylogenetic characterisation of the strain. The 16S rRNA gene phylogenetic tree inferred by Bayesian Inference, Neighbor-Joining and Maximum Parsimony methods showed that the strain clustered within the Scytonema sensu stricto clade. The phylogenetic distance and the positioning of the strain clearly indicated it to be different from other Scytonema species. Further analysis using rbcL phylogeny, folded secondary structures of the 16S-23S ITS, p-distance and percentage pairwise similarity matrix clearly distinguished the strain 10A1_PS from the other closely related species. In accordance with the International Code of Nomenclature for Algae, Fungi and Plants, we propose the name of the new species to be Scytonema pachmarhiense.

Rapid diversification and hybridization have shaped the dynamic history of the genus Elaenia

Multi-locus data have proven invaluable in phylogenetic reconstruction and species delimitation. However, the mixed genetic signal from different loci can make inference of evolutionary history challenging and may produce incongruences depending on analytical and marker choice. Aside from incomplete lineage sorting (ILS) following diversification events that have had little time for deep differentiation, the most common causes of incongruent phylogenies are genetic introgression confounding a bifurcating evolutionary trajectory. In this study, we used multi-locus analytical approaches on sequence data of nine loci from 80 individuals of over 20 Neotropical Elaenia flycatcher species to examine the systematics, molecular phylogeny and species limits of this complex genus. Our results provide a robust phylogeny and estimates of species limits within Elaenia, but point to important cases of incongruences among phylogenies based on different analytical approaches. Simulations and estimates of divergence times provide reasonable explanations for the incongruent placement of some Elaenia taxa, pointing to multiple cases of both ILS and introgression within the genus. Molecular dating of major evolutionary events revealed intensive diversification during the Pleistocene, suggesting a central role of climate oscillations in the evolution of Elaenia flycatchers.

On the identity of Schistidium malacophyllum Herzog (Grimmiacaea, Bryophyta)

Schistidium Bruch & Schimper (in Bruch et al. 1845: 93) is one of the most complex and difficult moss genera, and is still poorly known and understudied taxonomically in South America. In the Neotropics, there are around twenty names for this genus without a real status acknowledged (Churchill et al., 2000) as no taxonomical or nomenclatural revision was ever conducted.

Pollen morphology of some taxa of Thlaspi L. sensu lato (Brassicaceae) from Turkey, and its taxonomical importance

ABSTRACTIn this study, the pollen morphology of 22 Turkish taxa (12 of which are endemic) of the taxonomically complex genus Thlaspi L. sensu lato was studied with light microscopy (LM) and scanning electron microscopy (SEM). We found that the pollen of Thlaspi are usually bilateral symmetric and anisopolar. They are prolate, subprolate, perprolate or spheroidal, with the polar axis ranging from 14.13 to 28.36 µm and equatorial axis from 8.75 to 19.48 µm. Pollen are usually tricolpate, but some of them are 1–2- or 4-colpate. The ornamentation of pollen of the examined taxa is usually micro or macro reticulate, and rarely foveolate. The exine thickness ranges from 1.59 to 2.75 µm, and the intine thickness from 0.54 to 0.94 µm. As a result of this study, some of the pollen characters such as the sizes of pollen and colpus, ornamentation of exine, apocolpidium, and shape and diameter of amb are found to be significant morphological characters for taxonomic use.

DNA barcoding a taxonomically complex hemiparasitic genus reveals deep divergence between ploidy levels but lack of species-level resolution

DNA barcoding is emerging as a useful tool not only for species identification but also for studying evolutionary and ecological processes. Although plant DNA barcodes do not always provide species-level resolution, the generation of large DNA barcode data sets can provide insights into the mechanisms underlying the generation of species diversity. Here, we study evolutionary processes in taxonomically complex British Euphrasia (Orobanchaceae), a group with multiple ploidy levels, frequent self-fertilization, young species divergence and widespread hybridization. We use a phylogenetic approach to investigate the colonization history of British Euphrasia, followed by a DNA barcoding survey and population genetic analyses to reveal the causes of shared sequence variation. Phylogenetic analysis shows Euphrasia have colonized Britain from mainland Europe on multiple occasions. DNA barcoding reveals that no British Euphrasia species has a consistent diagnostic sequence profile, and instead, plastid haplotypes are either widespread across species, or are population specific. The partitioning of nuclear genetic variation suggests differences in ploidy act as a barrier to gene exchange, while the divergence between diploid and tetraploid ITS sequences supports the polyploids being allotetraploid in origin. Overall, these results show that even when lacking species-level resolution, analyses of DNA barcoding data can reveal evolutionary patterns in taxonomically complex genera.

Different Natural Selection Pressures on the atpF Gene in Evergreen Sclerophyllous and Deciduous Oak Species: Evidence from Comparative Analysis of the Complete Chloroplast Genome of Quercus aquifolioides with Other Oak Species.

Quercus is an economically important and phylogenetically complex genus in the family Fagaceae. Due to extensive hybridization and introgression, it is considered to be one of the most challenging plant taxa, both taxonomically and phylogenetically. Quercus aquifolioides is an evergreen sclerophyllous oak species that is endemic to, but widely distributed across, the Hengduanshan Biodiversity Hotspot in the Eastern Himalayas. Here, we compared the fully assembled chloroplast (cp) genome of Q. aquifolioides with those of three closely related species. The analysis revealed a cp genome ranging in size from 160,415 to 161,304 bp and with a typical quadripartite structure, composed of two inverted repeats (IRs) separated by a small single copy (SSC) and a large single copy (LSC) region. The genome organization, gene number, gene order, and GC content of these four Quercus cp genomes are similar to those of many angiosperm cp genomes. We also analyzed the Q. aquifolioides repeats and microsatellites. Investigating the effects of selection events on shared protein-coding genes using the Ka/Ks ratio showed that significant positive selection had acted on the atpF gene of Q. aquifolioides compared to two deciduous oak species, and that there had been significant purifying selection on the atpF gene in the chloroplast of evergreen sclerophyllous oak trees. In addition, site-specific selection analysis identified positively selected sites in 12 genes. Phylogenetic analysis based on shared protein-coding genes from 14 species defined Q. aquifolioides as belonging to sect. Heterobalanus and being closely related to Q. rubra and Q. aliena. Our findings provide valuable genetic information for use in accurately identifying species, resolving taxonomy, and reconstructing the phylogeny of the genus Quercus.

A multivariate morphometric delimitation of species boundaries in the South American genus Nicoraepoa (Poaceae: Pooideae: Poeae)

A multivariate morphometric study of the genus Nicoraepoa was carried out to examine patterns of morphological variation among the species and to identify additional characters to allow a clearer delimitation among species. Nicoraepoa is a taxonomically complex genus comprising seven species endemic to South America. Although most of the species are well delimited, two of them, N. andina and N. chonotica, are morphologically similar and very difficult to separate. The morphological variation among species, with overlapping morphological characters, pseudovivipary and possible hybridization make species boundaries unclear. In the present paper, sixty-seven characters were scored for a total of 216 specimens and analyzed using ordination, cluster and discriminant analyses. Based on multivariate results, we recognized species groups and morphological diagnostic characters that allow clearer species delimitation. As a result, N. chonotica has been transferred to N. andina as a subspecies that inhabit southern Patagonia. Other taxa could be recognized and delimited by diagnostic characters: N. erinacea, N. pugionifolia, N. stepparia, N. subenervis subsp. spegazziniana and N. subenervis subsp. subenervis. Moreover, we discuss the possibility that a new species from Bolivia, based on only one specimen, closely related to N. subenervis should be ascribed in Nicoraepoa.

Metabolomic analysis applied to chemosystematics and evolution of megadiverse Brazilian Vernonieae (Asteraceae)

Vernonia sensu lato is the largest and most complex genus of the tribe Vernonieae (Asteraceae). The tribe is chemically characterized by the presence of sesquiterpene lactones and flavonoids. Over the years, several taxonomic classifications have been proposed for Vernonia s.l. and for the tribe; however, there has been no consensus among the researches. According to traditional classification, Vernonia s.l. comprises more than 1000 species divided into sections, subsections and series (sensu Bentham). In a more recent classification, these species have been segregated into other genera and some subtribes were proposed, while the genus Vernonia sensu stricto was restricted to 22 species distributed mainly in North America (sensu Robinson). In this study, species from the subtribes Vernoniinae, Lepidaploinae and Rolandrinae were analyzed by UHPLC-UV-HRMS followed by multivariate statistical analysis. Data mining was performed using unsupervised (HCA and PCA) and supervised methods (OPLS-DA). The HCA showed the segregation of the species into four main groups. Comparing the HCA with taxonomical classifications of Vernonieae, we observed that the groups of the dendogram, based on metabolic profiling, were in accordance with the generic classification proposed by Robinson and with previous phylogenetic studies. The species of the genera Stenocephalum, Stilpnopappus, Strophopappus and Rolandra (Group 1) were revealed to be more related to the species of the genus Vernonanthura (Group 2), while the genera Cyrtocymura, Chrysolaena and Echinocoryne (Group 3) were chemically more similar to the genera Lessingianthus and Lepidaploa (Group 4). These findings indicated that the subtribes Vernoniinae and Lepidaploinae are non-chemically homogeneous groups and highlighted the application of untargeted metabolomic tools for taxonomy and as indicators of species evolution. Discriminant compounds for the groups obtained by OPLS-DA were determined. Groups 1 and 2 were characterized by the presence of 3′,4′-dimethoxyluteolin, glaucolide A and 8-tigloyloxyglaucolide A. The species of Groups 3 and 4 were characterized by the presence of putative acacetin 7-O-rutinoside and glaucolide B. Therefore, untargeted metabolomic approach combined with multivariate statistical analysis, as proposed herein, allowed the identification of potential chemotaxonomic markers, helping in the taxonomic classifications.

A new species and some additions to the genus Oxytropis DC. (Fabaceae) in Iran

The complex genus Oxytropis of Iran was revised by the present author in 2013. The new species O. sutakensis Maassoumi is described here based on recent collections from high lands of the central Elburz Mountains, province Mazandaran. Also some new records, new synonyms, as well as further additions and remarks are given for the genus in Iran.

Coupling molecular data and experimental crosses sheds light about species delineation: a case study with the genus Ciona

Molecular studies sometimes reveal evolutionary divergence within accepted species. Such findings can initiate taxonomic revision, as exemplified in the formerly recognized species Ciona intestinalis. While an increasing number of studies have examined the ecology, reproductive barriers and genetics of C. intestinalis and C. robusta, there are still much uncertainties regarding other species of this genus. Using experimental crosses and mitochondrial data, we investigated the evolutionary relationships among four native and introduced Ciona spp., found in sympatry in the Mediterranean Sea or English Channel. Outcome of 62 bi-parental reciprocal crosses between C. intestinalis, C. robusta, C. roulei and C. edwardsi showed that C. edwardsi is reproductively isolated from the other taxa, which is in agreement with its distinct location in the phylogenetic tree. Conversely, hybrids are easily obtained in both direction when crossing C. intestinalis and C. roulei, reinforcing the hypothesis of two genetically differentiated lineages but likely being from a same species. Altogether, this study sheds light on the evolutionary relationship in this complex genus. It also calls for further investigation notably based on genome-wide investigation to better describe the evolutionary history within the genus Ciona, a challenging task in a changing world where biological introductions are shuffling species distribution.

Habenaria ocadiziana (Habenariinae: Orchidaceae) a new and unusual species from western Mexico

The genus Habenaria Willdenow (1805: 5,44) is one of the most diverse and most complex genus in the Orchidaceae, with approximately 800 species. It has a Pantropical geographical distribution. (Ames 1910, Williams 1951, McVaugh 1985, González 1993, and Batista et al. 2011a, 2011b). Recently Habenaria luquanensis G.W.Hu in Long et al. (2015: 190) was described from China, H. fimbriatiloba (Kolanowska 2016: 96) from Nepal and H. reflexicalcar J.A.N.Bat. & B.M.Carvalho in Batista et al. (2016: 278), H. hippocrepica J.A.N.Bat & Bianch in Batista et al. (2016: 282), H. quadriferricola J.A.N.Bat. & B.M.Carvalho in Batista et al. (2016: 286) and H. espinhacensis J.A.N. Bat. & A.A.Vale from Brazil in Batista et al. (2016: 288). However, a new species has been discovered recently, H. yookuaaensis Mejía-Marín, Espejo, López-Ferr. & R.Jiménez in Mejía-Marín et al. (2017: 74) increasing the number of known taxa in Mexico.

Micromorphological Studies of the Genus Ipomoea L. (Convolvulaceae) in Nepal

Ipomoea is a large and complex genus, which comprises the largest number of species within the family Convolvulaceae. Globally, the genus consists of about 600 species of vines and shrubs, which are widely distributed throughout the tropics and the subtropics. In Nepal, the genus comprises 15 species, which are distributed throughout the tropical, subtropical and temperate region of the country. Besides few enumerations and floristic surveys, no comprehensive anatomy and pollen characters of 16 species of Ipomoea occurring in Nepal to evaluate the qualitative and quantitative differences in these characters. We found that the all species of Ipomoea have paracytic type stomata. However, there is considerable variation in the size and frequency of the stomata. The size and shape of the epidermal cells also varies from species to species. Ipomoea nil has the highest stomatal frequency, while I. purpurea has the lowest frequency. All species of Ipomoea have globose, isopolar, echinate, pentoporate and radially symmetrical pollen grains. I. quamoclit has the largest pollen, while I. aquatica has the smallest pollen. The anatomy of stem shows no distinct structural differences among species. Although no qualitative differences in the studied characters are found among species, there is considerable variation in the quantitative characters, such as the size of stomata, frequency of stomata and pollen size. These characters could have important taxonomic and ecological implications and therefore, are as valuable as the morphological characters.

GENETIC DIVERSITY OF CROCUS SATIVUS AND ITS CLOSE RELATIVE SPECIES ANALYZED BY iPBS-RETROTRANSPOSONS

Saffron (Crocus L.) is a member of Crocoideae, the biggest of four subfamilies in the Iridaceae family. It has 2n = 3x = 24 chromosomes and is triploid; thus, it is sterile. In previous research, different molecular DNA markers were used but molecular characterization and genetic diversity of this complex genus have not yet been clarified. Therefore, current study aimed to determine the molecular characterization of saffron and its close relative species using inter-primer binding site (iPBS)-retrotransposon markers. Eighty-three iPBS-retrotransposon primers were used in 28 C. sativus genotypes and 17 close relative species of saffron to identify their genetic diversity. Sixteen polymorphic iPBS-retrotransposon primers generated a total of 401 polymorphic scorable bands. The mean PIC value, Nei’s genetic diversity and Shannon’s information index (I) were calculated as 0.85, 0.16 and 0.29, respectively. The results of the Unweighted Pair Group Method with Arithmetic mean UPGMA dendrogram and Principal Coordinates Analysis PCoA analysis indicated a spatial representation of the relative genetic distances among 28 saffron samples and the 17 close relative species were categorized under two distinct groups. Saffron genotypes showed very limited genetic variation and according to the iPBS-retrotransposon data, its close relatives were C. cartwrightianus and C. pallasii subsp. pallasii.

Comparative analysis of avian poxvirus genomes, including a novel poxvirus from lesser flamingos (Phoenicopterus minor), highlights the lack of conservation of the central region

BackgroundAvian poxviruses are important pathogens of both wild and domestic birds. To date, seven isolates from subclades A and B and one from proposed subclade E, have had their genomes completely sequenced. The genomes of these isolates have been shown to exhibit typical poxvirus genome characteristics with conserved central regions and more variable terminal regions. Infection with avian poxviruses (APVs) has been reported in three species of captive flamingo, as well as a free-living, lesser flamingo at Kamfers dam, near Kimberley, South Africa. This study was undertaken to further characterise this virus which may have long term effects on this important and vulnerable, breeding population.ResultsGene content and synteny as well as percentage identities between conserved orthologues was compared between Flamingopox virus (FGPV) and the other sequenced APV genomes. Dotplot comparisons revealed major differences in central regions that have been thought to be conserved. Further analysis revealed five regions of difference, of differing lengths, spread across the central, conserved regions of the various genomes. Although individual gene identities at the nucleotide level did not vary greatly, gene content and synteny between isolates/species at these identified regions were more divergent than expected.ConclusionBasic comparative genomics revealed the expected similarities in genome architecture but an in depth, comparative, analysis showed all avian poxvirus genomes to differ from other poxvirus genomes in fundamental and unexpected ways. The reasons for these large genomic rearrangements in regions of the genome that were thought to be relatively conserved are yet to be elucidated. Sequencing and analysis of further avian poxvirus genomes will help characterise this complex genus of poxviruses.

Taxonomy of Dichanthelium hirstii (Poaceae), a very rare and disjunct witch-grass of the eastern U.S.

After a careful range-wide study of specimens and a review of the taxonomic literature, we have determined that Dichanthelium hirstii (Swallen) Kartesz is taxonomically valid at the rank of species, and is a distinctive member of this complex genus. It is also one of the rarest plants in eastern North America.