Molecular Phylogenetic Analysis Research Articles

Hesperis sivasica (Brassicaceae), A new crucifer species from inner Anatolia

Hesperis sivasica, from the Kangal district of Sivas Province in inner Anatolia (Türkiye), is described as a new species based on morphological and molecular evidence. Although it is not morphologically closely related to the known species of Hesperis, it resembles H. kotschyi in trichome types but differs from it in pedicel, flowers, and fruit characteristics. In molecular phylogenetic analyses based on the Nuclear-encoded ribosomal internal transcribed spacer (ITS) region, H. sivasica belongs to the same clade as H. bottae and H. thyrsoidea, but it is easily distinguishable from both species based on life form, trichome types, flowers, and fruit characters. Diagnostic morphological characters, full description, SEM microphotographs, and detailed field photographs are provided. Remarks on the new species' habitat, ecology, phenology, distribution, and conservation status are also given.

Calycosiphonia or Kupeantha (Coffeeae, Rubiaceae)? A morphological and molecular study of a new species from the Albertine Rift

Field work in the Kibira National Park (Burundi), located in the Kivu-Ruwenzori system of the Afromontane Region, revealed the existence of a new species clearly belonging to the Argocoffeopsis-Calycosiphonia clade (Coffeeae, Rubiaceae). The species shows striking heterophylly: the plagiotropous branches have several nodes bearing reduced or even scaly leaves. For the rest, it shares characters with Calycosiphonia and Kupeantha. Therefore, a morphological comparison with the clade is done, as well as molecular phylogenetic analyses. The morphology of the novelty is closer to Kupeantha than to Calycosiphonia, inter alia because the anthers have no transverse septa, in contrast to the multilocellate anthers of Calycosiphonia. However, the molecular data advocate for a position in Calycosiphonia – a result weakening the morphological distinction between Calycosiphonia and Kupeantha. The former genus is no longer restricted to species with transverse septa in the anthers and with placental outgrowths around the seed. The new species is formally described as Calycosiphonia albertina Ntore & Robbr. sp. nov. Nomenclaturally, this placement is also the most conservative option. A taxonomic treatment, illustrations, a geographical distribution map, and a preliminary conservation assessment are provided. The previous inclusion of Calycosiphonia pentamera in Kupeantha based on morphology is here corroborated by molecular analyses.

First Pangenome of Corynebacterium rouxii, a Potentially Toxigenic Species of Corynebacterium diphtheriae Complex

First Pangenome of Corynebacterium rouxii, a Potentially Toxigenic Species of Corynebacterium diphtheriae Complex

A new species of Liobagrus Hilgendorf, 1878 (Teleostei, Siluriformes, Amblycipitidae) from the lower Changjiang River basin in southeast China

A new catfish species, Liobagrus chenhaojuni Chen, Guo & Wu, sp. nov., is described from the Tiaoxi River, a tributary of Taihu Lake, located in Zhejiang Province, China. This description is based on morphological characteristics and phylogenetic analysis. This species belongs to a group defined by the presence of a smooth posterior edge of the pectoral-fin spine and can be distinguished from other species in the group by a unique combination of characteristics, including: an upper jaw longer than the lower jaw; maxillary barbels reaching the middle of the pectoral fin; irregular blotches present on the lateral body; a rounded caudal-fin with a length ranging from 16.5% to 19.9% of the standard length; 39 to 41 post-Weberian vertebrae; and 15 to 17 anal-fin rays. The validity of this new species is further supported by the molecular phylogenetic analysis based on Cytb sequences.

Molecular characteristics and phylogenetic analysis of pigeon paramyxovirus type 1 isolates from pigeon meat farms in Shanghai (2009–2012)

The majority of pigeon paramyxovirus type 1 (PPMV-1) strains are generally non-pathogenic to chickens; however, they can induce severe illness and high mortality rates in pigeons, leading to substantial economic repercussions. The genomes of 11 PPMV-1 isolates from deceased pigeons on meat pigeon farms during passive monitoring from 2009 to 2012 were sequenced and analyzed using polymerase chain reaction and phylogenetic analysis. The complete genome lengths of 11 isolates were approximately 15,192 nucleotides, displaying a consistent gene order of 3′-NP-P-M-F-HN-L-5′. ALL isolates exhibited the characteristic motif of 112RRQKRF117 at the fusion protein cleavage site, which is characteristic of velogenic Newcastle disease virus. Moreover, multiple mutations have been identified within the functional domains of the F and HN proteins, encompassing the fusion peptide, heptad repeat region, transmembrane domains, and neutralizing epitopes. Phylogenetic analysis based on sequences of the F gene unveiled that all isolates clustered within genotype VI in class II. Further classification identified at least two distinct sub-genotypes, with seven isolates classified as sub-genotype VI.2.1.1.2.2, whereas the others were classified as sub-genotype VI.2.1.1.2.1. This study suggests that both sub-genotypes were implicated in severe disease manifestation among meat pigeons, with sub-genotype VI.2.1.1.2.2 displaying an increasing prevalence among Shanghai’s meat pigeon population since 2011. These results emphasize the value of developing pigeon-specific vaccines and molecular diagnostic tools for monitoring and proactively managing potential PPMV-1 outbreaks.

Molecular identification and characterizations of rhizobacterial isolates collected from lentil rhizosphere of Indo-gangetic plains.

Plant growth promoting rhizobacteria (PGPR) are also known to colonize in the soil rhizosphere and prevent the development of other soil borne pathogens residing in the root surface. These microorganisms play a vital role in growth and development of the plant and also enhances the soil fertility by enriching the soil with different beneficial nutrients. This study was aimed at isolation of different rhizobacteria and their molecular characterization in search of efficient bacterial strains with multiple growth regulating activities. A total 36 bacteria were isolated from lentil root nodule as well as soil from different lentil growing fields with a view to screen/evaluate their plant growth promoting potential. Morphological characterization of isolated rhizobacterial candidates were done by observing the colonies on YEMA and nutrient agar media. Determination of CFU, Congo red test and gram staining tests were done to further screen them according to their morphology. All the isolates were then undergone molecular phylogenetic analysis using the partial sequences of the 16S rDNA. Based upon the Gram staining test, all the isolates were negative in gram reaction except six Bacillus isolates, PSB2 and AB3. Results of Ribosomal Database Project (RDP) and Basic Local Alignment Search Tool for Nucleotide Sequences (BLASTn) from 16S rDNA gene sequences showed that these isolates are genetically diverse. A total of 15 isolates of Rhizobium, 6 isolates of Bacillus, 3 isolates of Pseudomonas, 2 isolates of Phosphate Solubilizing Bacteria, 4 isolates of actinomycetes were identified by molecular sequencing of their 16S rDNA region and comparing them with the other isolates enlisted in the database of NCBI for the similarity percentage, query coverage. The purpose of the present study was to select native rhizosphere bacteria from the lentil nodule and soil of Lentil field and to evaluate their plant growth promoting potential as an alternative of chemical fertilizer for sustainable, environment friendly agriculture and assessment of their phylogenetic characterization.

Molecular Detection and Phylogenetic Analysis of the alkB Gene in Klebsiella oxytoca Strains Isolated from the Gut of Tenebrio molitor.

The challenge in polystyrene disposal has caused researchers to look for urgent innovative and ecofriendly solutions for plastic degradation. Some insects have been reported to use polystyrene as their sole carbon source, and this has been linked to the presence of microbes in their guts that aid in plastic digestion. Thus, this study focuses on the molecular detection and phylogenetic analysis of the alkane-1-monooxygenase (alkB) gene in Klebsiella oxytoca strains isolated from the gut of Tenebrio molitor. The alkB gene encodes for alkane-1-monooxygenase, an enzyme involved in the oxidation of inactivated alkanes. This gene can be used as a marker to assess bacteria's ability to biodegrade polystyrene. Three bacterial strains were isolated from the guts of T. molitor mealworms and were confirmed using polymerase chain reaction (PCR) of the 16S ribosomal RNA gene. The primers used in the amplification of the 16S ribosomal RNA region were designed using NCBI, a bioinformatics tool. To detect the presence of the alkB gene in the isolated bacterial strains, a set of primers used in the amplification of this gene was manually designed from the conserved regions of the alkB nucleotide sequences of eleven bacterial species from GenBank. TCOFFE online tool was used to align the alkB sequences of the bacteria, while Jalview and ConSurf were used to view the alignment. The amplified alkB gene was then sequenced using the Sanger sequencing technique, blasted on NCBI to look for similar sequences, and a phylogenetic tree was constructed. Based on the 16S ribosomal RNA gene sequences, the isolated bacterial strains were confirmed to be Klebsiella oxytoca NBRC 102593, Klebsiella oxytoca JCM 1665, and Klebsiella oxytoca ATCC 13182. The alkB gene sequence identical to fourteen alkB gene sequences derived from Actinobacteria whole genome was detected in Klebsiella oxytoca for the first time to the best of our knowledge. The novel nucleotide sequence was published in the NCBI database under accession number OP959069. This gene sequence was found to be for the enzyme alkane-1-monooxygenase and may be one of the enzymes responsible for polystyrene degradation by the putative Klebsiella oxytoca ATCC 13182 in T. molitor.

Evaluation and Control of Alternaria tenuissima Causing Leaf Spots in Blue Honeysuckle in China.

Blue honeysuckle is emerging as a popular edible fruit and is also used in folk medicine. However, from June to August 2021, a serious leaf-spot disease affected the yield and quality of blue honeysuckle in Harbin, Heilongjiang Province, China; the species and characteristics of the pathogens responsible for the disease were unknown. In this study, 30 fungal isolates were obtained from infected blue honeysuckle leaves and identified as Alternaria tenuissima based on morphological and molecular characteristics and phylogenetic analyses. To the best of our knowledge, this is one of the first studies to identify A. tenuissima as the causal agent of blue honeysuckle leaf spots in China. Pathogenicity tests of the isolates revealed that most isolates were moderately pathogenic. All blue honeysuckle cultivars tested were found to be susceptible to 30 A. tenuissima isolates. In addition, elder, Dahurian rose fruit, sea buckthorn, rowan, hawthorn, bird cherry, and sorb could be infected by A. tenuissima isolates, while European cranberry bush and Nanking cherry were not infected. A. tenuissima isolates were highly sensitive to prochloraz (EC50 ≤ 0.50 μg ml-1) with 86.21% efficacy at 400 μg ml-1 in the field trials. Therefore, crop rotation and application of chemical fungicides are considered to control the disease-causing leaf spots in blue honeysuckle. These results provide a basis for controlling A. tenuissima in blue honeysuckle in China.

Molecular phylogenetic analysis of the East Asian hemicultrine fishes (Teleostei: Cyprinidae: Xenocypridinae), with suggestions to their generic classification and redescription of the recently described species Hemiculter yungaoi Vasil'eva et al. 2022.

The hemicultrine fishes are a group of small-sized cyprinids, widely distributed but endemic to East Asian rivers and lakes. Till now, the taxonomic boundaries and relationships within this group remain poorly explored. In the present study, we study the phylogeny of this group, providing suggestions for classification of the hemicultrine group. Using two mitochondrial and three nuclear genes, and samples representing all genera, our results showed that the group consists of seven major lineages, of which four (Hemiculterella, Hainania, Pseudolaubuca, and Anabarilius) were monophyletic and three (Hemiculter, Toxabramis, and Pseudohemiculter) were not. Based on the phylogenetic tree, we redefined the genera. We revive the genus Siniichthys, which has three species, Siniichthys bleekeri, Siniichthys lucidus, and S. varpachovskii, that were previously treated as members of the genus Hemiculter but showed distant relationships to the genus Hemiculter in our phylogenetic tree. With the new results, a diagnostic key for clades of the hemicultrine group is provided. Furthermore, we provide more detailed information on diagnostic features of the recently described species Hemiculter yungaoi (Vasil'eva et al., 2022). This work will facilitate future systematic studies, pave the way for evolutionary studies, and provide valuable information for the urgent conservation of hemicultrine fishes.

Two new species of Dictyota (Dictyotales, Phaeophyceae), D. dimorphosa sp. nov. and D. recumbens sp. nov., based on morphological and molecular investigations

ABSTRACT The brown algal genus Dictyota (Dictyotales, Phaeophyceae) is widespread, particularly in warm temperate and tropical waters, and plays a vital role in coastal ecosystems. This study reassessed the taxonomy of Dictyota, focusing on specimens from Myanmar and Japan, using a combination of morphological and molecular analyses. Molecular phylogenetic analyses using concatenated DNA sequences of rbcL, psaA, psbA, cox1 and cox3 genes revealed that Dictyota specimens from Myanmar, Japan, and other regions, belong to nine different clades, each representing a different species. Based on morphological and molecular data, seven out of these nine clades are identified as known species, while the remaining two clades are described as new species D. recumbens sp. nov. (=D. sp. A) and D. dimorphosa sp. nov. (=D. sp. B). Dictyota recumbens is characterized by the recumbent thallus, with transverse yellowish-green iridescent lines, and the formation of solitary spores irregularly distributed over the thallus. Dictyota dimorphosa is characterized by two morphological forms: decumbent and erect thalli, with bluish iridescence mainly in the decumbent thallus, and the formation of spores in oval ring shapes distributed over both thallus surfaces. Dictyota recumbens was typically found in tropical regions, while D. dimorphosa appears to be a cool-warm temperate species, distributed from northeastern Hokkaido to southern Kyushu with an extension along South Korea. Our molecular phylogenetic analyses have revealed the existence of several species whose names appeared in multiple clades, suggesting the potential for future increases in species diversity and the presence of cryptic species within certain groups.

Integrative Taxonomy of Urocleidoides spp. (Monogenoidea, Dactylogyridae) Parasites of Pseudanos trimaculatus (Characiformes: Anostomidae) from Eastern Amazon, Brazil.

Two new species of Urocleidoides are described from the gills of Pseudanos trimaculatus (Characiformes: Anostomidae) from the coastal drainages of the Eastern Amazon, Brazil. Urocleidoides itabocaensis n. sp. is characterized by having a sclerotized, tubular, sigmoid male copulatory organ (MCO), a circular sclerotized tandem brim associated with the base of the MCO; an accessory piece articulated with the MCO, aV-shaped, divided into two subunits, distal subunit spoon-shaped; and a vaginal pore dextroventral with opening marginal. Urocleidoides omphalocleithrum n. sp. is characterized by presenting a C-shaped or sigmoid MCO; anaccessory piece articulated with the MCO, L-shaped, divided into two subunits, distal subunit gutter-shaped; a vaginal pore dextroventral with opening marginal; and aventral bar broadly V-shaped, with anteromedial projection. Molecular phylogenetic analysis based on partial 28S rDNA and COI mtDNA genes indicate that U. itabocaensis n. sp. and U. omphalocleithrum n. sp. are closely related and appear as a sister group to other Urocleidoides species (U. paradoxus, U. digitabulum and U. sinus) parasitizing anostomid fishes. This study represents the first record of monogenoids from the gills of P. trimaculatus for the Eastern Amazon.

Two new species of Platanthera (Orchidaceae, Orchidoideae) from Xizang, China

Two new orchid species, Platanthera linzhiensis, P. deergongensis, are described and illustrated from Motuo, Xizang, China. P. linzhiensis is closely related to P. uniformis, but differs from it by lip yellowish green, spur yellow, nearly as long as ovary, connective obtuse-truncate, not protruding from anther, column lateral appendages ovate to oblong, slightly shorter than the anther. P. deergongensis is morphologically similar to P. contigua, but is distinguished from it by having white lip, obtuse-truncate connective and ovate to oblong column lateral appendages. Molecular phylogenetic analysis based on six markers (nrITS, psaB, matK, psbA-trnH, rbcL, trnL-F) revealed that P. linzhiensis and P. deergongensis formed a clade with high support, and are close to P. superantha.

A new species of Platanthera (Orchidaceae, Orchideae) from southeast of Xizang, China

A new species of orchid, Platanthera medogensis, was described and illustrated from Xizang Autonomous Region, China. P. medogensis is close to P. bakeriana and P. chiloglossa, but is readily distinguished from the latter by having ovate-lanceolate lip concave at base with two calli, linear visidium, two stigmas below the rostellum. Molecular phylogenetic analysis based on five markers (nrITS, matK, psbA-trnH, rbcL, trnL-F) revealed that P. medogensis is sister with P. exelliana by full support.

Molecular phylogeny and secondary structure analysis of hop stunt viroid (HSVd) associated with Mulberry (Morus alba) in India.

Hop stunt viroid (HSVd), a small, single stranded, circular, non-coding infectious RNA known to cause infection in various economically important crop plants. In the present investigation, a study was conducted in the southern part of Karnataka districts of India to detect the possible association of HSVd infection in mulberry plants. A total of 41 mulberry plants showing typical viroid-like symptoms along with asymptomatic samples were collected and screened using conventional Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) using a specific set of HSVd-Fw/ HSVd-Re primers. Out of 41 samples, the study confirmed the presence of HSVd in six samples of mulberry collected from Ramanagara (1 sample), Chikkaballapur (3 samples) and Doddaballapura (2 samples) regions with an expected HSVd amplicon size of ∼ 290-300 nucleotides. The mechanical transmission of HSVd was also confirmed on cucumber (cv. Suyo) seedlings through bioassay, which was reconfirmed by RT-PCR. The amplicons were cloned, sequenced, and the representative nucleotide sequences were deposited in the NCBI GenBank. Subsequently, molecular phylogenetic analysis showed that HSVd mulberry isolates from this study were most closely related to grapevine isolates, indicating a common origin. On the other hand, it was shown to belong to a different group from mulberry isolates so far reported from Iran, Italy, Lebanon, and China. The secondary structure analysis of HSVd mulberry Indian isolates exhibited substitutions in the terminal left, pathogenicity, and variable regions compared to those of the Indian grapevine isolates. As far as this study is concerned, HSVd was detected exclusively in some mulberry plants with viral-like symptoms, but the pathogenesis and symptom expression needs to be further investigated to establish the relationship between HSVd and the disease symptoms in the mulberry plants.

A new name and two new combinations in Leucheria Lag. (Asteraceae; Nassauvieae)

Molecular phylogenetic analysis has demonstrated that Polyachyrus Lag. species must be reclassified in Leucheria Lag. Here, Polyachyrus cinereus Ricardi & Weldt is renamed as Leucheria duraniorum, and Polyachyrus gayi J.Rémy and Polyachyrus poeppigii Kunze ex Less. subsp. multifidis (D.Don) Ricardi & Weldt are recombined in Leucheria.

Impatiensbeipanjiangensis (Balsaminaceae), a new species from Guizhou, China.

Impatiensbeipanjiangensis Jian Xu & H. F. Hu (Balsaminaceae), a new species of Impatienssubg.Clavicarpa discovered in Guizhou, China, is described and illustrated in this study along with its molecular phylogenetic analysis. I.beipanjiangensis is similar to I.liboensis, I.chishuiensis and I.clavigera in morphology, but I.tubulosa has the closest relationship to it. However, there are various ways in which the new species can be easily distinguished from these four species: Inferior nodes swollen rhizoid, pale green and with hooked outer sepals, longer lateral united petals, subovate auricle, deeper lower sepal and shorter spur that is reflexed towards the lower sepal. Furthermore, I.beipanjiangensis is distinguished from other Impatiens species, based on morphological, micromorphological and palynological evidence and molecular data (PP 0.967).

A new species of Habenaria (Orchidaceae, Orchidoideae, Orchideae) from Yunnan, China

A new species of Orchidaceae, Habenaria tiechangensis, from Yunnan province is described and illustrated based on morphological characters and molecular phylogenetic analysis. The results indicated that it belongs to H. josephi group and is similar to H. diplonema but differs from the latter by having short and lanceolate lateral lobes of lip and a pair of distinctive horn-like stigmas.

Description of Pauronemoides siddiqii n. gen., n. sp. (Tylenchomorpha, Paurodontidae), a morphological and molecular phylogenetic study

Summary Three populations of Pauronemoides siddiqii n. gen., n. sp. were recovered from three different locations in northwestern and northern Iran from bark and soil samples. The new genus was described and illustrated based upon morphological and molecular characteristics. Pauronemoides n. gen. belongs to the family Paurodontidae and is characterised by the medium-sized body, asymmetrical knobs in stylet base, stem-like extension into intestine, post-vulval uterine sac (PUS) absent or rudimentary, different tail tip shape between sexes, and bursa enveloping tail or reaching to the tail end. The type species, Pauronemoides siddiqii n. gen., n. sp., is mainly characterised by 752-1281 μm body length in females and 660-1085 μm in males, six equally-sized lips, stylet 9-11 μm long with asymmetrical knobs, six incisures in lateral fields forming five bands, three of which (two outers and one central) are wider, and variably lengthened stem-like extension projecting into the intestine. Vulva situated posteriorly (V = 87.7-91.7%), PUS absent. Conical tail with widely rounded end, having a small mucron at tip in females, males with conical tail ending to a narrower tip and bursa enveloping tail completely. The type species of the new genus was compared with all known species of the genera Prothallonema, Paurodontus, Paurodontoides and Paurodontella. Pauronemoides siddiqii n. gen., n. sp. resembles Prothallonema macrocellum and P. mucronatum by having the bulb extension penetrating into the intestine, dimorphism in tail shape of both sexes and bursa enveloping tail, and Paurodontella iranica by tail shape dimorphism between sexes and bursa ending near tail tip. Therefore, the above-mentioned species are transferred to the new genus as Pauronemoides macrocellus n. gen., n. comb. (= Prothallonema macrocellum), P. mucronatus n. gen., n. comb. (= Prothallonema mucronatum) and P. iranicus n. gen., n. comb. (= Paurodontella iranica). In addition to morphological comparisons, molecular phylogenetic analyses were performed using two sequences of small subunit (SSU), and three partial sequences of D2-D3 expansion segments of the large subunit (LSU) rDNA, and the resulting topologies were discussed.

Meconopsis biluoensis (Papaveraceae), a new species revealed by population-level investigation.

Meconopsis biluoensis, a new species of Papaveraceae in an alpine meadow from Yunnan, Southwest China, is described and illustrated. Morphologically, it resembles Meconopsis georgei, while it is distinct in acaulescent and hispid with clearly expanded bases on the leaves. A genus-level molecular phylogenetic analysis supported the closest relationship between M. biluoensis and M. georgei. In a finer population-level molecular phylogenetic analysis using ribosomal DNA (rDNA) and the chloroplast genome, individuals from M. biluoensis and M. georgei were clearly separated, and the extremely short branch length indicated that the two species had a very short differentiation time. The species has currently been assessed as "endangered" (EN) due to its small-sized population and narrow distribution following the IUCN categories and criteria.

Host–pathogen interaction between the African fig fly, Zaprionus indianus, and its external mycobiome under laboratory conditions

AbstractThe African fig fly, Zaprionus indianus Gupta (Diptera: Drosophilidae), is an ecologically diverse pest species that interacts with and feeds on various microbial pathogens including bacteria and yeast found in decomposing fruits. However, the interaction of Z. indianus with its microbial community and microbial pathogens is obscure. To determine the presence of fungal pathogens, we collected wild Z. indianus from the northwestern part of the Indian subcontinent. Based on molecular identification and phylogenetic analysis, Debaryomyces hansenii (Zopf) Lodder & Kreger‐van Rij (isolate ziha1) was the most commonly observed fungus associated with Z. indianus. Furthermore, we identified two more opportunistic fungal pathogens: Aspergillus flavus Link (isolate zias2), and Pichia kudriavzevii Boidin, Pignal & Besson (isolate zibd3). The interaction of isolated fungi with Z. indianus was evaluated in terms of larval mortality, adult emergence, and fecundity. Debaryomyces hansenii ziha1 resulted in 90% emergence rate for adults, and did not cause significant mortality in the larval stage. In contrast, A. flavus zias2 and P. kudriavzevii zibd3 showed a significant reduction in fecundity and caused 99% and 74% larval mortality of Z. indianus, respectively. In the laboratory oviposition preference assay, mated females of Z. indianus preferred D. hansenii ziha1 supplemented food with a positive oviposition index compared to the uninfected control and compared to food infected with P. kudriavzevii zibd3 or A. flavus zias2. These findings underscore Z. indianus' potential to act as a reservoir for both symbiotic and pathogenic fungal species, some of which may be further harnessed for effective fruit fly pest control strategies.