Species Delimitation Research Articles

An analysis of the gaps in the South African DNA barcoding library of ticks of veterinary and public health importance.

Ticks transmit pathogens of veterinary and public health importance. Understanding their diversity is critical as infestations lead to significant economic losses globally. To date, over 90 species across three families have been identified in South Africa. However, the taxonomy of most species has not been resolved due to morphological identification challenges. DNA barcoding through the Barcode of Life Data Systems (BOLD) is therefore a valuable tool for species verifications for biodiversity assessments. This study conducted an analysis of South African tick COI barcodes on BOLD by verifying species on checklists, literature, and other sequence databases. The compiled list represented 97 species, including indigenous (59), endemics (27), introduced (2), invasives (1), and eight that could not be classified. Analyses indicated that 31 species (32%) from 11 genera have verified COI barcodes. These are distributed across all nine provinces with the Eastern Cape having the highest species diversity, followed by Limpopo, with KwaZulu-Natal having the least diversity. Rhipicephalus, Hyalomma, and Argas species had multiple barcode index numbers, suggesting cryptic diversity or unresolved taxonomy. We identified 21 species of veterinary or zoonotic importance from the Argasidae and Ixodidae families that should be prioritised for barcoding. Coordinating studies and defining barcoding targets is necessary to ensure that tick checklists are updated to support decision-making for the control of vector-borne diseases and alien invasives.

DNA barcodes are ineffective for species identification of Acropora corals from the aquarium trade.

Species identification of stony corals (Scleractinia), which are regulated under the Convention on International Trade in Endangered Species of Wild Fauna and Flora, is critical for effective control of harvest quotas, enforcement of trade regulations and species conservation in general. DNA barcoding has the potential to enhance species identification success, depending on the specific taxon concerned and genetic markers used. For Acropora, DNA barcoding, based on the mitochondrial putative control region (mtCR) and the nuclear PaxC intron (PaxC), has been commonly used for species identification and delimitation, but the reliability and robustness of these loci remain contentious. Therefore, we sought to verify the applicability of this approach. In this study, we obtained 127 Acropora colonies from the aquarium trade to test the effectiveness of barcoding mtCR and PaxC for species identification. We were able to recover sequences for both loci in over half of the samples (n = 68), while gene amplification and sequencing of mtCR (n = 125) outperformed PaxC (n = 70). Amongst the 68 samples with both loci recovered, just a single sample could be unambiguously identified to species. Preliminary identities, based on only one gene, were assigned for 40 and 65 samples with mtCR and PaxC, respectively. Further analyses of 110 complete mitochondrial genomes obtained from GenBank showed that, despite the full length of the sequences, only eight species were delimited, of which only three species were correspondingly monophyletic. Therefore, we conclude that the commonly used DNA barcoding markers for Acropora are ineffective for accurate species assignments due to limited variability in both markers and even across the entire mitochondrial genome. Therefore, we propose that barcoding markers should generally not be the only means for identifying corals.

An integrative approach to the study of Kempnyia Klapálek, 1914 (Plecoptera: Perlidae) from Brazil: Support for the description of four new species and a basis for future studies.

Kempnyia (Plecoptera: Perlidae) is an endemic genus of Brazilian stoneflies that has 36 valid species and is distributed primarily in the Atlantic Forest and the mountainous areas of Central Brazil, particularly in Goiás and Tocantins states. Despite being the Brazilian genus with the most DNA sequences available on GenBank, integrative studies on the genus began only recently, in 2014. In this context, herein we studied the morphology and molecular data of Kempnyia specimens deposited in the Aquatic Biology Laboratory (UNESP, Assis) and the Entomology Museum of the Federal University of Viçosa (UFVB, Viçosa) collections. For the integrative approach adopted, in addition to studying the specimens morphologically, we used sequences of the COI mitochondrial gene combined with the following species delimitation methods: Automatic Barcode Gap Discovery (ABGD), both primary (ABGDp) and recursive (ABGDr) partitions; Assemble Species by Automatic Partitioning (ASAP); Poisson Tree Processes (PTP) and the Bayesian implementation of the Poisson Tree Processes (bPTP). As a result, we provided 28 new COI sequences of 21 species and support the description of four new species, namely, K. guarani sp. nov., K. tupiniquim sp. nov., K. una sp. nov., and K. zwickii sp. nov., consequently increasing the known diversity of the genus to 40 species. We also discuss the morphological variations observed in other species of the genus and provide several new geographic records. Therefore, our study brings new insights into the values of intra- and interspecific molecular divergence within Kempnyia, serving as a basis for new studies.

Molecular phylogenetic reconstruction improves the taxonomic understanding of Indian Dipcadi (Asparagaceae) and reveals a new species from the bank of Hiranyakeshi River, Maharashtra, India.

Dipcadi (Scilloideae: Asparagaceae) is a genus of bulbous monocots with approximately 40 species, of which 13 occur in India. Species delimitation within the genus has been troublesome hindering a comprehensive phylogenetic analysis. The most recent phylogeny of the subfamily Ornithogaloideae included six species of Dipcadi only from Africa. Here, we reconstructed the phylogeny of Ornithogaloideae including 23 accessions comprising 13 recognized taxa (11 species and two varieties) of Indian Dipcadi. The phylogenetic analyses were based on nucleotide sequences of three plastid regions (rbcL, matK and trnL-F spacer) and one nuclear region (ITS). Pseudogaltonia clavata exhibited sister relationship to Dipcadi. Our combined nuclear + plastid dataset analyses revealed a monophyletic Dipcadi with five clades, Clade I-V. Clade I, II and III included mainly Indian species whereas Clade V included mostly African species. Clade IV comprised D. serotinum. Clade I included nine taxa including our newly described species, D. mukaianum. The new species was phylogenetically placed with D. erythraeum, D. saxorum and D. ursulae. Morphologically, the species resembled D. montanum and D. ursulae but differed in characters such as tepal cohesion, number of ovules per locule and foul-smelling flowers. Clade II and III included 11 and six taxa, respectively. D. erythraeum which has a native range from Egypt to western India was found in Clades I and V. The widespread Dipcadi species, viz. D. erythraeum and D. serotinum showed polyphyly however, the monophyly of Dipcadi is established. Our studies suggest that additional molecular markers (plastid as well asnuclear) should be tested for their taxonomy utility. Further work on the historical biogeography of Dipcadi on the subfamily Ornithogaloideae with more genetic data will yield insights how aridification of the landscape would have shaped the evolution of the geographical clades.

Taxonomic studies of Cycas debaoensis (Cycadaceae) from China

Traditionally, species delimitation based on morphological and distributional evidence often leads to over- or underestimation of species diversity. The primary distribution area of Cycas debaoensis includes two habitats, which were initially published as two separate species, i.e., C. debaoensis in the karst habitat, and C. panshuiensis, which was originally published as Cycas gracilis Y.Y. Huang, Y.C. Zhong et Z.F. Lu, in the sand habitat. However, field investigations and population sampling in these two habitats revealed a certain degree of morphological transition and variation among the populations. Subsequent population genetic analysis showed minimal genetic differentiation among the populations in the two habitats, suggesting that they should be merged as a single species. Additionally, the typification of the name C. debaoensis is also discussed.

Palyno-anatomical diversity and its implication in the taxonomy of some Plantaginaceae species

Palyno-anatomical diversity and its implication in the taxonomy of some Plantaginaceae species

Reference Intervals of Mass Coefficients and Absolute Weights of Mini Pigs’ Organs

Introduction. Measurement of weights and calculation of mass coefficients of the laboratory animals’ internal organs are the integral stages of toxicological research. However, the absence of the correct intra-laboratory reference intervals corresponding to the normal values established for the animal population of a research laboratory could hinder the analysis of the mass coefficient changes in the experiment. For example, the data on weights and mass coefficients of mini pigs’ organs is being an issue due to its insufficient availability in the open sources. At the same time, in the literature there is a lot of such kind of data referring to the industrial pig breeds. Due to the wide use of the mini pigs in the pre-clinical research and because in the pig species taxonomy they are considered to be a weight category representing the pigs with reduced mass of the body with similar morphology of the organs and body systems, we have set an objective to determine and calculate the reference intervals of mass coefficients of internal organs relative to the mass of the body and brain, as well as the absolute weights of mini pigs’ internal organs and compare the results with the data on mini and industrial pig breeds in the literature sources.Materials and Methods. The data on 29 males and 29 females of the Vietnamese lop-bellied mini pig breed aged 6 months and older, who used to be in control groups of the various experiments held at JSC “SPA “House of Pharmacy” (Leningrad region) in the period from January 2018 to March 2024, was used to calculate the reference intervals. The statistical analysis was peRussian Federationormed using Microsoft Excel and Reference Value Advisor v2.1 software in compliance with the CLSI guidelines. Calculation of the reference intervals for all parameters was carried out by a robust method, the compliance with the normal distribution law was determined by Anderson–Darling test, in case of abnormal distribution of data, calculation of the reference interval was carried out with the Box–Cox transformation.Results. The data on the absolute weights of organs and their coefficients relative to the body and brain masses were presented in the form of the lower and upper reference limits and confidence intervals for each of the limit. The reference intervals of masses of organs across all parameters in males and females had similar limits, the most comparable values were found for the heart and brain parameters. The calculated interval of the heart absolute weight in males was 28.3–253 g, that of the brain was 46.5–93.7 g; in females these intervals were 42.9–279 g and 55.5–81.8 g respectively. Upon comparing the obtained data with the literature sources, it was found that the majority of the absolute weights of all measured mini pigs’ organs had fitted in the limits of the reference values, whereas the masses of the lungs and liver were at the lower limit or below the calculated intervals. The values of the absolute weights of most of the organs of the industrial pig breeds were higher than that of mini pigs, which was due to the difference in the body size and mass of the studied animal breeds. When comparing the mass coefficients of organs in relation to the body mass, it was found that the coefficients of most organs of the industrial breeds and mini pigs, on the contrary, were within the calculated reference intervals or slightly exceeded them.Discussion and conclusion. The calculated reference intervals of the mass coefficients of some organs in relation to the body mass, as well as the absolute weights of the spleen in mini pigs are comparable with the data available in literature for the industrial meat pig breeds. At the same time, the data available in the literature sources on the absolute weights of organs and their mass coefficients relative to the body mass of mini pigs, in most cases, have fitted into the calculated intervals. To increase the prognostic value of the obtained reference intervals, the analysis of a larger size sample is necessary.

Gut Microbiome and colorectal cancer: discovery of bacterial changes with metagenomics application in Turkısh population.

Colorectal cancer (CRC) is the 3rd most common cancer in the world and colonic carcinogenesis is a multifactorial disease that involves environmental and genetic factors. Gut microbiota plays a critical role in the regulation of intestinal homeostasis. Increasing evidence shows that the gut microbiome plays a role in CRC development and may be a biomarker for early diagnosis. This study aimed to determine the clinical prognostic significance of gut microbiota in CRC patients in the Turkish population by metagenomic analysis and to determine the microbial composition in tumor tissue biopsy samples. Tissue biopsies were taken from the participants with sterile forceps during colonoscopy and stored at -80°C. Then, DNA isolation was performed from the tissue samples and the V3-V4 region of the 16S rRNA gene was sequenced on the Illumina MiSeq platform. Quality control of the obtained sequence data was performed. Operational taxonomic units (OTUs) were classified according to the Greengenes database. Alpha diversity (Shannon index) and beta diversity (Bray-Curtis distance) analyses were performed. The most common bacterial species in CRC patients and healthy controls were determined and whether there were statistically significant differences between the groups was tested. A total of 40 individuals, 13 CRC patients and 20 healthy control individuals were included in our metagenomic study. The mean age of the patients was 64.83 and BMI was 25.85. In CRC patients, the level of Bacteroidetes at the phylum taxonomy was significantly increased (p = 0.04), the level of Clostridia at the class taxonomy was increased (p = 0.23), and the level of Enterococcus at the genus taxonomy was significantly increased (p = 0.01). When CRC patients were compared with the control group, significant increases were detected in the species of Gemmiger formicilis (p = 0.15), Prevotella copri (p = 0.02) and Ruminococcus bromii (p = 0.001) at the species taxonomy. Metagenomic analysis of intestinal microbiota composition in CRC patients provides important data for determining the treatment options for these patients. The results of this study suggest that it may be beneficial in terms of early diagnosis, poor prognosis and survival rates in CRC patients. In addition, this metagenomic study is the first study on the colon microbiome associated with CRC mucosa in the Turkish population.

A new species of Malacoceros (Annelida, Polychaeta, Canalipalpata, Spionidae) from urban waters in Gabon

A new species of Malacoceros is described from estuarine equatorial waters in Libreville (Gabon, West Africa). During a recent environmental study aimed to assess the urban impact on an estuarine ecosystem near Libreville, the collection of sediment samples from the area was undertaken. The local invertebrate macrofauna had not been previously well studied, and to document the biodiversity, specimens were examined in more detail. A new species of Malacoceros was discovered, occurring in mangrove areas. The new species is described and illustrated in detail, and information on three molecular markers was retrieved and partially used for species delimitation analysis. The new species resembles Malacoceros indicus (Fauvel 1928) described from India but is easily distinguished by a very conspicuous morphological character, the presence of 7–11 large tubercles along the anterior margin of the prostomium. The presence of such conspicuous tubercles has never been observed before in Malacoceros. Maximum likelihood trees for species of Malacoceros and the close genera of Rhynchospio, for which we have data, are also provided. The suitability of characters used for species delimitation in Malacoceros is discussed.

Species and Speciation in the Termite-Cultivated Fungus Termitomyces

Termitomyces is a genus of basidiomycete fungi cultivated by termites of the subfamily Macrotermitinae. This symbiosis originated in central Africa, and subsequently, the fungus-growing termites have colonized almost the entire African continent including Madagascar as well as significant parts of Asia. Around 40 species of Termitomyces have been described based on morphology of the sexual fruit bodies, which are associated with some 330 species of fungus-growing termites distributed over 11 genera. However, the total number of fungal species may be higher as not all species regularly produce mushrooms, and morphological variation does not seem to be a reliable criterion for species delimitation in this group. In this study we estimated the total number of species based on ITS-barcode criteria and assessed host specificity and geographic differentiation to infer patterns of speciation. We estimated the total number of phylogenetic species using two methods of DNA sequence-based species delimitation; Automatic Barcode Gap Discovery (ABGD) and the Generalized Mixed Yule Coalescent (GMYC) model on a large dataset of over 1,500 ITS sequences from laboratory cultures, fungarium specimens and the public database NCBI Genbank. This resulted in an estimated 87 species hypotheses using ABGD and 94 species hypotheses using the GMYC model. A phylogenetic reconstruction was performed on representative sequences of the 87 species hypotheses identified by ABGD (the most conservative estimate) constrained by a well-supported phylogeny based on whole-genome data to address host specificity and geographical differentiation. Five main clades were recovered which generally were associated with species of one or two host genera, except for samples collected from the genera Microtermes and Ancistrotermes, which formed two separate non-sister clades. We did not find any evidence for long-term host fidelity as would be expected for species with strict uniparental vertical symbiont transmission. We found strict geographic separation between African and Asian species of Termitomyces and infer a minimum of seven inter-continental migrations. We show that epigeous fruiting of the T. microcarpus group has a single evolutionary origin in Africa and that fruiting in species of this group likely is induced by the fungus rather than by the host-termite species. In contrast, fruiting in the symbionts of some species of Microtermes and Macrotermes may be suppressed by the host-termite species, since mushrooms of certain fungal species are found when those species are associated with some termite-host genera, but never when associated with other host genera. We discuss some examples of incongruence between morphological and phylogenetic species concepts and give suggestions to improve the taxonomy of the genus Termitomyces.

Quantifying global redundant fisheries trade to streamline seafood supply chains.

Seafood plays an important role in sustainably feeding the world and is one of the most traded food products globally. However sustainability improvements are often focused on its production (e.g., aquaculture, fishing) rather than trade. Here, we quantify the magnitude and extent of global 'redundant two-way' seafood trade-the exchange of the same quantity of the same taxonomic species between two countries-to examine its prevalence and potential implications across the seafood supply chain. We focused on wild-caught seafood trade and found that redundant two-way trade has increased by 43%, between 2000 and 2015, making up 3.2% (7.7 Mt) of global seafood trade during that period. Although most countries were involved in redundant two-way seafood trade (111 of 212 analyzed), the majority occurred between five trade partners: Canada and the United States (15%), Germany and the Netherlands (11.8%); Denmark and Sweden (10.6%); Germany and Denmark (7.1%); and France and Norway (7%). Nearly 50% of redundant trade is made up of just four species including Atlantic herring, Atlantic cod, Skipjack tuna and Atlantic mackerel. While deficiencies in global seafood trade data mask seasonal and product heterogeneity, redundant trade could have implications for meeting conservation and sustainable development goals. Future research should build upon these findings to explore specific environmental, economic, and social implications associated with redundant two-way trade to benefit producers and consumers within the seafood supply chain.

Discovery of a novel spotted fever group Rickettsia, "Candidatus Rickettsia kedanie," in unfed larval chigger mites, Leptotrombidium scutellare.

Spotted fever group (SFG) rickettsia, the causative agent of SFG rickettsiosis, is predominantly carried by ticks, whereas Orientia tsutusgamushi, the causative agent of scrub typhus, is primarily transmitted by chigger mites in Japan. In this study, we attempted to isolate intracellular eubacteria from Leptotrombidium scutellare, a major vector of O. tsutsugamushi; moreover, we isolated an SFG rickettsia using a mosquito-derived cell line. Draft genome sequences of this unique isolate, by applying criteria for species delimitation, classified this isolate as a novel strain, proposed as "Rickettsia kedanie." Further genetic analysis identified conserved virulence factors, and the isolate successfully propagated in mammalian cells, suggesting its ability to cause diseases in humans. The presence of SFG rickettsia in unfed larvae implies potential dual-pathogen carriage and reflects a symbiotic relationship similar to that between the mites and O. tsutsugamushi, indicating possibility of its transovarial transmission from female adults. Furthermore, conserved genomic similarity of the novel isolate to known SFG rickettsia suggests potential multiple hosts, including chiggers and ticks. In the natural environment, ticks, chigger mites, and wild animals may carry new isolates, complicating the infection cycle and increasing the transmission risks to humans. This discovery challenges the conventional association of SFG rickettsia with ticks, emphasizing its implications for research and disease control. However, this study was confined to a particular species of chigger mites and geographic area, underscoring the necessity for additional studies to comprehend the ecological dynamics, host interactions, and health implications linked to this newly identified SFG rickettsia.

Challenges of molecular barcode-based identification of earthworm specimens for biodiversity assessment

Specimen identification at the species level is a critical challenge for understanding community structure and conserving biodiversity. The use of mitochondrial DNA barcodes, in addition to morphology, has proven to be a useful tool for earthworm identification, but it has also raised difficulties. Thus, approaches to delineating molecular operational taxonomic units (MOTUs) from cytochrome c oxidase subunit 1 (COI) or 16S rDNA sequence data often reveal more mitochondrial lineages than morphospecies, raising the question of whether these MOTUs should be used as taxonomic entities in community structure studies. Here, we used a newly acquired dataset of 576 COI barcodes of earthworms from Metropolitan France that were clustered in 36 MOTUS, corresponding to 21 morphospecies. We also incorporated data gathered from the literature to investigate this question. In order to match our MOTUs with already-described mitochondrial lineages, we downloaded reference sequences from the GenBank and BOLD platforms. In light of the difficulties encountered in recovering these sequences, we recommend that any new mitochondrial lineage described in a study be named consistently with previous works. Next, we analyzed the biological, ecological, and molecular data available in the literature on the different mitochondrial lineages that matched our MOTUs in order to determine if there was a consensus for species delimitation. Although the study specimens mainly belong to the Lumbricidae, which is one of the most studied families of earthworms, the data are often missing to determine if the MOTUs correspond to different species. Pending revision of the taxonomy, MOTUs for which mitochondrial divergence has been confirmed by morphological differences should be considered distinct taxonomic entities in community structure studies. In the absence of morphological differences and pending more data, we propose to distinguish for these analyses, within sexually reproducing morphospecies, the MOTUs for which mitochondrial divergence has been confirmed by multilocus nuclear data, while in the case of reproduction by parthenogenesis, ecological differences between MOTUs are necessary to consider them as different taxonomic entities.

Plastome evolution of Engelhardia facilitates phylogeny of Juglandaceae

BackgroundEngelhardia (Juglandaceae) is a genus of significant ecological and economic importance, prevalent in the tropics and subtropics of East Asia. Although previous efforts based on multiple molecular markers providing profound insights into species delimitation and phylogeography of Engelhardia, the maternal genome evolution and phylogeny of Engelhardia in Juglandaceae still need to be comprehensively evaluated. In this study, we sequenced plastomes from 14 samples of eight Engelhardia species and the outgroup Rhoiptelea chiliantha, and incorporated published data from 36 Juglandaceae and six outgroup species to test phylogenetic resolution. Moreover, comparative analyses of the plastomes were conducted to investigate the plastomes evolution of Engelhardia and the whole Juglandaceae family.ResultsThe 13 Engelhardia plastomes were highly similar in genome size, gene content, and order. They exhibited a typical quadripartite structure, with lengths from 161,069 bp to 162,336 bp. Three mutation hotspot regions (TrnK-rps16, ndhF-rpl32, and ycf1) could be used as effective molecular markers for further phylogenetic analyses and species identification. Insertion and deletion (InDels) may be an important driving factor for the evolution of plastomes in Juglandoideae and Engelhardioideae. A total of ten codons were identified as the optimal codons in Juglandaceae. The mutation pressure mostly contributed to shaping codon usage. Seventy-eight protein-coding genes in Juglandaceae experienced relaxed purifying selection, only rpl22 and psaI genes showed positive selection (Ka/Ks > 1). Phylogenetic results fully supported Engelhardia as a monophyletic group including two sects and the division of Juglandaceae into three subfamilies. The Engelhardia originated in the Late Cretaceous and diversified in the Late Eocene, and Juglandaceae originated in the Early Cretaceous and differentiated in Middle Cretaceous. The phylogeny and divergence times didn’t support rapid radiation occurred in the evolution history of Engelhardia.ConclusionOur study fully supported the taxonomic treatment of at the section for Engelhardia species and three subfamilies for Juglandaceae and confirmed the power of phylogenetic resolution using plastome sequences. Moreover, our results also laid the foundation for further studying the course, tempo and mode of plastome evolution of Engelhardia and the whole Juglandaceae family.

Phylogenetics, Molecular Species Delimitation and Geometric Morphometrics of All Reddish-Brown Species in the Genus Neotriplax Lewis, 1887 (Coleoptera: Erotylidae: Tritomini).

To date, five species of reddish-brown Neotriplax have been described, but their highly similar body color and other phenotypic traits make accurate taxonomy challenging. To clarify species-level taxonomy and validate potential new species, the cytochrome oxidase subunit I (COI) was used for phylogenetic analysis and the geometric morphometrics of elytron, pronotum, and hind wing were employed to distinguish all reddish-brown Neotriplax species. Phylogenetic results using maximum likelihood and Bayesian analyses of COI sequences aligned well with the current taxonomy of the Neotriplax species group. Significant K2P divergences, with no overlap between intra- and interspecific genetic distances, were obtained in Neotriplax species. The automatic barcode gap discovery (ABGD), assemble species by automatic partitioning (ASAP), and generalized mixed Yule coalescent (GMYC) approaches concurred, dividing the similar species into eight molecular operational taxonomic units (MOTUs). Geometric morphometric analysis using pronotum, elytron, hind wing shape and wing vein patterns also validated the classification of all eight species. By integrating these analytical approaches with morphological evidence, we successfully delineated the reddish-brown species of Neotriplax into eight species with three new species: N. qinghaiensis sp. nov., N. maoershanensis sp. nov., and N. guangxiensis sp. nov. Furthermore, we documented the first record of N. lewisii in China. This study underscores the utility of an integrative taxonomy approach in species delimitation within Neotriplax and serves as a reference for the taxonomic revision of other morphologically challenging beetles through integrative taxonomy.

A critical review of the edible seaweed Palmaria palmata (L.) Weber & Mohr and its bioactive compounds in the “omics” era

The red alga Palmaria palmata (“dulse”; Palmariaceae, Rhodophyta) has been used as food since the fifth century, especially in the North Atlantic region. Dulse is a good alternative to cereals due to its high nutritional profile. A critical review based on scientific and grey literature of dulse bioactive compounds and their activity identified key knowledge gaps. The review synthesis emphasizes the importance of species delimitation, microbial community characterization and multi-omics in the research of P. palmata. Recent advances and uncertainty in delimitating P. palmata are introduced in a phylogenetic context, and recommendations are given for future phytochemical studies. We refer to the concept of “seaweed holobiont” as the functional entity encompassing the seaweed and its associated microbiota, and call for action to characterize the microbial communities, since their interactions with the environment and seaweeds are important in seaweed well-being and postharvest quality changes (e.g. microbial spoilage and degradation of algal matrices). Finally, we discuss the status and trends of using multi-omics to address important research questions of P. palmata, and to help us understand the source, biosynthesis and function of its bioactive compounds.

Characterization, comparison, and phylogenetic analyses of chloroplast genomes of Euphorbia species

The genus Euphorbia (Euphorbiaceae) has near-cosmopolitan distribution and serves as a significant resource for both ornamental and medicinal purposes. Despite its economic importance, Euphorbia's taxonomy has long been challenged by the intricate nature of morphological traits exhibiting high levels of convergence. While molecular markers are essential for phylogenetic studies, their availability for Euphorbia has been limited. To address this gap, we conducted comparative analyses focusing on the chloroplast (CP) genomes of nine Euphorbia species, incorporating three newly sequenced and annotated accessions. In addition, phylogenetic informativeness and nucleotide diversity were computed to identify candidate markers for phylogenetic analyses among closely related taxa in the genus. Our investigation revealed relatively conserved sizes and structures of CP genomes across the studied species, with notable interspecific variations observed primarily in non-coding regions and IR/SC borders. By leveraging phylogenetic informativeness and nucleotide diversity, we identified rpoB gene as the optimal candidate for species delimitation and shallow-level phylogenetic inference within the genus. Through this comprehensive analysis of CP genomes across multiple taxa, our study sheds light on the evolutionary dynamics and taxonomic intricacies of Euphorbia, offering valuable insights into its CP genome evolution and taxonomy.

Molecular phylogenetics of the superfamily Stromboidea (Caenogastropoda): New insights from increased taxon sampling

AbstractThe superfamily Stromboidea is a clade of morphologically distinctive gastropods which include the iconic Strombidae, or ‘true conchs’. In this study, we present the most taxonomically extensive phylogeny of the superfamily to date, using fossil calibrations to produce a chronogram and extant geographical distributions to reconstruct ancestral ranges. From these results, we confirm the monophyly of all stromboidean families; however, six genera are not monophyletic using current generic assignments (Strombidae: Lentigo, Canarium, Dolomena, Doxander; Xenophoridae: Onustus, Xenophora). Within Strombidae, analyses resolve an Indo‐West Pacific (IWP) clade sister to an East Pacific/Atlantic clade, together sister to a second, larger IWP clade. Our results also indicate two pulses of strombid diversification within the Miocene, and a Tethyan/IWP origin for Strombidae—both supported by the fossil record. However, conflicts between divergence time estimates and the fossil record warrant further exploration. Species delimitation analyses using the COI barcoding gene support several taxonomic changes. We synonymise Euprotomus aurora with Euprotomus bulla, Strombus alatus with Strombus pugilis, Dolomena abbotti with Dolomena labiosa, and Dolomena operosa with Dolomena vittata. We identified cryptic species complexes within Terebellum terebellum, Lambis lambis, “Canarium” wilsonorum, Dolomena turturella and Maculastrombus mutabilis. We reinstate Rimellopsis laurenti as a species (previously synonymised with R. powisii) and recognise Harpago chiragra rugosus and Lambis truncata sowerbyi valid at the rank of species. Finally, we establish several new combinations to render Lentigo, Dolomena, and Canarium monophyletic: Lentigo thersites, Dolomena robusta, Dolomena epidromis, Dolomena turturella, Dolomena taeniata, Dolomena vanikorensis, D. vittata, “Canarium” wilsonorum, Hawaiistrombus scalariformis, Maculastrombus mutabilis, Maculastrombus microurceus.

Designing A Novel Primer Set for GAPDH Gene to Enhance Taxonomic and Phylogenetic Studies of Golovinomyces Species

Golovinomyces (Erysiphaceae, Ascomycota) is an obligate plant pathogenic group causing powdery mildew on diverse angiosperm plants, including economically significant crops. Despite advancements in the taxonomy and phylogeny of Golovinomyces species using ribosomal DNA markers (ITS and LSU), several taxonomic issues remain unresolved. Previously, the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene, which exhibits higher nucleotide variation, has been proposed as an additional marker for powdery mildew species. In this study, we designed a new primer set (GoGPD-F and GoGPD-R) to improve the PCR success and efficiency of the GAPDH gene across various Golovinomyces species and dried herbarium specimens. The primers were successful in amplifying and sequencing the GAPDH gene in sixteen Golovinomyces species, including six species not previously registered in GenBank and two undescribed species. This development is a significant contribution to future research on the identification, taxonomy, and phylogeny of Golovinomyces species, offering a more robust tool for resolving existing taxonomic issues.

Pan-Genome Provides Insights into Vibrio Evolution and Adaptation to Deep-Sea Hydrothermal Vents.

This study delves into the genomic features of 10 Vibrio strains collected from deep-sea hydrothermal vents in the Pacific Ocean, providing insights into their evolutionary history and ecological adaptations. Through sequencing and pan-genome analysis involving 141 Vibrio species, we found that deep-sea strains exhibit larger genomes with unique gene distributions, suggesting adaptation to the vent environment. The phylogenomic reconstruction of the investigated isolates revealed the presence of 2 main clades: The first is monophyletic, consisting exclusively of Vibrio alginolyticus, while the second forms a monophyletic clade comprising both Vibrio antiquarius and Vibrio diabolicus species, which were previously isolated from deep-sea vents. All strains carry virulence and antibiotic resistance genes related to those found in human pathogenic Vibrio species which may play a wider ecological role other than host infection in these environments. In addition, functional genomic analysis identified genes potentially related to deep-sea survival and stress response, alongside candidate genes encoding for novel antimicrobial agents. Ultimately, the pan-genome we generated represents a valuable resource for future studies investigating the taxonomy, evolution, and ecology of Vibrio species.