Molecular Variation Research Articles

Molecular characterization based on cytochrome C oxidase I gene of the family Channidae from different riverine systems of Odisha, India

This study focuses on four Channa species from the northern part of the Eastern Ghats in India: Channa punctata (Bloch, 1793); Channa striata (Bloch, 1793); Channa marulius (Hamilton, 1822) and Channa gachua (Hamilton, 1822). The aim is to determine whether their molecular divergence aligns with their morphological distinctiveness. The molecular analysis based on mitochondrial COI gene sequences revealed distinct clusters for each species and genus, with K2P distances ranging from 17.28 – 27.96%. Notably, C. marulius was positioned in a distinct clade separate from the C. punctata, C. striata, and C. gachua groups. Channa gachua clustered with Channa rara and Channa kelaartii, suggesting a close evolutionary relationship. Channa punctata and C. striata also clustered together, reinforcing their status as sister species. Species delimitation using the Assemble Species by Automatic Partitioning method identified 10 partitions, with the most reliable delimitation showing a clear separation of Channa species of Odisha. These findings align with recent analyses and confirm that the molecular divergence among the four species is consistent with their morphological differences. The study underscores the importance of molecular methods in resolving taxonomic ambiguities and understanding species diversity. It provides a foundational molecular database for Channa species, supporting future research on genetic divergence and contributing to conservation and aquaculture efforts.

Phylogeography of Cold Water Soft Coral Alcyonium spp. (Anthozoa, Octocorallia: Alcyonacea) Between South America and the West Antarctic Peninsula.

The Antarctic marine environment has a unique geologic and climatic history that has contributed to the evolution of high species diversity. Given the current trend of environmental warming, understanding the history of Antarctic species is crucial for predicting the impact of climate change on ecosystem function. Soft corals are a group of striking presence in the benthic marine assemblages in the Southern Ocean, which is recognized as a biodiversity hotspot. DNA sequences (Cox1, mtMutS, and 28S rDNA) were utilized for molecular phylogenetic reconstructions, species delimitations, and divergence estimations to investigate the spatial patterns of genetic diversity in Alcyonium species in the southern South American-Antarctic region. Significant genetic divergence was observed between regions, with a clear genetic break between South America and the West Antarctic Peninsula and the identification of four putative species. Divergence time estimates indicated that Alcyonium's diversification began about 41.1 million years ago (Ma), coinciding with the opening of the Drake Passage and the formation of the Antarctic Circumpolar Current (ACC, ~42 Ma). This indicates that Alcyonium has persisted insitu for an extensive period, enduring a wide range of environmental conditions.

Identification of N-phenyl-N-(quinolin-4-yl) amino carboxylic acids as URAT1 inhibitors with hypouricemic effects

Urate transporter 1 (URAT1) is a therapeutic target for the treatment of hyperuricemia and gout. However, the application of currently marketed URAT1 inhibitors is hampered by insufficient efficacy and poor safety profiles. A series of N-phenyl-N-(quinolin-4-yl) amino carboxylic acids were designed by adopting strategies of molecular hybridization, scaffold hopping, and functional variation. Most compounds showed apparent inhibitory activity against URAT1, and the most active compound 7 exhibited an IC50 of 0.18 μ M, which was comparable to the clinically available drug benzbromarone (IC50 = 0.39 μ M). When tested in parallel with benzbromarone, compound 7 showed significant uric acid-lowering effect in a hyperuricemia zebrafish model induced by potassium oxonate and xanthine sodium salt. Compound 7 was also more metabolically stable than benzbromarone in mouse liver microsomes. The results suggested potential therapeutic benefits of these compounds in the treatment of hyperuricemia and gout.

Анализ генетического разнообразия сортов масличного льна селекции ВНИИМК с применением молекулярно-генетических маркеров

Oil flax (Linum usitatissimum L.) is one of the most important technical crops. The success of the breeding work is reached mostly by the genetic diversity of used initial germplasm. The molecular-genetic markers determine this diversity. Five cultivars of oil flax: Danik, Snegurok, Nilin, Y 117, and August, bred at the V.S. Pustovoit All-Russian Research Institute of Oil Crops were used as research material. To estimate genetic structure of cultivars we used 40 plants of each cultivar. Ten microsatellite loci markers were used for analysis. The amplification was conducted in a termocycler MiniAmp (Thermo Scientific, USA). The electrophoretic segregation of amplicons was carried out in 8% polyacrilamide gel in the native conditions. The primary indicators of genetic varia-tion (a number of alleles per a locus (Na), an effective number of alleles (Ne), observed (Ho) and wanted (He) heterozigosity, an informative Shennon’s index (I), fixation index (F), percentage of polymorphic loci (%P), genetic distances (D) were determined, analysis of molecular variation and principle coordinate analysis were done. The indicators of intraspecific genetic diversity decreased in the direction of cultivar range Nilin, Danik, August, Y 117, and Snegurok. Snegurok is a cultivar of linear type with some number of non-typical plants. The cultivar Y 117 is divided into two main biotype. Nilin, Danik, and August do not possess clear-marked structure. Most of the total variation is conditioned by differences between cultivars. The genetic distances between cultivars are quite big and equal from 0.752 to 0.986. All cultivars are distant from each other by two main coordinates. The conducted research showed small intravarietal and signif-icant intervarietal genetic diversity of five oil flax cultivars bred at the V.S. Pustovoit All-Russian Re-search Institute of Oil Crops and their potential in as initial material for breeding of new cultivars.

Lipid profiles and DNA barcoding markers reveal the genetic delimitation between species of the Carapa genus native from the Amazon

Authentic identification of Amazonian tree species is important for conservation and their sustainable exploitation. This work aimed to characterize the inter- and intraspecific divergence in two taxonomic units of the genus Carapa using the lipidomic profile of the seed oils, analyzed by gas chromatography-mass spectrometry (GC-MS) and DNA barcoding molecular markers to identify and discriminate differences between Carapa species. Seeds and leaves of 53 individuals were collected and morphologically grouped into Carapa guianensis and Carapa vasquezii. The oils extracted from seeds were esterified, and their lipidomic profiles were analyzed. Two chloroplast genome regions (psbA-trnH and rbcL) were amplified for genetic diversity analyses and the barcoding-gap test. The lipidomic profile allowed the identification of 40 substances present in the C. guianensis and C. vasquezii oils, with 20 shared among the species independent of the region of collection, two occurring only in the oil of C. guianensis from Acre, four in samples of C. guianensis and C. vasquezii from Amazonas, and 16 substances occurring only in samples of C. vasquezii oil. C. vasquezii presented a greater diversity of terpenoids. The genome regions made it possible to obtain 16 distinct haplotypes for the two species (C. guianensis and C. vasquezii), 999 conserved sites, and 32 polymorphic sites. The species presented significant molecular divergence (FST=0.87), and the rbcL region was considered promising for barcode studies at levels ranging from 0.1 to 0.2% of genetic distance. The results suggest that the two species morphologically identified C. guianensis and C. vasquezii constitute genetically divergent biological groups.

Phylogenomics and adaptive evolution of hydrophytic umbellifers (tribe Oenantheae, Apioideae) revealed from chloroplast genomes

BackgroundTribe Oenantheae consists mainly of aquatic species within the Apioideae. The unique morphology and habitat distinguish this group from other Apioideae groups. However, the genomic information of these group species has not been widely developed, and the molecular mechanisms of adaptive evolution remain unclear.ResultsWe provide comparative analyses on 30 chloroplast genomes of this tribe representing five genera to explore the molecular variation response to plant adaptations. The Oenantheae chloroplast genomes presented typical quadripartite structures, with sizes ranging from 153,024 bp to 155,006 bp. Gene content and order were highly conserved with no significant expansion or contraction observed. Seven regions (rps16 intron–trnK, rpoB–trnC, trnE–trnT–psbD, petA–psbJ, ndhF–rpl32–trnL, ycf1a–rps15, and ycf1a gene) were identified as remarkable candidate DNA markers for future studies on species identification, biogeography, and phylogeny of tribe Oenantheae. Our study elucidated the relationships among the genera of tribe Oenantheae and subdivided the genera of Sium and Oenanthe. However, relationships among the Oenanthe I clade remain to be further clarified. Eight positively selected genes (accD, rbcL, rps8, ycf1a, ycf1b, ycf2, ndhF, and ndhK) were persuasively detected under site models tests, and these genes might have played roles in Oenantheae species adaptation to the aquatic environments.ConclusionsOur results provide sufficient molecular markers for the subsequent molecular studies of the tribe Oenantheae, and promote the understanding of the adaptation of the Oenantheae species to aquatic environments.

Secondary contact erodes Pleistocene diversification in a wide-ranging freshwater mussel (Quadrula).

The isolated river drainages of eastern North America serve as a natural laboratory to investigate the roles of allopatry and secondary contact in the evolutionary trajectories of recently diverged lineages. Drainage divides facilitate allopatric speciation, but due to their sensitivity to climatic and geomorphological changes, neighboring rivers frequently coalesce, creating recurrent opportunities of isolation and contact throughout the history of aquatic lineages. The freshwater mussel Quadrula quadrula is widely distributed across isolated rivers of eastern North America and possesses high phenotypic and molecular variation across its range. We integrate sequence data from three genomes, including female- and male-inherited mitochondrial markers and thousands of nuclear encoded SNPs with morphology and geography to illuminate the group's divergence history. Across contemporary isolated rivers, we found continuums of molecular and morphological variation, following a pattern of isolation by distance. In contact zones, hybridization was frequent with no apparent fitness consequences, as advanced hybrids were common. Accordingly, we recognize Q. quadrula as a single cohesive species with subspecific variation (Q. quadrula rumphiana). Demographic modeling and divergence dating supported a divergence history characterized by allopatric vicariance followed by secondary contact, likely driven by river rearrangements and Pleistocene glacial cycles. Despite clinal range-wide variation and hybridization in contact zones, the process-based species delimitation tool delimitR, which considers demographic scenarios like secondary contact, supported the delimitation of the maximum number of species tested. As such, when interpreting species delimitation results, we suggest careful consideration of spatial sampling and subsequent geographic patterns of biological variation, particularly for wide-ranging taxa.

Adaptation of Aglycosylated Monoclonal Antibodies for Improved Production in Komagataella phaffii.

Monoclonal antibodies (mAbs) are a major class of biopharmaceuticals manufactured by well-established processes using Chinese Hamster Ovary (CHO) cells. Next-generation biomanufacturing using alternative hosts like Komagataella phaffii could improve the accessibility of these medicines, address broad societal goals for sustainability, and offer financial advantages for accelerated development of new products. Antibodies produced by K. phaffii, however, may manifest unique molecular quality attributes, like host-dependent, product-related variants, that could raise potential concerns for clinical use. We demonstrate here conservative modifications to the amino acid sequence of aglycosylated antibodies based on the human IgG1 isotype that minimize product-related variations when secreted by K. phaffii. A combination of 2-3 changes of amino acids reduced variations across six different aglycosylated versions of commercial mAbs. Expression of a modified sequence of NIST mAb in both K. phaffii and CHO cells showed comparable biophysical properties and molecular variations. These results suggest a path toward the production of high-quality mAbs that could be expressed interchangeably by either yeast or mammalian cells. Improving molecular designs of proteins to enable a range of manufacturing strategies for well-characterized biopharmaceuticals could accelerate global accessibility and innovations.

Computational analysis of the deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) in TYR gene impacting human tyrosinase protein and the protein stability.

Tyrosinase, a copper-containing oxidase, plays a vital role in the melanin biosynthesis pathway. Mutations in the tyrosinase gene can disrupt the hydroxylation of tyrosine, leading to decreased production of 3,4-dihydroxyphenylalanine (DOPA). Consequently, this impairs the subsequent formation of dopaquinone, a key precursor in melanin pigment synthesis. This study aimed to identify the deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) within the TYR gene that exert an influence on the human TYR protein. Additionally, we evaluated the impact of 10 FDA-approved drugs on the protein stability of mutated structures, exploring the potential for inhibitory pharmaceutical interventions. Through various bioinformatics tools, we detected 47900 nsSNPs, particularly K142M, I151N, M179R, S184L, L189P, and C321R, which were found to be the most deleterious variants, decreasing the protein stability. These drugs (Sapropterin, Azelaic Acid, Menobenzone, Levodopda, Mequinol, Arbutin, Hexylresorcinol, Artenimol, Alloin and Curcumin) interacted with the binding sites in four mutant models K142M, I151N, M179R, and S184L proving that these ligands directly bind with the active site of mutant tyrosinase protein to inhibit it's working. On the other hand, two mutant models L189P and C321R did not show any binding site residue interaction with any ligands. In conclusion, this in-silico analysis of deleterious nsSNPs in the TYR gene, coupled with the evaluation of ligands/drugs on mutated tyrosinase structures not only advances our understanding of molecular variations but also highlights promising pathways for targeted inhibitory interventions in the intricate network of melanin biosynthesis.

Transcriptomic Analysis of the Amygdala in Subjects with Schizophrenia, Bipolar Disorder and Major Depressive Disorder Reveals Differentially Altered Metabolic Pathways.

The amygdala, crucial for mood, anxiety, fear, and reward regulation, shows neuroanatomical and molecular divergence in psychiatric disorders like schizophrenia, bipolar disorder and major depression. This region is also emerging as an important regulator of metabolic and immune pathways. The goal of this study is to address the paucity of molecular studies in the human amygdala. We hypothesize that diagnosis-specific gene expression alterations contribute to the unique pathophysiological profiles of these disorders. We used a cohort of subjects diagnosed with SCZ, BPD or MDD, and nonpsychiatrically ill control subjects (n = 15/group), together with our bioinformatic 3-pod analysis consisting of full transcriptome pathway analysis, targeted pathway analysis, leading-edge gene analysis and iLINCS perturbagen analysis. We identified altered expression of metabolic pathways in each disorder. Subjects with SCZ displayed downregulation of mitochondrial respiration and nucleotide metabolism pathways. In comparison, we observed upregulation of mitochondrial respiration pathways in subjects with MDD, while subjects with BPD displayed enrichment of pathways involved in carbohydrate metabolism. Several pathways associated with brain metabolism including immune system processes and calcium ion transport were also differentially altered between diagnosis groups. Our findings suggest metabolic pathways, including downregulation of energy metabolism pathways in SCZ and upregulation of energy metabolism pathways in MDD, are uniquely altered in the amygdala in these disorders, which may impact approaches for therapeutic strategies.

PATH-08. MOLECULAR DIVERGENCE RATES DIFFER BETWEEN BRAIN METASTASES AND EXTRACRANIAL DISEASE SITES ACROSS PRIMARY TUMOR HISTOLOGIES

Abstract Genomic alterations and molecular subgroups between extracranial disease sites and brain metastases often differ, yet the prevalence and clinical significance of divergent evolution in brain metastases is not fully understood. This study examined genomic alterations and molecular subgroup divergence rates between matched brain metastases and extracranial disease sites. A retrospective, two-center study was conducted on patients who underwent resection of brain metastases between 2014-2022 with clinical and matched genomic data and/or molecular markers available. The overall cohort comprised 256 patients with matched tumors from multiple cancer types, most commonly from breast (n=108, 42.2%), melanoma (n=83, 32.4%), and NSCLC (n=43, 16.8%). Targeted next-generation sequencing of over 500 oncogenes was performed on resected tumors as part of clinical care (n=41 patients with matched specimens). Molecular subgroups for breast, melanoma, and non-small cell lung cancer were also assessed by immunohistochemistry to evaluate rates of molecular subgroup discordance between sites. Subgroup discordance by immunohistochemistry was observed most frequently across breast cancer (22.2%, n=24/108) with loss of the estrogen receptor (ER) and progesterone receptor (PR) and gain of HER2 most frequently observed within brain metastases. Molecular subgroup discordance was rare within melanoma (7.3%, n=6/82) and NSCLC (14.0%, n=6/43) patients. When evaluating oncogenomic alterations from targeted DNA sequencing in 41 patients with matched specimens, 80.5% (33/41) of brain metastases demonstrated a unique oncogene alteration profile compared to an extracranial disease site. Fourteen patients (34.1%) had a gain of at least 1 targetable alteration within a brain metastasis that was not observed in an extracranial disease site. Brain metastases demonstrated high rates of genomic divergence compared to primary and extracranial metastatic disease sites. This data supports obtaining brain metastasis tissue and conducting molecular profiling of this tissue to help select optimal CNS penetrant systemic therapies for each patient.

A molecular assessment of species boundaries and relationships in the Australian brine shrimp Parartemia (Anostraca: Parartemiidae).

Australian salt lakes contain a diverse range of endemic invertebrates. The brine shrimp Parartemia is among the most speciose and salt-tolerant of these invertebrates. The morphotaxonomy of Parartemia is well established but there has only been limited molecular assessment of the phylogenetic relationships and boundaries of the morphospecies. We used multiple genetic markers (nuclear 28S and mitochondrial 16S and COI ) and tree-building methods (Bayesian inference and maximum likelihood) to investigate the phylogeny of Parartemia . We also used species delimitation methods to test the validity of morphological species designations. The data set included all but 2 of the 18 described Parartemia morphospecies, collected from a total of 93 sites from across southern Australia plus some sequences from GenBank. The results identified large amounts of molecular divergence (e.g. COI P- values of up to 25.23%), some groups of closely related species (which also usually shared some morphological similarities) and some distinctive species, although the relationships among divergent lineages were generally not well resolved. The most conservative set of results from the species delimitation analyses suggests that the morphotaxonomy is largely accurate, although many morphospecies comprised divergent genetic lineages separated by COI P- values of up to 17.02%. Two putative new morphospecies, three cryptic species and one synonymy were identified. Our findings improve the knowledge of Parartemia taxonomy and will facilitate the development of future studies and conservation of this taxon.

Occurrence of plant-parasitic nematodes on rice (Oryza sativa) in Kenya with a focus on Hirschmanniella oryzae

Summary Rice ranks as the third most important staple cereal food crop in Kenya, following maize and wheat. The demand for rice has been increasing at a faster rate than most cereals, occasionally requiring imports to meet local needs. In response, the Kenyan government has been implementing a programme to increase rice production by expanding irrigated lowland rice schemes from 32 988 to 171 676 ha, while increasing rain-fed upland production areas four-fold to 42 000 ha by 2030. However, with continued rice monocropping in irrigated lowland fields and intensification in rain-fed upland ecosystems, there is a growing concern that plant-parasitic nematodes may emerge as a significant problem across rice ecosystems. This study characterised the nematode genera associated with rice in Kenya and assessed their diversity and distribution across rice ecosystems, with a focus on Hirschmanniella species. Eleven nematode genera were identified in both ecosystems, indicating a relatively high diversity. These genera, ranked by prominence, included Hirschmanniella, Hoplolaimus, Pratylenchus, Helicotylenchus, Meloidogyne, Ditylenchus, Trichodorus, Xiphinema, Rotylenchus, Longidorus and Paratylenchus. The family Tylenchidae was also found to be an important component of the nematofauna. Both morphological and molecular analyses confirmed the presence of Hirschmanniella oryzae in irrigated lowland and rain-fed upland rice, which represents the first documented report for Kenya. A notably large molecular variation was also observed for these Kenyan populations on the 18S region, with intraspecific variation up to 10 bp difference. Understanding the diversity, distribution, and species composition of nematodes in rice ecosystems is important for raising awareness among plant protection services, farmers, cooperatives and extension agents about plant-parasitic nematodes and their challenges in rice production. Future research should build on this knowledge to support extensive studies on population dynamics and damage threshold, focusing on local rice cultivars to develop effective management strategies, including breeding programmes and other cultural practices.

Hidden diversity in anthropophilic sand flies of the Monticola Series (Diptera, Psychodidae)

The Monticola series comprises two anthropophilic and widely distributed species in Brazil: Pintomyia (Pifanomyia) monticola (Costa Lima, 1932) and Pintomyia (Pifanomyia) misionensis (Castro, 1959). They mainly occur in the Atlantic Rainforest, and it is known that Pi. monticola comprises at least two well-structured genetic lineages regarding a fragment of the cytochrome c oxidase subunit I (COI) gene. Here, we aim to elucidate the taxonomic status of this group using integrative taxonomy tools. Collections were performed in nine localities of four Brazilian states, and COI fragments were sequenced and merged with publicly available data. Several single-locus species delimitation algorithms, genetic distance metrics, phylogenetic trees, and haplotype networks were used to uncover cryptic diversity and population structure within Pi. monticola and Pi. misionensis. The resulting genetic clusters were then tested for morphological differences through linear and geometric morphometry of several characters. We analyzed 152 COI sequences, comprising 48 haplotypes. The maximum intraspecific p distances were 8.21% (mean 4.17%) and 9.12% (mean 4.4%) for Pi. monticola and Pi. misionensis, respectively, while interspecific ones ranged from 10.94 to 14.09% (mean 12.33%). Phylogenetic gene trees showed well-supported clades for both species, with clear structuring patterns within them. Species-delimitation algorithms split our dataset into at least three putative species for each taxon. Moreover, population structure analysis showed a strong correlation between Atlantic Forest areas of endemism as sources of molecular variation in Pi. monticola. Morphometric analyses were significant for wing shape variation and some linear measurements (mainly of the head) when comparing specimens of different genetic clusters for both taxa. These results indicate strong genetic structuring of Monticola series species, confirmed by morphometry, indicating two possible cryptic species complexes.

Solid‐Solid Phase Transformation Behavior of ϵ‐CL‐20 Induced by Typical Organic Solvents: A Theoretical and Experimental Study

AbstractThe solid‐solid phase transformation of ϵ‐CL‐20 induced by external conditions is one of the bottlenecks limiting the widespread applications of CL‐20‐based energetic materials. Herein, we report the investigation on the influence of solvent polarity on ϵ‐CL‐20 solid‐solid phase transformation behavior both theoretically and experimentally. Density functional theory (DFT) calculation was performed to evaluate the possibility of ϵ‐CL‐20 phase transformation induced by organic solvent molecules from the perspective of ϵ‐CL‐20 electronic structure and molecular structure variations. Additionally, experimental study of ϵ‐CL‐20 phase transformation induced by 1,2‐dichloroethane, ethanol, and methanol gas environment was conducted. Solvent with higher polarity was confirmed to significantly vary molecular surface electrostatic potential and molecular conformation of ϵ‐CL‐20 molecule. Furthermore, ϵ‐CL‐20 critical phase transformation temperature decreased when using inducing solvent with higher polarity. And the observed maximum phase transformation rate was the one induced by the highest polarity solvent. A four‐parameter model was established to describe the phase transformation process as a function of time based on the experimental results. Possible ϵ‐CL‐20 solid‐solid phase transformation mechanism was proposed. Hopefully, these results will be beneficial for the rational preparation and utilization of CL‐20‐based energetic materials.

Molecular compositional variation of organic matter deposited on the East Tasman Plateau during the Paleocene–Eocene Thermal Maximum

Molecular compositions in sediments collected by Ocean Drilling Program Leg 189 at Site 1172 in the Tasmanian Gateway, Australia have been characterised by gas chromatography–mass spectrometry to assess the impact of the Paleocene–Eocene Thermal Maximum (PETM) on organic matter origins and evolution. Total organic carbon (TOC) and sulfur contents reach the lowest values immediately before the initiation of the negative carbon isotope excursion (CIE) in the shallow marine environment on the East Tasman Plateau. The TOC content increases slightly while the sulfur content increases more substantially during deposition of the CIE, suggesting the occurrence of low-oxygen environments during the PETM event. The studied section is thermally immature, as shown by the dominance of biological configuration biomarkers such as 17β(H),21β(H)-hopanes (ββ) and hopenes. Changes in relative abundance of compound classes and isomer ratios are largely caused by the variation of source inputs and depositional conditions. Very low abundance of marine steroids during the CIE, but very enriched hopanoids, indicate low marine productivity, in accord with substantial remineralisation of organic matter in the bottom waters. The ββ-hopanes are the most abundant hopanoid series, followed by the neohop-13(18)-ene and hop-17(21)-ene series, further verifying the immaturity of the organic constituents in the samples. Hopane ratios (ββ/(βα + αβ) and βα/(βα + αβ) with different carbon numbers are systematically higher in sediments deposited during the CIE than those formed pre- and post-CIE, suggest increased bacterial inputs. Higher C30/C29 and C30/C31 hopanoid ratios in the CIE sediments are consistent with a greater contribution from in situ bacterial organic matter, rather than continental soil erosion by flooding. This is supported by the higher C27–32 hopanoids/(C27 + C29 + C31n-alkanes) ratio and sulfur content during the CIE. A relatively lower TOC content in the sediments formed during the PETM is inferred to have been caused by dilution by both enhanced detrital input and intensified bacterial consumption. This study demonstrates that the biomarker approach can play an important role in the identification of organic matter origin and characterisation of depositional environment for PETM sequences.

Evolutionary History and Ecology of Andrena (Foveoandrena) androfovea: A New Nearctic Mining Bee (Hymenoptera, Andrenidae) Species and Subgenus.

With about 1700 described species, the mining bee genus Andrena is a rapidly diversifying lineage and one of the most species-rich groups of bees. Recent phylogenomic advances have greatly improved our understanding of the phylogeny of the genus, yet many species still await description, subgeneric assignments that are in line with their evolutionary history, as well as study of their morphology and behavior. Here we provide a comprehensive account of a newly discovered species, Andrena androfovea n. sp. We sequence the genome of the new species and include it in the presently most comprehensive phylogenomic analysis of Andrena using ultraconserved element (UCE) sequence data, comprising 264 samples and 249 species. Given the recovered phylogenetic position of the new species, we establish a new subgenus, Foveoandrena, provide a detailed morphological description, and discuss the antiquity and historical biogeography of the lineage in light of molecular divergence time estimates. Lastly, we study and document the foraging behavior of the new species with photos and video footage, and discuss the species' unusual host plant associations with Chamaesaracha and Quincula, both Solanaceae. Being likely oligolectic on these plants, we present the first documented case of an Andrena species being narrowly associated with members of this plant family. By integrating multiple lines of documentation, our study provides a particularly detailed account of species discovery and description.

First isolation of the Sindbis virus in mosquitoes from southwestern Spain reveals a new recent introduction from Africa

Sindbis virus (SINV), is an Alphavirus of the family Togaviridae. This zoonotic arbovirus is transmitted by mosquitoes, primarily from the Culex genus, with bird species acting as amplifying vertebrate hosts. Occasionally it can also affect humans that are accidental hosts. SINV genotype I (SINV-I) has been isolated in mosquitoes and birds in South Africa and Northern Europe, producing fever outbreaks. In the last decades, there were several detections of SINV in Europe. In 2022, during the West Nile virus (WNV) mosquito surveillance program in Andalucía (Spain) implemented by the regional health administration, we detected the presence of both SINV and WNV in a Culex perexiguus pool, representing the first detection of SINV in Spain. After this finding, we screened 1149 mosquito pools to determine the status of SINV circulation in western Andalucía. We identified for the first time the presence of SINV in five different mosquito species. Culex perexiguus presented the highest infection rate by SINV. In addition, SINV was geographically widespread and distributed in four out of the five Andalucía's provinces studied, with Cadiz presenting the highest infection rate. All SINV genomes from Southwestern Spain characterised in this study belonged to SINV-I, previously detected in Europe and Africa. These isolated SINV-I strains presented low molecular variation among them and in the phylogenomic analyses they formed a monophyletic group that clustered with strains from Algeria and Kenya. These results suggest that, around 2017, a single new SINV introduction into the European continent occurred, probably from Northern (Algeria) or Central Africa.

Molecular Variation and Phylogeny of Thymidylate Kinase Genes of Candidatus Phytoplasma ziziphi from Different Resistant and Susceptible Jujube Cultivars in China.

The thymidylate kinase (tmk) gene is indispensable for the proliferation and survival of phytoplasma. To reveal the molecular variation and phylogeny of the tmk genes of Candidatus phytoplasma ziziphi, in this study, the tmk genes of 50 phytoplasma strains infecting different resistant and susceptible jujube cultivars from different regions in China were amplified and analyzed. Two sequence types, tmk-x and tmk-y, were identified using clone-based sequencing. The JWB phytoplasma strains were classified into three types, type-X, type-Y, and type-XY, based on the sequencing chromatograms of the tmk genes. The type-X and type-Y strains contained only tmk-x and tmk-y genes, respectively. The type-XY strain contained both tmk-x and tmk-y genes. The type-X, type-Y, and type-XY strains comprised 42%, 12%, and 46% of all the strains, respectively. The type-X and type-XY strains were identified in both susceptible and resistant jujube cultivars, while type-Y strain was only identified in susceptible cultivars. Phylogenetic analysis indicated that the tmk genes of the phytoplasmas were divided into two categories: phylo-S and phylo-M. The phylo-S tmk gene was single-copied in the genome, with an evolutionary pattern similar to the 16S rRNA gene; the phylo-M tmk gene was multi-copied, related to PMU-mediated within-genome transposition and between-genome transfer. Furthermore, the phylogenetic tree suggested that the tmk genes shuttled between the genomes of the Paulownia witches' broom phytoplasma and JWB phytoplasma. These findings provide insights into the evolutionary and adaptive mechanisms of phytoplasmas.

Astrocyte regional specialization is shaped by postnatal development.

Astrocytes are an abundant class of glial cells with critical roles in neural circuit assembly and function. Though many studies have uncovered significant molecular distinctions between astrocytes from different brain regions, how this regionalization unfolds over development is not fully understood. We used single-nucleus RNA sequencing to characterize the molecular diversity of brain cells across six developmental stages and four brain regions in the mouse and marmoset brain. Our analysis of over 170,000 single astrocyte nuclei revealed striking regional heterogeneity among astrocytes, particularly between telencephalic and diencephalic regions, at all developmental time points surveyed in both species. At the stages sampled, most of the region patterning was private to astrocytes and not shared with neurons or other glial types. Though astrocytes were already regionally patterned in late embryonic stages, this region-specific astrocyte gene expression signature changed dramatically over postnatal development, and its composition suggests that regional astrocytes further specialize postnatally to support their local neuronal circuits. Comparing across species, we found divergence in the expression of astrocytic region- and age-differentially expressed genes and the timing of astrocyte maturation relative to birth between mouse and marmoset, as well as hundreds of species differentially expressed genes. Finally, we used expansion microscopy to show that astrocyte morphology is largely conserved across gray matter regions of prefrontal cortex, striatum, and thalamus in the mouse, despite substantial molecular divergence.