Search Results (559)

Disparities in the functional classification of secretory genes among aphid taxa may be attributed to variations in coding sequences and gene expression profiles. However, the driving factors that regulate sequence evolution remain unclear. This study aimed to investigate the differences in coding sequences and expression patterns of secretory genes between the rose grain aphid (Metopolophium dirhodum) and the pea aphid (Acrythosiphon pisum), with a particular focus on their roles in evolutionary adaptations and functional diversity. The study involved the rearing of aphids, RNA extraction, de novo transcriptome assembly, functional annotation, secretory protein prediction, and comparative analysis of coding sequences and expression patterns across various functional categories using bioinformatics tools. The results revealed that metabolic genes exhibited greater coding sequence divergence, indicating the influence of positive selection. Moreover, significant expression divergence was noted among functional categories, particularly in metabolic and genetic information processing genes, which exhibited higher variability. This study enhances our understanding of the molecular mechanisms that contribute to phenotypic and genetic diversity among aphid species. This study elucidates the relationship between variations in coding sequences and differences in gene expression among functional categories, thereby establishing a foundation for future studies on gene evolution in response to environmental pressures. Full article

The Millard’s rat (Dacnomys millardi), a threatened murid endemic to Southeast Asian montane rainforests and the sole member of its monotypic genus, faces escalating endangered risks as a Near Threatened species in China’s Biodiversity Red List. This ecologically specialized rodent exhibits diagnostic morphological adaptations—hypertrophied upper molars and cryptic pelage—that underpin niche differentiation in undisturbed tropical/subtropical forests. Despite its evolutionary distinctiveness, the conservation prioritization given to Dacnomys is hindered due to a deficiency of data and unresolved phylogenetic relationships. Here, we integrated morphological analyses with the first complete mitogenome (16,289 bp in size; no structural rearrangements) of D. millardi to validate its phylogenetic placement within the subfamily Murinae and provide novel insights into genetic diversity erosion. Bayesian and maximum likelihood phylogenies robustly supported Dacnomys as sister to Leopoldamys (PP = 1.0; BS = 100%), with an early Pliocene divergence (~4.8 Mya, 95% HPD: 3.65–5.47 Mya). Additionally, based on its basal phylogenetic position within Murinae, we propose reclassifying Micromys from Rattini to the tribe Micromyini. Codon usage bias analyses revealed pervasive purifying selection (Ka/Ks < 1), constraining mitogenome evolution. Genetic diversity analyses showed low genetic variation (CYTB: π = 0.0135 ± 0.0023; COX1: π = 0.0101 ± 0.0025) in fragmented populations. We propose three new insights into this genetic diversity erosion. (1) Evolutionary constraints: genome-wide evolutionary conservation and shallow evolutionary history (~4.8 Mya) limited mutation accumulation. (2) Anthropogenic pressures: deforestation-driven fragmentation of habitats (>20,000 km²/year loss since 2000) has reduced effective population size, exacerbating genetic drift. (3) Ecological specialization: long-term adaptation to stable niches favored genomic optimization over adaptive flexibility. These findings necessitate suitable conservation action by enforcing protection of core habitats to prevent deforestation-driven population collapses and advocating IUCN reclassification of D. millardi from Data Deficient to Near Threatened. Full article

As distant hybridization has profound implications for evolutionary biology, aquaculture, and biodiversity conservation, this study aims to elucidate patterns of maternal inheritance, genetic divergence, and phylogenetic relationships by synthesizing mitochondrial genome (mitogenome) data from 74 distant hybrid fish species. These hybrids span diverse taxa, including 48 freshwater and 26 marine species, with a focus on Cyprinidae (n = 35) and Epinephelus (n = 14), representing the most frequently hybridized groups in freshwater and marine systems, respectively. Mitogenome lengths were highly conserved (15,973 to 17,114 bp); however, the genetic distances between hybrids and maternal species varied from 0.001 to 0.17, with 19 hybrids (25.7%) showing distances >0.02. Variable sites in these hybrids were randomly distributed but enriched in hypervariable regions, such as the D-loop and NADH dehydrogenase subunits 1, 3 and 6 (ND2, ND3, and ND6) genes, likely reflecting maternal inheritance (reported in Cyprinus carpio × Carassius auratus). Moreover, these genes were under purifying selection pressure, revealing their conserved nature. Phylogenetic reconstruction using complete mitogenomes revealed three distinct clades in hybrids: (1) Acipenseriformes, (2) a freshwater cluster dominated by Cypriniformes and Siluriformes, and (3) a marine cluster comprising Centrarchiformes, Pleuronectiformes, Scombriformes, Cichliformes, Anabantiformes, Tetraodontiformes, Perciformes, and Salmoniformes. The prevalence of Cyprinidae hybrids underscores their importance in aquaculture for hybridization, where traits such as rapid growth and disease resistance are enhanced. In contrast, marine hybrids are valued for their market value and adaptability. While mitogenome data robustly support maternal inheritance in most cases, exceptions suggest complex mechanisms, such as doubly uniparental inheritance (DUI), in distantly related crosses. Moreover, AT-skew of genes in hybrids revealed a paternal leakage of traits in mitogenomes. This study also highlights ecological risks, such as genetic swamping in native populations, emphasizing the need for responsible hybridization practices. These findings advance our understanding of the role of hybridization in fish evolution and aquaculture, providing a genomic framework and policy recommendations for optimizing breeding programs, hybrid introduction, and mitigating conservation challenges. Full article

Previous phylogeographic study of the root vole (Alexandromys oeconomus) revealed four mitochondrial cytochrome b lineages—North and Central European, North (=Central) Asian and Beringian. Three of them were studied in detail, while the North Asian lineage, which occupies the most extensive territory and is considered to be the place of origin for the species, was understudied. In the framework of the current study, we obtained 95 new sequences (34 localities) from the wide territory of Northern Asia and in total, examined 940 specimens from 181 localities throughout the species’ distribution range. The North Asian lineage was found to be more diverse than the Beringian and the European lineages. Southern Siberia and especially the Altai–Sayan region displayed the highest haplotype and nucleotide diversity, suggesting the region’s role as a genetic diversity hotspot. We suppose that the expansion of the North Asian lineage started from Western Transbaikalia. Its representatives colonised the territory from the Urals to the northern shore of the Okhotsk Sea, and then spread in the opposite direction, to Southern Siberia. As a result, a mixture of haplogroups is observed in the Altai–Sayan region. According to the BEAST analysis calibrated with the first A. oeconomus records, the MRCA of North Asian and Beringian lineages is dated back to ~0.82 Mya, and the first divergence within the North Asian lineage may have occurred ~0.6 Mya. When compared with colonisation times of other representatives of the Arvicolinae subfamily, our dating seems to be overestimated. In this regard, molecular data for dated fossil remains of the root vole are essential for subsequent studies. Full article

Cherry laurel (Prunus laurocerasus) is an understudied, highly polyploid (22×) species that is widely used as an ornamental shrub and as a fruit-bearing plant in Türkiye. We analyzed 43 accessions—33 ornamental cultivars and 10 fruit-bearing selections—by examining size variations in 10 simple sequence repeat (SSR) markers and the first intron region of the self-incompatibility ribonuclease (S-RNase) gene. A total of 498 alleles were detected across 11 loci, with the highest number of alleles observed at the S-locus. The SSR loci amplified between 4 (ASSR63) and 17 (BPPCT039) alleles per accession, with eight of the 11 primers generating more than 12 alleles per accession. Two markers, BPPCT040 and CPSCT021, uniquely distinguished all tested accessions. Of the alleles, only 178 (36%) were shared between the ornamental and fruit-bearing groups, reflecting significant genetic differentiation. A dendrogram and principal coordinate analysis revealed three distinct groups. Group 1 included most Hungarian and some European cultivars. Groups 2 (Western European cultivars) and 3 (Turkish selections) exhibited higher average allele numbers, suggesting greater genetic diversity in these groups. Our results indicate that cultivated cherry laurels originate from a broad genetic base and show clear genetic divergence between ornamental and fruit-bearing selections, likely due to differing long-term selection pressures. The observed genetic variability is consistent with the polyploid nature of the species and supports the presumed self-incompatible phenotype. This is the first study to report SSR fingerprints for ornamental cultivars and fruit-bearing selections, providing a potential tool for use in breeding programs. Full article

The Tsushima leopard cat (Prionailurus bengalensis euptilurus), an endangered feline endemic to Tsushima Island, Japan, faces critical threats due to its small and isolated population. Understanding its demographic history and genetic differentiation from continental populations is essential for conservation planning. In this study, we performed whole-genome sequencing of four Tsushima individuals and applied demographic inference methods, including pairwise sequentially Markovian coalescent (PSMC) and Sequentially Markovian Coalescent (SMC++), to reconstruct the historical effective population size (Ne) and estimate divergence times. PSMC revealed a population expansion between 200,000 and 100,000 years ago, followed by a long-term decline. SMC++ inferred a continuous decline and estimated that the divergence from the Korean leopard cat population occurred approximately 30,000–20,000 years ago. Genetic diversity analysis showed that the Tsushima population has significantly lower heterozygosity and higher inbreeding levels than continental populations. Genetic clustering based on genome-wide SNPs indicated that the Tsushima population is genetically closest to the Korean population, forming a northern cluster distinct from southern populations, such as Borneo and the Malay Peninsula. These findings provide valuable insights into the evolutionary history and genetic status of the Tsushima leopard cat and contribute critical data for the design of future conservation strategies targeting this unique insular lineage. Full article

Horizontal gene transfer (HGT), the non-Mendelian transfer of genetic material between organisms, is relatively frequent in prokaryotes, whereas its extent among eukaryotes remains unclear. Here, we raise the hypothesis of a possible cross-phylum HGT event involving 5S ribosomal DNA (rDNA). A specific type of 5S rDNA sequence from the anuran Xenopus laevis was highly similar to a 5S rDNA sequence of the genome of its flatworm parasite Protopolystoma xenopodis. A maximum likelihood analysis revealed phylogenetic incongruence between the gene tree and the species trees, as the 5S rDNA sequence from Pr. xenopodis was grouped along with the sequences from the anurans. Sequence divergence analyses of the gene region and non-transcribed spacer also agree with an HGT event from Xenopus to Pr. xenopodis. Additionally, we examined whether contamination of the Pr. xenopodis genome assembly with frog DNA could explain our findings but found no evidence to support this hypothesis. These findings highlight the possible contribution of HGT to the high diversity observed in the 5S rDNA family. Full article

Avian metapneumovirus subtype B (aMPV/B) is an economically significant pathogen in poultry, causing respiratory and reproductive disorders. In this study, 167 clinical samples were collected from commercial poultry farms across Thailand to investigate the prevalence, genetic diversity, and evolutionary dynamics of aMPV/B. Nested RT-PCR targeting the G gene revealed a positivity rate of 34.13% (57/167). Phylogenetic and Median-joining network analyses of sequenced amplicons identified two distinct Thai lineages: one genetically similar to vaccine strains and another of unknown origin. Divergence time analysis using a Bayesian framework estimated the time to the most recent common ancestor (tMRCA) of these lineages around 2006, with further sub-lineage diversification occurring around 2009 and 2016. These findings suggest that the circulating Thai aMPV/B strains likely stem from limited introduction events followed by local evolution. Lineage-specific amino acid substitutions within the G gene were identified, which may affect antigenic properties and immune recognition. This study highlights the molecular heterogeneity and ongoing diversification of aMPV/B in Thailand and underscores the need for sustained genomic surveillance and regionally tailored vaccination strategies. Full article

The Dalbergia genus, a morphologically diverse group within the Fabaceae family, encompasses species of significant value in furniture production and medicinal and aromatic applications. The taxonomy of Dalbergia has relied on morphological traits, chloroplast (cp) DNA fragments, and cp genomic data. However, genomic resources for tropical liana species within this genus remain scarce. In this study, we assembled and analyzed the cp genomes of 3 liana species—Dalbergia peishaensis, D. pinnata, and D. tsoi—and compared them with those of 26 other Dalbergia species to explore their cp genome characteristics and evolutionary patterns. We employed a combination of traditional cp genome analysis and methods adapted from plant whole-genome sequencing. Phylogenetic analysis revealed that D. peishaensis has a close relationship with D. cultrata, forming a recently diverged clade, whereas D. tsoi and D. pinnata are positioned within a basal clade of the Dalbergia genus, suggesting an earlier divergence. The Dalbergia cp genomes exhibit considerable variation in size, with evidence of pseudogenization, gene loss, and duplication observed in the three liana species. Notably, the infA gene, previously reported as absent in the chloroplast genomes of Dalbergia species, was identified in the cp genomes of these three liana Dalbergia species. A total of 4533 simple sequence repeats (SSRs) were identified, providing valuable insights into cp genome evolution and facilitating future population genetics studies, particularly when combined with the high structural variation observed in the genus through whole-genome analysis methods. Additionally, seven highly divergent regions were identified as potential DNA barcode hotspots. This study enhances the genomic characterization of liana Dalbergia species and offers a robust framework for future plant cp genome analyses by integrating methodologies originally developed for whole-genome studies. Full article

The nopal cactus, a plant from the Cactaceae family, holds significant economic and nutritional value for Mexico. This study aimed to enhance the genetic diversity and morphological traits of Opuntia velutina, a species cultivated as a vegetable nopal. A total of 1050 in vitro O. velutina explants were exposed to 15 different doses of gamma radiation from ⁶⁰Co gamma, ranging from 5 to 125 Gy. The lethal dose was above 50 Gy, with an LD₅₀ of 22.8 Gy for stimulating in vitro shoot growth. Shoots derived from doses between 5 and 50 Gy were subjected to in vitro shoot proliferation across four consecutive generations to stabilize morphological traits. Cluster analysis categorized the 178 irradiated shoots into 13 distinct morphological groups (CG1–CG13). Twenty-seven shoots exhibiting significant morphological improvements, such as a 50–100% increase in cladode length, up to a six-fold increase in shoot number, and up to a seven-fold increase in root number, were selected for molecular analysis of genetic diversity. Six primers were used with the Inter Simple Sequence Repeat (ISSR) molecular markers to examine genetic uniformity, yielding 54.5% polymorphic bands, indicating a high level of genetic variation. Both a UPGMA dendrogram and STRUCTURE-based Bayesian analysis confirmed the genetic divergence among the selected mutant lines. Overall, gamma irradiation effectively enhanced both phenotypic and genotypic diversity in O. velutina. This study corroborates that in vitro mutagenesis through gamma radiation is a viable strategy for generating novel genotypes with breeding potential within the Opuntia genus. Full article

Citrus tatter leaf virus (CTLV), a major pathogen threatening global citrus production, remains poorly characterized in terms of its regional genetic diversity and evolutionary dynamics. To address this gap, we conducted a comprehensive population genetic analysis of CTLV in Zhejiang Province, China, using 181 coat protein (CP) gene sequences—the largest regional CTLV dataset to date. Our analyses uncovered substantial genetic diversity among Zhejiang CTLV isolates. Phylogenetic reconstructions revealed that these isolates span multiple clades, closely aligning with global CTLV population structures, indicative of recurrent viral introductions and extensive regional circulation. Population structure analyses revealed significant genetic differentiation driven by geography, with Jinhua isolates forming a distinct cluster, and by host species, with Citrus reticulata ‘Criton’ isolates diverging from those in other citrus varieties. Selection pressure analysis indicated that while most CP polymorphic sites were under purifying selection, several clade-specific codons showed signatures of positive selection. These results offer new insights into CTLV’s population structure and localized evolutionary trajectories, enhancing our understanding of its regional adaptation and informing strategies for disease management and control of this globally significant pathogen. Full article

Edge populations can harbor unique genetic diversity shaped by historical isolation and play a key role in species’ resilience and range expansion under ongoing climate warming. The Aesculapian snake (Zamenis longissimus) reaches the northern limit of its range in Central Europe, where isolated populations may provide key insights into the species’ evolutionary potential and conservation priorities. In Bohemia (the western Czech Republic), only one reproducing population, in the vicinity of Stráž nad Ohří (SO), had previously been confirmed north of the species’ continuous distribution. Here, we report two additional reproducing populations recently discovered through long-term monitoring: one at the Želinský meander (ZM) and another in Central Bohemia (CB). The ZM population is autochthonous, viable, and genetically remarkable, harboring two divergent mitochondrial haplotypes: the widespread Eastern phylogeographical clade haplotype E1 and a novel haplotype, W10, belonging to the Western clade. This represents the first confirmed record of a Western clade haplotype in the Czech Republic, and only the second known locality within the species’ entire range where both clades coexist. In contrast, the CB population—founded by human-mediated translocation from SO—is expanding dynamically and is represented solely by E1, the only haplotype previously recorded in the country. Our study highlights the importance of incorporating genetic data into conservation planning and understanding species’ evolutionary potential. The mitochondrial diversity uncovered at the ZM exemplifies how historical processes, isolation, and lineage mixing shape contemporary genetic structure. Preserving such populations, which retain unique evolutionary diversity, will be critical for maintaining the resilience of Z. longissimus in Central Europe. More broadly, disjunct northern populations may serve as reservoirs of genetic diversity, enhancing adaptive potential and supporting future range expansion under climate change. Recognizing and conserving this diversity is essential not only for local persistence but also for species-level resilience in a rapidly changing environment. Full article

Rice blast disease, caused by the ascomycete fungus Magnaporthe oryzae (syn. Pyricularia oryzae), poses a severe threat to global rice production. Southern China, a major rice-growing region characterized by diverse agroecological conditions, faces substantial challenges from blast disease, yet our understanding of the genetic structure of M. oryzae populations in this region remains limited. Here, we analyzed 885 M. oryzae strains from 18 nurseries across four rice ecological regions in Southern China using a panel of genome-wide SNP markers. Phylogenetic and principal component analyses revealed three distinct clonal lineages: lineage I (58.19%), lineage II (21.36%), and lineage III (20.45%). Lineage I exhibited a broader geographic distribution compared to the other two lineages. Host-adapted divergence was observed across rice subspecies, with lineage III predominantly associated with japonica growing-regions, while lineages I and II mainly colonized indica rice-growing regions. Genetic diversity exhibited significant spatial heterogeneity, with the nucleotide diversity (π) ranging from 0.17 in South China to 0.32 in the Middle–Lower Yangtze River region, reflecting differential cropping systems. The predominantly negative Tajima’s D values across populations suggested recent expansion or selective sweeps, likely driven by host resistance pressures. High genetic differentiation between lineage I and other lineages contrasted with low divergence between lineages II and III, indicating distinct evolutionary trajectories. Furthermore, an uneven distribution of mating types among three genetic lineages was observed, suggesting limited sexual recombination within clonal lineages. The information obtained in this study may be beneficial in devising suitable strategies to control rice blast disease in Southern China. Full article

Background: Gloriosa superba L., commonly known as Glory Lily, is a medicinally valuable perennial climber native to tropical and subtropical regions of India. It is known for its rich alkaloid content, including colchicine and colchicoside, which contribute to its therapeutic potential in treating various ailments. Despite its pharmacological significance, genomic research on G. superba remains limited due to the lack of genetic markers, hindering molecular studies and breeding advancements. Methods: This study utilized a previously reported de novo transcriptome assembly of G. superba, identifying 14,672 EST-SSRs as genomic markers to assess genetic variations across different accessions. Genetic diversity was examined using SSR markers, while 20 morphological traits were systematically evaluated across 19 G. superba accessions from diverse geographic regions to provide insights into trait variability. Results: The most highly variable traits included plant height, number of leaves per plant, number of branches per plant, fresh pod yield, fresh seed yield, dry seed yield, number of pods per plant, leaf width, and internodal length, with coefficients of variation (CV) ranging from 63.53% to 22.45%. Intermediate CV values (10.05% to 18.75%) were observed in eight traits, while three traits (days to flowering, days to 50% flowering, and colchicine content) had low variation (<5%). Principal component analysis (PCA) accounted for 51.3% of phenotypic variation, with PC1 and PC2 contributing 29.4% and 21.9%, respectively. Clustering analysis grouped the 19 G. superba accessions into two main clusters and four sub-clusters, highlighting significant genetic divergence, with the highest dissimilarity (81.45%) observed between accessions from Arrupukottai and Pachmarhi. SSR analysis using 112 markers revealed high polymorphism but a relatively low heterozygosity index (H = 0.277) and PIC values of individual SSRs ranged from 0.26069 in RGM-51635 to 0.4534 in RGM-24219. Conclusions: The genetic divergence observed among the collected G. superba ecotypes provides valuable insights for future breeding programs aimed at enhancing cultivation efficiency and developing superior varieties with improved yield and colchicine content. Full article

Rodents are among the most abundant and ecologically diverse mammals, playing key roles in terrestrial ecosystems and often serving as reservoirs for various zoonotic and wildlife pathogens. Among these are protozoan parasites of the genera Hepatozoon and Theileria, which are known to infect a wide range of domestic and wild animals worldwide. However, little is known about the diversity and phylogenetic relationships of these hemoprotozoans in rodent hosts, particularly in the Arabian Peninsula. The aim of this study was to investigate the presence and genetic diversity of Hepatozoon sp. and Theileria sp. in rodents from different regions of Saudi Arabia and to determine potential reservoir species. A total of 111 rodents were captured and identified by molecular analysis of the mitochondrial 16S rRNA gene. Screening for parasites was performed using PCR amplification of the 18S rRNA gene, followed by sequencing, haplotype analysis, and phylogenetic reconstruction using both maximum likelihood and Bayesian inference methods. Our results represent the first molecular detection of Hepatozoon sp. in Arvicanthis niloticus (31.3%), Gerbillus cheesmani (26.5%), G. nanus (28.5%), and Rattus rattus (32.0%) and of Theileria sp. in G. nanus (21.5%) and R. rattus (24.0%) in Saudi Arabia. Haplotype network analysis revealed seven distinct Hepatozoon haplotypes forming a star-like cluster, suggesting host specificity. One divergent haplotype (Hap_2), 19 mutation steps apart, may represent a novel lineage. Phylogenetic analyses grouped Saudi Hepatozoon sequences with those from reptiles and rodents, forming a clade distinct from sequences isolated from felids and canids. In contrast, Theileria sequences showed low diversity, clustering with a single widespread haplotype found in rodents and ruminants in several regions. These findings significantly expand the current knowledge on rodent-associated apicomplexan parasites in Saudi Arabia, revealing novel Hepatozoon haplotypes and highlighting the role of rodents in the transmission of reptile-associated Hepatozoon spp. This study provides basic molecular data crucial to understanding host–parasite relationships and the potential public and veterinary health implications of these parasites in arid ecosystems. Full article