Durum wheat, the world's second most cultivated wheat species, is a staple crop, critical for global food security, including in Ethiopia where it serves as a center of diversity. However, climate change and genetic erosion threaten its genetic resources, necessitating genomic studies to support conservation and breeding efforts. This study characterized genome-wide diversity, population structure (STRUCTURE, principal coordinate analysis (PCoA), neighbor-joining trees, analysis of molecular variance (AMOVA)), and selection signatures (FST, Hardy-Weinberg deviations) in Ethiopian durum wheat by analyzing 376 genotypes (148 accessions) using an Illumina Infinium 25K single nucleotide polymorphism (SNP) array. A set of 7842 high-quality SNPs enabled the assessments, comparing landraces with cultivars and breeding populations. Results revealed moderate genetic diversity (mean polymorphism information content (PIC) = 0.17; gene diversity = 0.20) and identified 26 loci under selection, associated with key traits like grain yield, stress tolerance, and disease resistance. AMOVA revealed 80.1% variation among accessions, with no significant differentiation by altitude, region, or spike density. Landraces formed distinct clusters, harboring unique alleles, while admixture suggested gene flow via informal seed exchange. The findings highlight Ethiopia's rich durum wheat diversity, emphasizing landraces as reservoirs of adaptive alleles for breeding. This study provides genomic insights to guide conservation and the development of climate-resilient cultivars, supporting sustainable wheat production globally.

Genetic diversity in Schistosoma mansoni populations can impact the prevalence of resistance-conferring alleles, affecting treatment outcomes and control measures. Understanding how parasites are structured across and within populations is important to monitor and manage treatment impacts and the spread of drug resistance. This study assessed the genetic diversity and structure of S. mansoni populations under treatment using multi-locus microsatellite markers. Egg-positive stool samples from school-aged children in schistosomiasis-endemic communities were analyzed to obtain a binary matrix for GenAlEx 6.502 analysis. The markers were 78.57% polymorphic, with a mean allele number ranging from 2.50 to 4.75. Average population metrics were as follows: different alleles (Na) = 3.179, effective alleles (Ne) = 2.282, expected heterozygosity (He) = 0.442, and genetic identity (I) = 0.800, indicating high diversity. Diversity indices were particularly high in Tomefa (I = 0.931, He = 0.499), Manheam (I = 1.074, He = 0.557), and Adakope (I = 0.778, He = 0.448). Analysis of molecular variance revealed low differentiation among populations (4% of total variance, P = 0.001) and high differentiation among individuals (88% of total variance, P = 0.001), with FST = 0.04 and high gene flow (Nm = 5.959). A neighbor-joining tree and principal coordinate analysis indicated low population structuring. The Mantel test showed no significant correlation between genetic and geographic distances (r = 0.006, P = 0.148). The findings suggest high genetic diversity and gene flow, supporting the potential spread of alleles that may confer traits like drug resistance. An integrated approach is needed to achieve sustainable control of schistosomiasis.IMPORTANCEThis study is crucial as it provides a detailed analysis of Schistosoma mansoni genetic diversity and population structure in schistosomiasis-endemic communities under treatment. By employing multi-locus microsatellite markers, the research highlights significant genetic variation within and among populations, revealing high levels of genetic diversity and gene flow, as well as the presence of private alleles. These findings emphasize the potential for the emergence and spread of drug resistance and virulence traits, which can impact treatment efficacy and control measures. The absence of significant geographic isolation in population structure further emphasizes the need for a comprehensive approach to schistosomiasis control, as genetic factors rather than geographic barriers may drive resistance dynamics. This study informs strategies for sustainable control by integrating genetic insights into disease management efforts.

Two fish species Acanthurus mata and Ephippus orbis of the order Acanthuriformes were collected from Gopalpur-onsea, Bay of Bengal, where they were recorded for the first time. Both the fishes were identified using the conventional taxonomic methods followed by the molecular taxonomic method of DNA barcoding using the mitochondrial cytochrome c oxidase subunit I (COI) gene. All COI barcodes produced in this investigation were matched with reference sequences of anticipated species by morphological identification. Based on DNA barcodes, neighbour-joining, and maximum likelihood phylogenetic trees were constructed, and all of the specimens found were clustered according to their species-level taxonomic categorisation. To derive haplotype diversity, a median-joining network was built. The current study additionally looked at the number of variable sites, parsimony informative sites, nucleotide diversity, and variation in amino acids. Significant genetic variations were detected among A. mata species from various geographic regions. However, E. orbis still has highly conserved natural populations with no significant variations. The findings of this work provide information on the phylogeny, population dynamics, divergence time, and genetic diversity of both fish species as well as substantial validation for the use of DNA barcode sequences for tracking species diversity.

Walnut (Juglans regia L.), a key economic tree species, plays an essential role in China's forestry sector. Our previous surveys indicated that the incidence of walnut branch blight reaches up to 60% in Chengkou County and Beibei District, Chongqing City, China. Over the past two years, branch blight has been frequently observed from July to December on both young and old branches, with a high incidence leading to fruit drop rates of up to 60% or even total crop failure, highlighting this disease as one of significant threats to the sustainable development of the walnut industry. In the field, symptoms on infected stems progressed from reddish-brown to dark brown, and longitudinal cracking. Four infected stems were collected from the walnut variety Yucheng No. 1 in Chengkou County and Beibei District. Twenty-six pathogenic fungi were isolated by tissue isolation method, including fifteen fungi with similar culture morphology. The pathogen was identified through microscopic examination, morphological characterization, pathogenicity tests, and the cloning of polygenic genes. Microscopic examination of the pure culture after 7 days of growth revealed that the pycnidia were ellipsoidal, with colorless, transparent conidia that were either spindle-shaped or oval, containing 1 to 2 oil droplets. 7-day-old conidia (n = 20) measured 4.3 to 8.5 μm in length and 1.5 to 2.8 μm in width. The culture was subsequently purified by single-spore separation. The strain CKZ4-3 was successfully reisolated from symptomatic plants, and display white, sparse mycelia on potato dextrose agar (PDA) medium. Following, the isolate CKZ4-3 was selected for further investigation. The pathogenicity test was conducted by using the needle pricking method to create small wounds on six healthy Yucheng No. 1 trees planted in an experimental field, and then inoculating the bacterial pellets and blank PDA on these wounds. Results showed that isolate CKZ4-3 induced necrotic lesions on the stems, causing them to turn dark brown and spread vertically, with necrotic spots ranging from 5 to 12 mm. The strain CKZ4-3 was successfully reisolated from symptomatic plants by single-spore separation, fulfilling Koch's postulates. Genomic DNA was extracted from cultures aged seven days. DNA was extracted and the ITS, TUB, GAPDH, Apn and EF1-α genes were amplified using primers ITS1/ITS4 (White et al. 1990), T1/T2 (Glass et al. 1995), GDF/GDR (Templeton et al. 1992), Apn2-F/R(Udayanga et al. 2014), and EF1-728F/EF1-986R (Udayanga et al. 2014) respectively. Sequence analysis using BLASTn in GenBank revealed that the ITS-rDNA, TUB2, Apn and EF1-α sequences of CKZ4-3 showed 99% (579/584 nt), 99% (533/539 nt), 99% (533/539 nt), 98% (750/768 nt) and 92% (320/349 nt)similarity, respectively, to Diaporthe eres (accession GQ281804, MZ724024, KJ380958 and KJ210550). The ITS (PP785566), TUB2 (PV052969), GAPDH (PV052972), Apn2 and EF1-α sequences of isolate CKZ4-3 clustered with Diaporthe eres using "Construct/Test Neighbor-joining Tree" in MEGA11. Previous studies have recognized Diaporthe as a major pathogenic group responsible for walnut branch blight (Chen et al. 2014; Wu et al. 2016; Liu et al. 2020; López-Moral et al. 2020). However, this study provides the first report of Diaporthe eres causing necrotic lesions on walnut branches in Chongqing city, China. The findings of this study will contribute to the theoretical framework for the comprehensive management of walnut branch blight, underscoring the need for effective disease control strategies in walnut-producing regions worldwide.

In China and Southeast Asia, black goats command higher selling prices. However, the blind breeding practices carried out by farmers pose a threat to the original genetic diversity of the population. Therefore, the objective of this study is to conduct a systematic detection of the genetic diversity of native black goat breeds, aiming to provide a reference for the protection and improvement of these valuable native black goat breeds. Genetic diversity and population structure of 18 black goat breeds were estimated by utilizing 16 microsatellite markers. Subsequently, data analysis was carried out with the assistance of software like Phylip, Fstat, Arlequin, Structure. For the purpose of visualization, ITOL and Structure Selector were used to present the results in a visual manner. The mean number of alleles per population ranged from 4.75 to 9.56, with an average of 6.38. The observed heterozygosity of each breed ranged from 0.46 to 0.68, all of which were lower than the expected heterozygosity. The inbreeding coefficient (FIS) of the 18 breeds ranged from -0.003 to 0.376. Among them, the FIS values of Meigu goat (MG), Yimeng black goat, Yunling goat, Guizhou black goat and Ziwuling black goat were significantly higher than those under random rearrangement (p<0.05). All pairwise Fixation index between the Chinese black goat populations reached a significant level (p<0.05). Finally, the results of Bayesian model-based clustering and a neighbor-joining tree based on Nei's genetic distance showed these eighteen breeds can be further classified into seven genetic clusters. All breeds showed high genetic diversity. MG had excessive inbreeding, and CZ and LZ were at risk of losing original genetic traits. Similar geographical and climatic conditions might lead to similar genetic materials in different breeds.

In response to the emerging threat of insecticide resistance in malaria vectors, insecticides are being repurposed for vector control or developed de novo. Good stewardship of these finite new resources is essential if disease control programmes are to remain effective. This is dependent on timely data to help guide evidence-based decision-making for National Malaria Control programmes (NMCPs). By embedding genomics into cluster randomized control trials (cRCTs), we can perform surveillance and early detection of insecticide resistance variants to new and repurposed chemicals in natural field conditions, supporting effective stewardship.The LLIN Evaluation Uganda Project (LLINEUP) trial evaluated the efficacy of pyrethroid-piperonyl butoxide (PBO) and pyrethroids-only long-lasting insecticidal nets (LLINs). It was conducted in Uganda between 2017-2020 and was the largest cRCT to date, covering 40% of the country in 104 health sub-districts. We embedded genomic surveillance within LLINEUP to detect and track insecticide resistance variants. At baseline and throughout the trial, we sampled Anopheles mosquitoes with Prokopack aspirators and performed Illumina whole-genome sequencing.We show that An. funestus populations were relatively unaffected by the interventions, compared to An. gambiae s.l., which were markedly reduced six months following LLIN deployment. Standard approaches for describing genetic diversity and population structure e.g. fixation index (FST), Principal Component Analysis (PCA) and Neighbour-Joining (NJ) trees, were consistent with the density observations and suggestive of a single large An. funestus population in Uganda with little genetic differentiation. Genome-wide selection scans revealed strong signals of selection at the Resistance to pyrethroid-1 (RP1) locus and Cyp9k1, both loci previously implicated in pyrethroid resistance. We report two additional loci, eye diacylglycerol kinase (Dgk) (≅ 13.5Mb on the X chromosome) and O-mannosyl-transferase (TMC-like) (≅ 67.9Mb on 3RL) that showed signals of selection. Known DDT and permethrin resistance-associated variants at the Gste2 locus, L119F and L119V, were also identified. Over the trial period, changes in haplotype frequencies were observed in regions under selection, with more pronounced shifts in the PBO arm. Notably, there were significant reductions in the frequencies of swept haplotypes (measured by delta (Δ) H12) in the Dgk and Cyp6p9a regions, while significant increases in haplotype frequency were observed at Gste2 and Cyp9k1 loci.Our findings reveal the differential impact of the trial on An. gambiae s.l. and An. funestus densities and the differing responses of An. funestus populations to pyrethroid and pyrethroid-PBO selection pressure. These insights underscore the potential value of tailored, species- and region-specific vector control strategies, supported by regional genetic surveillance, to better control insecticide resistance evolution and spread. By embedding genomic surveillance in cRCTs we can facilitate the discovery of putative resistance variants and can provide evidence of their impact on vector control tool efficacy; both of crucial importance to evidence-based deployment of vector control tools by NMCPs.

The genus &lt;i&gt;Monoraphidium&lt;/i&gt; is a green microalgae distributed globally in freshwater ecosystems, and it is difficult to classify morphologically. Molecular genetic markers have been used for their taxonomy, although they have not been thoroughly evaluated. Here, we investigated three nuclear rRNA molecules (18S, internal transcribed spacer [ITS] + 5.8S, and 28S) and four chloroplast genes (&lt;i&gt;psbB&lt;/i&gt;, &lt;i&gt;psbC&lt;/i&gt;, &lt;i&gt;rbc&lt;/i&gt;L, and &lt;i&gt;tufA&lt;/i&gt;) using 16 &lt;i&gt;Monoraphidium&lt;/i&gt; strains consisting of 9 species. Upon comparisons of genetic diversity and marker performance evaluation, we found that ITS was the best marker for &lt;i&gt;Monoraphidium&lt;/i&gt; to discriminate each species, followed by &lt;i&gt;tufA&lt;/i&gt;. The taxonomic discrimination power of the ITS was supported by the neighbor-joining tree. In addition, a secondary structure of ITS2 combined with compensatory base changes showed the distinct differences among individual species of &lt;i&gt;Monoraphidium&lt;/i&gt;. These suggest that ITS may be the best marker for species differentiation of the coccoid green algae &lt;i&gt;Monoraphidium&lt;/i&gt;.

The northeast region of China plays a crucial role in crop production. The leaf beetle Monolepta hieroglyphica (Motschulsky, 1858) (Coleoptera: Chrysomelidae) has emerged as a potential threat to food security in the region. With a wide distribution spanning Asia and Russia, this beetle affects various crops. However, limited information is available regarding its occurrence patterns and genetic diversity among major crops in the region. Based on systematic observations across various hosts, coupled with genetic variation analysis using mitochondrial DNA markers, the main results were as follows. Leaf beetle occurrence varied among hosts, peaking from late July to mid-August, with maize and soybean fields exhibiting higher infestation rates compared with other crops. Notably, late-cultivated maize fields harbored the highest beetle numbers due to the species' preference for young leaves. The host transfer trajectory may have originated in soybean and weeds, with subsequent alternation between host plants and other crops, before the final migration to cabbage and late-cultivated maize fields. Genetic analysis revealed nine COI haplotypes, four COII haplotypes, eleven Cytb haplotypes, and twenty-one combined haplotypes. No clear relationship existed between genetic diversity and occurrence, and no distinct host-based genetic patterns emerged from neighbor-joining tree and haplotype network analyses. High gene flow rates were observed, likely contributing to decreased genetic variation. An analysis of molecular variance results indicated major genetic variation within populations, although genetic distance and haplotype distribution indicated divergence among host populations. These results provide foundational data for developing effective M. hieroglyphica pest management strategies.

The European species of the Cheilosia subgen. Neocheilosia Barkalov, 1983 (Diptera, Syrphidae) are revised. The identities of Cheilosia morio (Zetterstedt, 1838) and of its synonyms are reviewed, and C. scanica Ringdahl, 1937 is established as a junior synonym of C. morio. Cheilosia luteicornis (Zetterstedt, 1838) is re-installed as the name for C. morio of authors pro parte, not Zetterstedt. Cheilosia morio and C. luteicornis are redescribed, and lectotypes are designated for Eristalis lineata Wahlberg, 1843 and for E. luteicornis Zetterstedt, 1838 in order to ensure the consistent future interpretation of the names. The hitherto unknown male of Cheilosia barovskii Stackelberg, 1930 is described, and the female of C. barovskii is redescribed. We also provide updated distributional records and an identification key. Finally, we present a Neighbor-Joining tree for mtDNA COI barcodes of four species of the subgen. Neocheilosia.

Fraxinus platypoda Oliv. (Oleaceae), an ecologically and economically valuable tree species with key distribution areas in northwestern China, faces conservation challenges due to its fragmented groups and scarce individual numbers. To investigate the genetic consequences of this demographic crisis, we analyzed 65 individuals from 11 natural groups in this region using whole-genome resequencing. We identified a total of 60,503,092 single nucleotide polymorphisms (SNPs), and after further filtering, retained 3,394,299 SNPs for subsequent analysis. Population structure analysis (Neighbor-Joining tree, STRUCTURE, and kinship coefficients) revealed two distinct genetic clusters (K = 2), with principal component analysis (PCA) confirming this subdivision. Cluster I, composed of eight individuals from Groups 3, 5, 8, and 11, is highly differentiated from Cluster II and may be ancestral to it. Among the 11 groups, Groups 3 and 11 show a high genetic diversity and differentiation, with Tajima’s D &gt; 0, indicating a long evolutionary history and balancing selection. The remaining nine groups have a low diversity, low differentiation, and frequent gene flow, with Tajima’s D &lt; 0, suggesting directional selection. A mantel test showed no significant link between genetic variation and geographic isolation (p = 0.460). The high differentiation of Cluster I and gene flow of Cluster II are maintained by factors like evolutionary history and reproductive systems. Groups 3 and 11 are highlighted as important genetic resources deserving priority protection. This study offers key genomic data for conserving fragmented tree species and future adaptability research.

Potato (Solanum tuberosum L.), as one of the major food crops, is cultivated in both temperate and subtropical climatic regions worldwide. During the field survey conducted in December 2023, black to brown colored spots with dark brown to black margins were observed in the leaves of the potato cultivar Kufri Jyothi, grown annually to monitor pest and disease incidence at the Indian Council of Agricultural Research (ICAR) - Central Potato Research Institute (CPRI) Research Station, Ooty, Tamil Nadu, India (Latitude - 11.370796 N, Longitude - 76.664094 E, Elevation - 2110 m above mean sea level. As the disease progressed, the spots were scattered throughout the leaves and coalesced to form necrotic lesions. The disease incidence reached 40 - 45%, attributed by airborne inoculum spread. Tissues collected from the margin of the infected leaf (5 × 5 mm) were surface disinfected with 1% NaOCl for 1 min, 70% ethanol for 30 sec and rinsed with sterilized water for three consecutive times before incubation at 25 ± 1°C on the potato dextrose agar (PDA) medium for pathogen culturing. Five cultures were obtained through single spore isolation and denoted as PTAA-01 to PTAA-05. The colony morphology of all five isolates was identical, with a greyish-brown and black appearance on the upper and undersides of the Petri dishes. The mycelia were septate, light grey and had a geniculate brown conidiophore with a short conidial chain. Conidia were brown, short-beaked, obclavate to obpyriform in shape, one to six and zero to two transverse and oblique septa. The dimensions of the conidia (n = 50) are 18 - 53 x 9 - 14 (length × width) µm. Morphological characters of the pathogen were consistent with Alternaria alternata (Fr.) Keissl, described earlier by Simmons (2007). Genomic DNA was extracted from the representative isolate PTAA-01 using CTAB method (Murray and Thompson 1980). PCR was performed with primers ITS1 / ITS4 targeting internal transcribed spacer (ITS) sequence (White et al. 1990), gpd1/gpd2 for glyceraldehyde-3-phosphate dehydrogenase (GAPDH), PG3/PG2b for endopolygalacturonase (EndoPG), Alt a1F/Alt a1R for Alternaria major allergen gene and EF1-728F/EF1-986R for translation elongation factor (TEF) 1-α (Woudenberg et al. 2015). Amplified products were sequenced and deposited in NCBI GenBank with accession numbers; PP864706 (ITS), PP943430 (GAPDH), PP968830 (EndoPG), PQ031066 (Alt a1) and PQ031067 (TEF1-α) and all shared > 99% identity with A. alternata (GenBank accession numbers: MN919390, KX226447, KP123997, OK040811, and MZ648042), respectively. A neighbour-joining phylogenetic tree was constructed based on concatenated sequences of ITS, GAPDH, EndoPG, Alt a1, and TEF1-α using MEGA 11, where PTAA-01 isolates formed a clade with the strain of CBS 916.96 of A. alternata. For pathogenicity test, the conidial suspension (106 spores/ml) prepared from 15 days old culture was spray inoculated on one-month-old potato cultivar Kufri Jyothi in triplicates and maintained under glasshouse condition with an ambience of 16 h photoperiod, 20 - 25°C temperature and > 70% relative humidity. Symptoms appeared on the 5th day after inoculation and were identical to the natural symptoms observed earlier in the field. The reisolated pathogen had morphological and molecular procedures identical to those of A. alternata, fulfilling Koch's postulate test. While Lingwal et al. (2022) reported brown leaf spots of potatoes in Eastern parts of India, our study marks the first report in Southern India alerting the potato growers of this specific region to the A. alternata outbreak.

The SH3 genes are a group of well-studied antifungal coffee defense genes, which have been localized to a region in chromosome 3. A previous study screened this region for other antifungal defense genes, particularly, those implicated in defense against coffee leaf rust (CLR) and coffee berry disease (CBD). Three candidate defense gene loci have been identified, namely, an ethylene-responsive transcription factor 1B (ERF1B) gene, a chalcone synthase 2-like (CHS2) gene, and a major allergen Pru ar 1-like gene. For this study, the main goal is to evaluate and compare the sequences of these selected loci from a sample of Philippine coffee accessions, which consist of the four main varieties utilized in local production: Arabica (Coffea arabica), Robusta (C. canephora), Liberica (C. liberica var. liberica) and Excelsa (C. liberica var. dewevrei). DNA was extracted from young leaves and subjected to PCR amplification using newly designed primers. The PCR products were run through agarose gel electrophoresis after which, gel portions containing the target bands were excised and processed for bidirectional sequencing. Consensus sequences were constructed from the raw sequences using UGENE. Due to probable primer specificity issues, the CHS2 sequences were excluded from further analysis. In order to analyze the ERF1B and Pru ar 1-like gene sequences, MEGA11 was used for multiple sequence alignment, protein sequence prediction, and construction of neighbor-joining trees. The sequences were also cross-referenced against the GenBank database using BLAST. Results show that several of the sequences represent novel orthologs, especially those obtained from the Liberica and Excelsa samples. Furthermore, orthologs which are most likely linked to conferring greater resistance were determined. Most notable among these are the ERF1B sequences of a Red Bourbon (A-RB, NSIC-2008-Cf-A-05) and a Mundo Novo (A-MN) sample. Despite originating from Arabica samples, the A-RB and A-MN ERF1B orthologs show greater similarity to their counterparts in Liberica/Excelsa and Robusta samples, respectively. These orthologs are recommended for follow-up studies through additional in silico analysis and genotype-phenotype association so they can definitively be considered as target genes in future coffee breeding programs.

Lilium 'Siberia', is extensively cultivated and has high economical value in China due to its popularity as an ornamental lily. In August 2023, lily basal rot was observed on about 60% of two-year-old plants at the Liaoning Academy of Agricultural Sciences Multiplex greenhouse ( in an area of about 2000 m2 ) . Initial symptoms appeared on the base of the bulbs as brown lesions that expanded over time, and later the leaves turned yellow and about one month latter the whole plant died. To isolate the causal pathogen, tissues were collected from 5 symptomatic plants with basal rot. The infected bulbs were surface-sterilized with 75 % ethanol solution for 30 s after initial rinsing, followed by triple sterile-water washes, specimens were dried aseptically prior to pathogen isolation. Tissue sections 5 mm × 5 mm were transferred from plant lesion margins onto potato dextrose agar (PDA) medium after surface sterilization. Cultures were maintained at 25℃ for pathogen isolation. After 7 days, 3 consistent surface morphology strains(H1, H2 and H3) were prepared based on single spore isolates. After 10 to 15 days, mycelium had fully covered the plates. The hyphae were branched, septate, smooth, hyaline, Conidia were black, solitary, globose or subglobose, glossy aseptate of 8.3 - 11.4 μm × 12.4 - 14.9 μm (n=50) in size, and produced at the tips of hyaline and ampulliform conidiophores. The fungus showed similar morphological characteristics to Nigrospora oryzae (Wang et al. 2017). For molecular confirmation of the species identity, genomic DNA of three isolates (H1, H2 and H3) were extracted by the CTAB method (O'Donnell et al., 1998), and portions of three genes, the Intemal Transcribed Spacer (ITS) of the ribosomal RNA, the Translation Elongation Factor subunit 1-alpha (TEF1-ɑ) and the beta-tubulin (TUB2) genes were amplified by the PCR using the primers ITS1/ITS4,EF1-728F/EF-2 and Bt-2a/Bt-2b (Wang et al. 2017). A BLASTn analysis showed that the identity of the nucleotide sequences of isolates (H1, H2 and H3) were 99%(500/501bp; 488/488 bp; 495/499bp) for ITS, 99% (461/461 bp;466/467 bp;467/467 bp) for TEF1- ɑ; and 99% (331/333 bp; 376/384 bp; 381/388 bp) for the TUB2 sequences, with N. oryzae LC2702 in GenBank. The resulting sequences were submitted to GenBank under accession numbers PP203296, PP784618, PP784619 for ITS; PP417827, PP869279, PP886084, for TEF1-ɑ; PP448183, PP869277, PP869278 for TUB2 of isolates H1, H2 and H3 respectively. A neighbor-joining phylogenetic tree showed that the three isolates from Siberian lily clustered with the N.oryzae clade.Therefore, the isolates H1, H2 and H3 were identified as N. oryzae based on morphology and molecular evidence. One representative isolate(H1) was used for completing the Koch's postulates. A pathogenicity test was made on 1-year-old healthy Siberia lily bulbs, the bulbs were disinfected, using a sterile needle to prick the base of the bulbs, then they were planted in sterilized soil. A conidial suspension (1 × 106 conidia/ml) was used to water the planted lily bulbs once every 5 days, and the controls were watered with sterile water. Each treatment contained 30 bulbs, and experiment was repeated three times. After 15 days of inoculation at 25℃, the bulbs inoculated with H1 began to turn black and to rot, and black perithecia were visible. The control plants did not show disease and no pathogen was isolated from them. We reisolated the pathogen from infected tissues, after observation of the morphological characteristics and ITS sequence ( PQ686265 ) the reisolated fungus was identified as Nigrospora oryzae. According to Koch's Postulates, Nigrospora oryza was the pathogen causing lily basal rot. To our knowledge, this is the first report of basal rot on Lilium'Siberia'(Lilium spp.) caused by Nigrospora oryzae in China.

The recent emergence of new HIV-1 recombinant strains presents a new challenge to the control of HIV-1/AIDS and the development of an effective vaccine. We employed a near full-length genomic sequence analysis of a newly identified CRF85_BC recombinant strain in Ningxia, China, to determine its recombination pattern. Blood samples were collected from HIV-infected or AIDS patients in Ningxia in 2023. CRF85_BC subtype strains were detected from three samples using an in-house method, and one sample's near full-length genome sequence was also obtained. MEGA11, jpHMM, and Simplot software were used to identify subtypes and analyze recombination patterns. Neighbor-joining phylogenetic tree analysis showed that HIV-1 pol region sequences of three samples were CRF85_BC subtypes. One near full-length genome sequence of the recombinant strain was obtained, and jpHMM preliminarily judged that the recombinant strain was inserted with two subtype B fragments and two CRF01_AE fragments based on subtype C as the backbone. Further analysis using Simplot software revealed that the recombinant strain was the second-generation recombinant strain of CRF85_BC and CRF01_AE, and the recombination mode was based on the full-length genome of CRF85_BC, and CRF01_AE gene fragments that were inserted at positions 7365-8279 and 8431-9492, respectively. The results of the fragment phylogenetic tree verified its accuracy. One CRF01_AE and CRF85_BC second-generation recombinant strain was found in HIV-1 infected people in Ningxia, indicating that new HIV-1 recombinant strains continuously emerge and circulate in this region. Genomic surveillance of these recombinants should inform targeted interventions, such as prioritized contact tracing, to mitigate the formation of transmission clusters.

Guava (Psidium guajava L.) is one of the economically major fruit crops, abundant in nutrients and found growing in tropical-subtropical regions around the world. Ensuring sufficient genomic resources is crucial for crop species to enhance breeding efficiency and facilitate molecular breeding. However, genomic resources, especially microsatellite or simple sequence repeat (SSR) markers, are limited in guava. Therefore, novel genome-wide SSR markers were developed by utilizing chromosome assembly (GCA_016432845.1) of the "New Age" cultivar through GMATA, a comprehensive software. The software evaluated about 397.8 million base pairs (Mbp) of the guava genome sequence, where 87,372 SSR loci were utilized to design primers, ultimately creating 75,084 new SSR markers. After in silico analysis, a total of 75 g-SSR markers were chosen to screen 35 guava genotypes, encompassing wild Psidium species and five jamun genotypes. Of the 72 amplified novel g-SSR markers (FHTGSSRs), 53 showed polymorphism, suggesting significant genetic variation among the guava genotypes, including wild species. The 53 polymorphic g-SSR markers had an average of 3.04 alleles per locus for 35 selected guava genotypes. Besides, in this study, the mean values recorded for major allele frequency, gene diversity, observed heterozygosity, and polymorphism information content were 0.73, 0.38, 0.13, and 0.33, respectively. Among the wild Psidium species studied, the transferability of these novel g-SSR loci across different species was found to be 45.83% to 90.28%. Furthermore, 17 novel g-SSR markers were successfully amplified in all the selected Syzygium genotypes, of which only four markers could differentiate between two Syzygium species. A neighbour-joining (N-J) tree was constructed using 53 polymorphic g-SSR markers and classified 35 guava genotypes into four clades and one outlier, emphasizing the genetic uniqueness of wild Psidium species compared to cultivated genotypes. Model-based structure analysis divided the guava genotypes into two distinct genetic groups, a classification that was strongly supported by Principal Coordinate Analysis (PCoA). In addition, the AMOVA and PCoA analyses also indicated substantial genetic diversity among the selected guava genotypes, including wild Psidium species. Hence, the developed novel genome-wide genomic SSRs could enhance the availability of genomic resources and assist in the molecular breeding of guava.

Next-generation sequencing (NGS) technologies have revolutionized livestock genomics by enabling rapid, high-resolution genotyping of local populations with thousands of single nucleotide polymorphisms (SNPs), offering unprecedented accuracy and cost efficiency. This study presents the first comprehensive genomic assessment of the Denizli (DNZ) and Gerze (GRZ) chicken breeds, comparing them to commercial broiler and layer hybrid lines using the double digest restriction-site associated DNA sequencing (ddRADseq) technique. A total of 94,208 bi-allelic SNPs were common between DNZ and GRZ, while 33,284 SNPs were retained among all populations after the quality filtering process. Genetic diversity parameters were higher in native Turkish chicken breeds compared to hybrid lines in which minor allele frequency (MAF) was higher than 0.3 in DNZ and GRZ while it was lower than this value in commercial hybrid lines. Notably, DNZ displayed the highest observed (0.386) and expected (0.375) heterozygosity, whereas the broiler hybrid line showed the lowest heterozygosity (0.254), suggesting inbreeding depression (FIS = 0.241). The negative inbreeding coefficient values occurring due to random mating were observed in DNZ and GRZ chicken breeds, while this value was estimated at 0.118 in the layer hybrid line. Population structure analyses such as principal component analyses (PCA), genetic distance-based neighbor-joining (NJ) tree, ADMIXTURE, and TreeMix algorithm revealed that DNZ and GRZ were genetically distinct from both each other and commercial hybrid lines. The results of this study confirm that comprehensive conservation strategies are efficient approaches to keeping genetic variability at an optimal level without inbreeding. Moreover, this study demonstrates the efficacy of ddRADseq in generating high-throughput genotypic data, providing a cost-effective framework for genomic diversity and population structure studies in indigenous chicken breeds.

Abstract The study of small rodents is challenging because of the difficulty of observing and sampling them in the wild. Although noninvasive approaches have proven effective for large mammals, such an approach has rarely been applied to rodents. Here, we describe a novel noninvasive approach for sampling rodent hairs in tropical forest and caves in Gabon, and present cytochrome b sequence data from hair samples obtained using this technique. Twenty-six unknown rodent hair samples were randomly selected for this study from a larger set of samples collected from 2 sites in Gabon (Lastoursville and Franceville). These samples were captured using 3 types of hair traps made from 20 cm long cylindrical tubes of plastic sheathing composed of either: (i) 50-mm diameter red electric cable; (ii) gray polyvinyl chloride (PVC) pipes; or (iii) a larger PVC pipe of 100-mm diameter. Traps were placed along ~200 m long transects laid either on the forest floor, on tree trunks, or within caves and baited with a tethered palm nut. From this sample subset, we were able to obtain a 429-bp fragment of the mitochondrial cytochrome b gene from 17 samples. Nearly all samples could be identified to the species level using a neighbor-joining tree analysis based on published sequences. Five murid rodents were identified (Praomys petteri, P. missonei, Lophuromys spp., Malacomys longipes, and Grammomys spp.) and 1 Red-legged Sun Squirrel (Heliosciurus rufobrachium). This study shows that it is possible to amplify and sequence hair samples collected noninvasively from small forest rodents in the tropics and that such an approach could provide important genetic data on species that would otherwise be difficult to study.

Acer truncatum, originating in China, is an ornamental tree species with high economic value. In September 2022, a new leaf spot disease was observed on seedlings of A. truncatum in a tree nursery from the Jiangsu Academy of Forestry (118°45'517.30″E, 24 31°51'27.94″N) in China. According to statistics, 62.5% of 1600 A. truncatum seedlings suffered from the disease. The first symptoms were black to brown spots appearing on the infected leaves. Subsequently, the spots gradually expanded into larger areas, and finally the entire leaf turned yellow and fell off. The diseased leaves were collected and sections of 3 to 4 mm were excised from the margins between healthy and diseased tissues, surface sterilized in 75% ethanol for 30 sec. and 1.5% NaClO for 90 sec., rinsed three times in sterilized distilled water, plated on potato dextrose agar (PDA) and incubated at 25℃ in darkness. Pure cultures were obtained by monosporic isolation. Six fungal cultures with similar morphological characteristics were obtained from the infected tissues, and they accounted for 70% of the total isolates. Colonies were initially white but turned dark gray following 7 days of incubation at 25°C in the dark. To induce sporulation, colonies were grown on 2% water agar and incubated under UVA light at 25°C for two weeks. The conidiophores produced conidia, and conidia were hyaline, unicellular, nonseptate, ellipsoidal to fusiform, externally smooth, thin-walled, and were 15.3 to 20.4 × 4.5 to 7.4 μm (n=35, counted from the two selected isolates). These characteristics were consistent with the description of Neofusicoccum sp. (Kirk et al. 2008). Isolates YBF2-1 and YBF5-1 were selected as representative for molecular identification. The internal transcribed spacer region (ITS), the translation elongation factor 1-alpha gene (EF1-α), and the beta-tubulin gene (TUB2), using the primer pairs ITS1/ITS4 (White et al. 1990), EF1-728F/EF1-986R (Alves et al. 2008), and Bt2a/Bt2b (Glass and Donaldson 1995) were amplified, respectively. The obtained ITS (GenBank Accession No. PP980685, PQ222752), EF1-α (No. PQ009204, PQ227810), and TUB2 sequences (No. PP993456, PQ227811) all showed >99% homology with several GenBank sequences of Neofusicoccum parvum (MK370685, KC818612 for ITS; MH118932, KJ126847 for EF1-α; and MN318109, OL456719 for TUB2, respectively). A neighbor-joining phylogenetic tree was generated by combining all sequenced loci in MEGA7. The two isolates were identified as N. parvum. To test pathogenicity, 15 leaves on three one-month-old A. truncatum seedlings (five leaves from each seedling) were wounded with a sterile needle inoculated with 20 μL conidia suspension (1×106 spores/mL) on the left sides of the leaves, using isolate YBF2-1, while the same size droplet of sterilized water was used on the right sides of leaves. Each plant was separately covered with clear polyethylene bags to maintain about 80% relative humidity at 25℃. After 5 days of inoculation, typical symptoms were found on the left sides of treated leaves, and no symptoms occurred on the right sides of the leaves (the control). The inoculation experiment was conducted three times. Subsequently, the same fungus was reisolated and identified from six leaves of three inoculated seedlings. This is the first report of N. parvum on A. truncatum in the world, and it provides an important reference for the biology and epidemiology of N. parvum.

Sugarcane, an economically significant crop, is facing huge challenges from sugarcane mosaic disease (SMD), primarily caused by RNA viruses. During a regular field disease survey of sugarcane in China in June 2023, sugarcane (LC05-136) leaves from Nanning, Guangxi provinces, displayed a mild mosaic pattern. This differs from typical symptoms of sugarcane streak mosaic virus (SCSMV), sugarcane mosaic virus (SCMV), or sorghum mosaic virus (SrMV). To identify the causing pathogen, we purified virions from sugarcane leaves using the method described before. Total RNA was extracted from purified suspension using QIAamp MinElute Virus SpinKit following the manufacturer's protocol (Qiagen). Initially, RNA was reverse transcribed using Superscript III reverse transcriptase (Life Technologies) with the primer primK random. Subsequently, cDNA synthesis of the second strand was performed with Klenow enzyme (NEB) and used a specific primer A to amplify. An RNA-Seq library was constructed with VAHTS®UniversalPlusDNALibrary PrepKit for Illumina (Vazyme). The product was analyzed through high-throughput sequencing (HTS) using a DNBSEQ-T7 platform by Chengdu Xinshiji Biotechnology Co., LTD, yielding 108,896,756 raw reads (length 150 nt, total size >10 Gb) and 373968 viral effective reads were identified by Kraken2. Next, Diamond was employed to align the contigs with the NR virus library and aligned by BLASTn. HTS resulted in the identification of five contigs (ranging from 662 to 6697 nt) of sugarcane mild mosaic virus (SCMMV, genus Ampelovirus (related, unclassified viruses), family Closteroviridae). By rapid amplification of 5' and 3' cDNA ends (Vazyme), the full length of SCMMV sequence was confirmed showing by BLASTn with a higher identity (98.69%) to a SCMMV isolate PSR07106 (GenBank accession no.MN116751.1), thus we designated it as SCMMV-GX1 isolate (GenBank accession no. PP920681). Neighbor-joining tree analysis of full-length genomes of SCMMV indicates that SCMMV-GX1 is most closely related to SCMMV-PSR07106 but forms a distinct branch. This suggests SCMMV-GX1 has some variations compared to those from other regions. To ascertain whether SCMMV is widespread in sugarcane plantations, we collected 28 leaf samples (included the sample through HTS) from sugarcane plants in Hainan, Guangxi, and Yunnan provinces. These samples, which exhibited varying levels of mosaic symptoms, were analyzed using RT-PCR with specific primers (SCMMV-TF and SCMMV-TR) targeting the 264-bp conserved P24 gene of SCMMV. Amplicons of expected size were obtained from 11 samples: Hainan (4/6), Guangxi (3/8), and Yunnan (4/14) and confirmed by sequencing. Based on sampling data, the estimated field incidence of SCMMV is approximately 2%. It has been reported that both SCMMV and SCBV can be transmitted by pink sugarcane mealybug (Saccharicoccus sacchari). Thus, we tested our samples for the presence of SCBV by PCR and identified a co-infection rate of 72.73% for both SCMMV and SCBV across all the samples. Furthermore, SCMMV-GX1 sample was SCBV-negative and the mild mosaic symptoms were probably caused only by SCMMV. Notably, SCMMV has been previously identified in Africa, the Caribbean, America, and Southeast Asia, and this study represents the first report of SCMMV in China.

BackgroundEthiopian mustard (Brassica carinata (A) Braun) is a promising oilseed crop with the potential for sustainable biofuel and bio-industrial applications. Despite the presence of diverse germplasms in Ethiopia, their genetic diversity remains largely unexplored. This study evaluated the genetic diversity and population structure of 188 B. carinata genotypes using high-density Single Nucleotide Polymorphism (SNP) markers generated though DArTseq™ Genotyping-by-Sequencing (GBS). Of the 15,515 identified DArTSeq SNPs, 3,793 high-quality markers were retained and used to analyze the genetic diversity and population structure.ResultsThe results from STRUCTURE, principal coordinate analysis (PCoA), and neighbor-joining tree analyses revealed two slightly distinct subpopulations, with Pop1 predominantly comprising genotypes from the Oromia and Amhara regions (86.17%), whereas Pop2 primarily consisted of released varieties, suggests the influence of targeted selection. Despite the presence of subpopulations, PCoA indicated a relatively limited overall genetic diversity among the genotypes. Analysis of Molecular Variance (AMOVA) revealed higher genetic variation within populations (65.19%) than between populations (34.81%), resulting in low genetic differentiation (PhiPT = 0.02) and high gene flow (Nm = 5.74). Notably, subpopulation formation was not strongly correlated with geographical origin, highlights that factors beyond geography, such as gene flow and selection pressure, may have played a significant role in shaping the observed genetic diversity. Genetic diversity indices revealed a slightly low-to-moderate variation within the B. carinata populations, as evidenced by the slightly low expected heterozygosity (He = 0.21) and moderate polymorphic information content (PIC = 0.36).ConclusionOverall, this study revealed a moderate level of genetic diversity within the evaluated B. carinata genotypes. The results offer valuable insights into the genetic structure of this species and highlight the need for targeted strategies to enhance genetic diversity in future breeding initiatives and conservation efforts.