Bp Sequence Research Articles

Analysis of Multiple PCR Bands in Drimia Species Obtained by R-Gene Specific Degenerate Primers

Many studies confirmed that degenerate primers LM638 and LM637 amplify NBS-LRR Type R gene encoding sequences in both monocots and dicots. In addition, these primers also amplify nonspecific multiple bands along with specific amplification. The current study aims to explore the structure, role and reason for nonspecific bands in the amplification. The genomic DNA-degenerate PCR method was used to isolate the NBS-LRR type R-genes in Drimia species (synonym Urginea). Agarose gel electrophoresis was carried out for separation and visualization of amplified bands. The kit-based gel extraction method was followed to purify the PCR bands. Purified PCR bands were subjected to TA cloning. The plasmids which contain desired PCR bands were sequenced using the Sanger sequencing method. Multiple sequence alignment tool CLUSTALW was used to align sequences and MISA-Web tool was used to identify simple sequence repeats (SSR). The results of the study revealed that multiple sequence analysis of PCR bands of 600bp/500bp showed random deletions, presence of indels and frameshift mutations in the alignment. The sequence alignment also showed monomorphic sites between two sequences. Both 600 and 500bp were devoid of simple sequence repeats and the ORF finder confirmed the presence of irregular stop codons in the 600 bp sequences. The multiple sequence alignment tool was used in disclosing the structure and ancestor relationship between aligned Drimia sequences. The current study would help to explore pseudo genes in the genome of Drimia and to differentiate the orthologous and paralogous relationships in the sequences.

Cloning and characterization of heat shock transcription factor 1 and its functional role for Hsp70 production in the sea slug Onchidium reevesii

To investigate the regulatory role of heat shock transcription factor 1 of sea slug Onchidium reevesii (OrHSF1) on Hsp70 expression in the sea slug under stress , the OrHSF1 gene was cloned and bioinformatics analysis was performed, then the gene and protein expressions by RNA interference (RNAi) mediated knockdown of OrHSF1 expression were measured to clarify the regulatory relationship between OrHSF1 and Hsp70 under low-frequency noise (LFN) stress. Our study was the first to clone a 1572 bp sequence of the OrHSF1 gene, with the sequence coding for amino acids (CDS) being 729 bp, encoding 243 amino acids. O. reevesii shared a close evolutionary relationship with mollusks such as the Aplysia californica. OrHSF1 gene is widely expressed in different tissues of sea slugs, with the highest expression in the intestine and the lowest in the reproductive glands. Furthermore, we used RNA interference (RNAi) as a tool to silence the OrHSF1 gene in the central nervous system (CNS) and the results indicated that gene silencing was occurring systematically in the CNS and the suppression of OrHSF1 expression by RNAi-mediated gene silencing altered the expression of Hsp70; besides, the expression trends of OrHSF1 gene and Hsp70 were consistent in the 3 and 5-day RNAi experiment. Moreover, in sea slugs injected with siHSF1 and exposed to LFN, the mRNA expression and protein expression of Hsp70 in the CNS were significantly decreased compared to the low-frequency noise group (P < 0.05). This study demonstrated that OrHSF1 regulates Hsp70 expression in marine mollusks under low-frequency noise, and HSF1-Hsp70 axis plays a key role in stress response.

Parasitological and molecular identification of cestode Bothriocephalus scorpii sensu stricto in the new host Chelidonichthys lucerna (L. 1758) (Triglidae, Scorpaenoidei) from the North Sea

A specimen of female tub gurnard (Chelidonichthys lucerna) caught as bycatch in commercial saithe, Pollachius virens, fisheries near the Shetland Islands was identified as a new definitive host for the cestode Bothriocephalus scorpii (Bothriocephalidea) sensu stricto. It was also the first Cestoda species recorded in tub gurnard. However, as shown in our study, the identification of complex species such as Bothriocephalus scorpii based only on external characteristics had to be supplemented with molecular marker analysis to determine the taxonomic status of the specimen. Therefore, to successfully identify the parasite specimen, DNA was extracted from it, and a partial sequence of lsrDNA was amplified and the PCR product was subjected to 2 × 300 bp PE sequencing with 10,000× coverage on MiSeq. A BLAST search using the 346 bp sequence showed 100% similarity to the lsrDNA sequence of B. scorpii deposited in GenBank under accession number AF286942. Relatedness between the sequence of B. scorpii found in our study and the 20 most similar records from GenBank was identified using a phylogenetic tree constructed under maximum likelihood. Our study proves that next-generation sequencing of partial lsrDNA supplemented the morphological identification of the parasite specimen and can be applied in future parasitological studies.

Molecular characterization of gonadotropin-releasing hormone receptor and its expression profiling in response to HCG stimulation in striped murrel, Channa striata (Bloch, 1793)

The gonadotropin releasing hormone receptors (GnRHR) play an important role in the activation of GnRH and elicit the release of gonadotropins that plays an important role in maturation and spawning. In the present work, molecular characterization of the GnRHR gene of snakehead murrel, Channa striata was carried out. The full-length cDNA of GnRH receptors of the 1581 bp sequence, which encodes 440 amino acids was identified by RACE-PCR. Signal peptide analysis confirmed that GnRHR is a non-secretory protein, and hydropathy profiles indicated its hydrophobic nature. The deduced amino acid sequences of the GnRHR showed the expected conserved domains, which include seven membrane-spanning domains, two potential N-linked glycosylation sites (631 Asp, 561 Asp), and 32 sites phosphorylation sites of serine and threonine residues. A homology search of GnRHR cDNA sequence revealed 88 % identity with Channa argus, followed by 85 % and 83 % sequence identities with Lates calcarifer, and Anabas testudineus at the protein level. Phylogenetic analysis depicted a close association with Channa argus and other fish species. Our findings showed differential GnRHR expression during different reproductive stages, with higher expression after HCG administration. Expression profiling revealed that GnRHR is highly expressed in the brain and testis at 16 h post-HCG injection, while it was neutrally regulated in female ovarian tissues. This study provides full-length coding sequence information of the GnRHR gene and will help to understand the reproductive biology of murrel using expression studies and devise strategies for induced breeding.

A novel RofA-family transcriptional regulator, GadR, controls the development of acid resistance in Listeria monocytogenes.

The ability to survive the acidic conditions found in the stomach is crucial for the food-borne pathogen Listeria monocytogenes to gain access to the mammalian gastrointestinal tract. Little is currently known about how acid resistance is regulated in this pathogen and why this trait is highly variable between strains. Here, we used comparative genomics to identify a novel RofA-family transcriptional regulator, GadR, that controls the development of acid resistance. The RofA family of regulators was previously found only in a small group of bacterial pathogens, including streptococci, where they regulate virulence properties. We show that gadR encodes the dominant regulator of acid resistance in L. monocytogenes and that its sequence variability accounts for previously observed differences between strains in this trait. Together, these findings significantly advance our understanding of how this important pathogen copes with acid stress and suggest a potential molecular target to aid its control in the food chain.

Regulatory effect of NK homeobox 1 (NKX2.1) on melanocortin 4 receptor (Mc4r) promoter in Mandarin fish.

The melanocortin 4 receptor (MC4R) is a G protein-coupled transporter that mediates the regulation of thyroid hormones and leptin on energy balance and food intake. However, the mechanisms of transcriptional regulation of Mc4r by thyroid hormone and leptin in fish have been rarely reported. The messenger RNA expression of Mc4r gene was significantly higher in brain than those in other tissues of mandarin fish. We analyzed the structure and function of a 2029 bp sequence of Mc4r promoter. Meanwhile, overexpression of NKX2.1 and incubation with leptin significantly increased Mc4r promoter activity, but triiodothyronine showed the opposite effect. In addition, mutations in the NKX2.1 binding site abolished not only the activation of Mc4r promoter activity by leptin but also the inhibitory effect of thyroid hormones on Mc4r promoter activity. In summary, these results suggested that thyroid hormones and leptin might regulate the transcriptional expression of Mc4r through NKX2.1.

McAPRR2: The Key Regulator of Domesticated Pericarp Color in Bitter Gourd.

Pericarp color is a crucial commercial trait influencing consumer preferences for bitter gourds. However, until now, the gene responsible for this trait has remained unidentified. In this study, we identified a gene (McAPRR2) controlling pericarp color via a genome-wide association study (GWAS) utilizing the resequencing data of 106 bitter gourd accessions. McAPRR2 exhibits three primary haplotypes: Hap1 is a wild type with a green pericarp, Hap2 is a SA (South Asian) and SEA (Southeast Asia) type with a green pericarp, and Hap3 is primarily a SEA type with a light green pericarp. The McAPRR2 haplotype is significantly correlated with both pericarp color and ecological type. Importantly, McAPRR2 with the light green pericarp demonstrated premature termination due to a 15 bp sequence insertion. The phylogenetic tree clustered according to pericarp color and ecological type, using SNPs located in the McAPRR2 gene and its promoter. High πwild/SEA and πSA/SEA values indicate high nucleotide diversity between wild and SEA types and between SA and SEA types in the McAPRR2 gene. The haplotypes, phylogenetic tree, and nucleotide diversity of McAPRR2 suggest that McAPRR2 has undergone domestication selection. This study identifies McAPRR2 as the key gene determining pericarp color in bitter gourds and introduces a novel insight that McAPRR2 is subject to domestication selection.

Global analysis of seed transcriptomes reveals a novel PLATZ regulator for seed size and weight control in soybean.

Seed size and weight are important factors that influence soybean yield. Combining the weighted gene co-expression network analysis (WGCNA) of 45 soybean accessions and gene dynamic changes in seeds at seven developmental stages, we identified candidate genes that may control the seed size/weight. Among these, a PLATZ-type regulator overlapping with 10 seed weight QTLs was further investigated. This zinc-finger transcriptional regulator, named as GmPLATZ, is required for the promotion of seed size and weight in soybean. The GmPLATZ may exert its functions through direct binding to the promoters and activation of the expression of cyclin genes and GmGA20OX for cell proliferation. Overexpression of the GmGA20OX enhanced seed size/weight in soybean. We further found that the GmPLATZ binds to a 32-bp sequence containing a core palindromic element AATGCGCATT. Spacing of the flanking sequences beyond the core element facilitated GmPLATZ binding. An elite haplotype Hap3 was also identified to have higher promoter activity and correlated with higher gene expression and higher seed weight. Orthologues of the GmPLATZ from rice and Arabidopsis play similar roles in seeds. Our study reveals a novel module of GmPLATZ-GmGA20OX/cyclins in regulating seed size and weight and provides valuable targets for breeding of crops with desirable agronomic traits.

Two different types of tandem sequences mediate the overexpression of TinCYP51B in azole-resistant Trichophyton indotineae.

Trichophyton indotineae is an emerging dermatophyte that causes severe tinea corporis and tinea cruris. Numerous cases of terbinafine- and azole-recalcitrant T. indotineae-related dermatophytosis have been observed in India over the past decade, and cases are now being recorded worldwide. Whole genome sequencing of three azole-resistant strains revealed a variable number of repeats of a 2,404 base pair (bp) sequence encoding TinCYP51B in tandem specifically at the CYP51B locus position. However, many other resistant strains (itraconazole MIC ≥0.25 µg/mL; voriconazole MIC ≥0.25 µg/mL) did not contain such duplications. Whole-genome sequencing of three of these strains revealed a variable number of 7,374 bp tandem repeat blocks harboring TinCYP51B. Consequently, two types of T. indotineae azole-resistant strains were found to host TinCYP51B in tandem sequences (type I with 2,404 bp TinCYP51B blocks and type II with 7,374 bp TinCYP51B blocks). Using the CRISPR/Cas9 genome-editing tool, the copy number of TinCYP51B within the genome of types I and II strains was brought back to a single copy. The azole susceptibility of these modified strains was similar to that of strains without TinCYP51B duplication, showing that azole resistance in T. indotineae strains is mediated by one of two types of TinCYP51B amplification. Type II strains were prevalent among 32 resistant strains analyzed using a rapid and reliable PCR test.

First Report of Muskmelon Fruit Rot Caused by Fusarium sulawesiense in China.

Muskmelon(Cucumis meloL.) is a widely cultivated and economically important fruit crop worldwide. In June 2022, fruitrot symptoms were observed on ripening muskmelons (cv. Boyang) in Shouguang City (36.81°N 118.90°E) of China. To determine the causal agent, we surveyed 200 muskmelon plants in about 1000 m2 of planting area and collected diseased muskmelons. Approximately 20% of muskmelon fruits had symptoms, and yield loss averaged 20%. Water-soaked lesions were observed on the surface and the fruit rotted from inside. Lesions were covered with white mycelium. Rotted fruit were surface-disinfested with 1% NaOCl for 1 min, 75% ethanol for 30 s, and washed three times with sterile water. Pieces (1 cm3) were cut from the disinfested fruit, placed on potato dextrose agar (PDA), and incubated at 25°C for 1 week. Ten isolates with similar morphology were obtained and isolates SG66 and SG68 were selected for further characterization. Colonies maintained on PDA in the dark had an average radial growth rate of 10-12 mm/d at 25°C. Surface was white, velvety to felty mycelium. Reverse was white to pale wheat. Diffusible pigments were absent. On carnation leaf agar, sporodochia appeared as slimy dots, macroconidia were 3- to 5-septate, 20-35 × 3-5 μm, falcate, with a pronounced dorsiventral curvature, with blunt to papillate apical cell, and barely to distinctly notched basal cell. Microconidia and chlamydospores were not observed. These morphological characteristics were consistent with descriptions of Fusarium sp. DNA was extracted from isolates SG66 and SG68 using a CTAB method. Nucleotide sequences of the internal transcribed spacers (ITS) (White et al. 1990), calmodulin (CAM), RNA polymerase II second largest subunit (RPB2), and translation elongation factor 1-α gene (TEF1) (Xia et al. 2019) were amplified using generic primers, the products sequenced, and sequences deposited in GenBank (ITS: OP251362, OP251363; CAM: OP266024, OP266025; RPB2: OP266028, OP266029; TEF1: OP266026, OP266027). Isolates SG66 and SG68 clustered with Fusarium sulawesiense (85% bootstrap) (Maryani et al. 2019). The Fusarioid-ID database pairwise alignment of ITS (526 bp), CAM (534 bp), RPB2 (861 bp), and TEF1 (636 bp) sequences from isolate SG66 showed 99.6% (98.9% coverage), 100% (100% coverage), 100% (100% coverage) and 100% (98.4% coverage) similarity with the corresponding sequences (GQ505730, LS479422, LS479855 and GQ505641), respectively, of the reference strains of F. sulawesiense (InaCC F940 and NRRL 34059). To perform a pathogenicity test, 10 μl of conidial suspensions (1 × 106 conidia/ml) were injected into ten muskmelon fruit using a syringe, and ten control fruit were inoculated with 10 μl of sterile distilled water. The test was repeated three times. After 7 days at 25°C, the pulp of all inoculated muskmelons began to rot, and the lesion expanded from the inside to the fruit surface at the injection site and became covered with white mycelia. No symptoms developed on the control fruit. The fungus was successfully re-isolated from infected tissues and confirmed as F. sulawesiense by morphological and phylogenetic analyses. F. sulawesiense has previously been reported onyellow melon (Canary) in Brazil (Lima et al. 2021) and on a range of hosts, including Luffa aegyptiaca, in China (Wang et al. 2019). To our knowledge, this is the first report of muskmelon fruit rot caused by F. sulawesiense in China.

Fusarium pernambucanum Causing Leaf Yellow Spot on Melon (Cucumis melo L.), a New Disease in China.

Melon (Cucumis melo L.) is a member of the Cucurbitaceae family, and is an important economic and horticultural crop. In March 2022, melon plants in greenhouses exhibited severe leaf yellow spot symptoms in Changjiang County (109°13'N, 19°28'E), Hainan Province. The incidence of the disease was about 30-50%. Lesions initially appeared as yellow dots on leaves and expanded irregularly. Gradually, brown spots appeared, and finally the whole leaves turned yellow and resulted in blighting and death of foliage (Figure 1.). A total of four symptomatic plants were sampled from about 0.2 ha of an area. Symptomatic leaves were excised, surface disinfected with 2% (w/v) NaOCl, rinsed three times with sterile distilled water, and placed on potato dextrose agar (PDA) followed by incubation at 25°C in the dark for 5 days. The pure cultures were obtained by the hyphal-tip method. A total of eight fungal isolates with similar colony characteristics were recovered from the four symptomatic plants. Three DNA fragments (ITS, TEF1, and RPB2) of the eight isolates showed 100% sequence identity based on the molecular identification methods described below. Therefore, one of the isolates, M2JP-3, was chosen for identification and test of the pathogenicity. The colony of M2JP-3 on PDA at 25°C for 5 days was white with yellow-brown pigmentation in the center (Figure 2A-B). From 10-day-old cultures grown on CLA (Fisher et al. 1982), macroconidia (n = 50) were falcate, slender, curved dorsiventrally, tapering towards both ends, 3 to 7 septate, and measured 24.5 to 52.1 x 3.7 to 4.7 μm. The microconidia (n = 50) were straight or slightly curved, septate 0 to 2, and measured 9.9 to 16.3 x 2.5 to 3.7 μm (Figure 2C-E). For molecular identification, genomic DNA was extracted using the method previously described (Khan et al. 2021),the internal transcribed spacer (ITS), translation elongation factor 1α (TEF1) and DNA-dependent RNA polymerase subunit II (RPB2) were amplified, respectively, using primers ITS1/ITS4 (White et al. 1990), EF1/ EF2 (O'Donnell et al. 1998), and 5F2/7cR (Reeb et al. 2004). The 529 bp (ITS), 723 bp (TEF1), and 965bp (RPB2) sequences were deposited in GenBank with acce. nos. OP303211, OP312675 and OP312674, respectively. A phylogenetic tree was constructed using the concatenated three gene sequences of M2JP-3 and that of the Fusarium incarnatum-equiseti species complex (FIESC) (Xia et al. 2019) based on Maximum Likelihood (Figure 3). M2JP-3 was grouped together with the F. pernambucanum strain NRRL 32864 (accession no. GQ505702 for ITS, GQ505613 for TEF1and GQ505791 for RPB2), and shared 100% concatenated sequence identity. For pathogenicity tests of M2JP-3, seeds of melon cultivar Jinmeiren were surface disinfected and sowed in soil in three replicated pots in a greenhouse at 26 °C under natural light. Healthy leaves of the melon plants were wounded with needles and inoculated with mycelial plugs of M2JP-3 or PDA plugs as control. . Symptoms similar to the original greenhouse symptoms were observed at 7 days after inoculation (Figure 4). The control leaves were asymptomatic. The same fungus was reisolated from the inoculated leaves, as identified based on morphology and molecular evidence, which confirmed the Kochs' postulates. To our knowledge, this is the first time Fusarium pernambucanum has been recorded causing leaf yellow spot disease on melon. Further, findings of the present study will help to develop effective disease management strategies against Fusarium pernambucanum Leaf Yellow Spot on melon in China.

Development of a Sensitive, Easy and High-Throughput Compliant Protocol for Maize and Soybean DNA Extraction and Quantitation Using a Plant-Specific Universal Taqman Minor Groove Binder Probe.

We report the optimization of a high-throughput, compliant DNA extraction method that uses standard format 96-well plates and a commercial automated DNA purification system (ABI PRISM® 6100 Nucleic Acid PrepStation). The procedure was set up for maize and soybean, the most common GMO crops and the main ingredients of several foodstuffs, and compared with an EU-validated CTAB-based method. Optimization of the DNA extraction was achieved by applying self-prepared buffers (for DNA extraction, binding, and washing) on the PrepStation loaded with proprietary glass-fiber-coated purification plates. Quantification of extracted DNA was performed by real-time PCR using previously reported endogenous soybean lectin and maize starch synthase genes and a novel plant-specific universal TaqMan MGB probe that targets the 18S rRNA multiple copy gene. Using serial dilutions of both maize and soybean genomic DNAs, we show low PCR sensitivity and efficiency for the official TransPrep DNA extraction protocol compared to the CTAB-based one. On the other hand, using serial dilutions of a standard reference plasmid containing a 137 bp sequence cloned from the 18S rRNA plant-specific ribosomal gene, we demonstrate the high PCR sensitivity and efficiency of the optimized DNA extraction protocol setup with self-prepared buffers. The limits of detection and quantification of the 18S rDNA reiteration were consistent with the calculated values, supporting the suitability of the DNA extraction procedure for high-throughput analyses of large populations and small amounts of tissue.

Identification of a candidate sex-determining gene, ptf1aY, in the Chinese longsnout catfish (Leiocassis longirostris) through high-throughput sequencing

Identifying sex-specific molecular markers and elucidating sex determination mechanisms are critical in sex-controlled breeding in aquaculture. Chinese longsnout catfish (Leiocassis longirostris) is characterized by rapid male growth, suggesting that all-male production will be economically desirable in aquaculture. In this study, novel sex-specific sequences were identified in the Chinese longsnout catfish by using comparative genomics with high-throughput sequencing. Based on the variable regions between the X (1513 bp) and Y (862 bp) sequences, a pair of Y-specific primers was designed to discriminate the genetic sex of Chinese longsnout catfish. The specificity and universality of these primers were verified in two breeding and three wild populations. Sequence analysis revealed that the 1513 and 862 bp were pancreas transcription factor 1a (ptf1a) homologous genes, implying that Chinese longsnout catfish possess an XY sex-determination system, with ptf1a as the sex-linked gene. Two ptf1a cDNA sequences were isolated and named ptf1aX and ptf1aY based on their sites on the X and Y chromosomes. The ptf1aY gene is a truncated copy of ptf1aX on the Y chromosome. The proteins encoded by ptf1aX (263 aa) and ptf1aY (199 aa) showed high sequence identity (65.40 %). Expression analysis showed that ptf1aY mRNA was specifically detected in the testes, and ptf1aX was expressed in the both ovaries and testes. Thus, ptf1aY is a candidate male sex-determining gene in the Chinese longsnout catfish. Our study greatly contributes to understanding sex determination mechanisms and developing all-male population of Chinese longsnout catfish.

Multiple piroplasm parasites (Apicomplexa: Piroplasmida) in northeastern populations of the invasive Asian longhorned tick, Haemaphysalis longicornis Neumann (Ixodida: Ixodidae), in the United States.

Piroplasms, which include the agents of cattle fever and human and dog babesiosis, are a diverse group of blood parasites of significant veterinary and medical importance. The invasive Asian longhorned tick, Haemaphysalis longicornis, is a known vector of piroplasms in its native range in East Asia and invasive range in Australasia. In the USA, H. longicornis has been associated with Theileria orientalis Ikeda outbreaks that caused cattle mortality. To survey invasive populations of H. longicornis for a broad range of piroplasms, 667 questing H. longicornis collected in 2021 from 3 sites in New Jersey, USA, were tested with generalist piroplasm primers targeting the 18S small subunit rRNA (395–515 bp, depending on species) and the cytochrome b oxidase loci (1009 bp). Sequences matching Theileria cervi type F (1 adult, 5 nymphs), an unidentified Theileria species (in 1 nymph), an undescribed Babesia sensu stricto (‘true’ Babesia, 2 adults, 2 nymphs), a Babesia sp. Coco (also a ‘true Babesia’, 1 adult, 1 nymph), as well as Babesia microti S837 (1 adult, 4 nymphs) were recovered. Babesia microti S837 is closely related to the human pathogen B. microti US-type. Additionally, a 132 bp sequence matching the cytochrome b locus of deer, Odocoileus virginanus, was obtained from 2 partially engorged H. longicornis. The diverse assemblage of piroplasms now associated with H. longicornis in the USA spans 3 clades in the piroplasm phylogeny and raises concerns of transmission amplification of veterinary pathogens as well as spillover of pathogens from wildlife to humans.

First morphometric and molecular characterization of Fasciola spp. in Northwest Tunisia.

The aim of this study was to characterize the Tunisian Fasciola spp. flukes by morphometric and molecular analyses. Flukes were collected from livers of sheep slaughtered in Sejnane slaughterhouses (Bizerte gouvernorate, Northwest Tunisia) between January and March 2021.Five morphometric parameters were determined for all the liver flukes, as follows: (i) total body length (BL), (ii) distance between ventral sucker and the tail (VS-T), (iii) distance between oral sucker and ventral sucker (OS-VS), (iv) abdomen diameter (AD), (v) tail diameter (TD) and the body length to width ratio (BL/BW). Molecular identification of the fluke specimens was carried out by polymerase chain reaction, restriction fragment polymorphism (PCR-RFLP) of a 680 bp sequence of the internal transcribes spacer 1 (ITS1) gene and by amplification, sequencing, and phylogenetic analysis of a 500 bp sequence of the ITS2 gene. Morphometric measurements showed that the mean of the total body length of the adult flukes was 21.1 ± 2.7 mm with minimum and maximum lengths of 13 and 31 mm, respectively. The PCR-RFLP analysis revealed a single profile consisting of three bands of approximately 370, 100, and 60 bp. Fasciola sequences described in the present study (GenBank numbers: OQ457027 and OQ457028) showed 99.58-100% identity to Fasciola hepatica. In conclusion, the results of this study show that molecular and phylogenetic analyses confirm the presence of a single species of F. hepatica in the Sejnane region Northwest of Tunisia. However, further studies are needed to identify the occurrence of Fasciola species in other Tunisian regions.

Isolation and protein MdtQ analysis of outer membrane vesicles released by carbapenem-resistant Klebsiella pneumoniae

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has emerged as a leading public health problem, and is increasingly being reported worldwide with resistance to a wide spectrum of antibiotics. Recent reports have demonstrated that the outer membrane vesicles (OMVs) of gram-negative bacteria are potent resistance factors, but their role in the drug resistance of CRKP has not been elucidated. In order to investigate the effects of OMV components on drug resistance and to explore the mechanism of antimicrobial resistance in CRKP, we isolated the OMVs through ultracentrifugation, separated the OMV proteins through mass spectrometry (MS), and performed bioinformatics analysis. A total of 3,192 proteins were detected by nano LC-MS/MS analysis, with 108 (61.4%) cytoplasmic proteins, 50 (28.4%) cytoplasmic membrane proteins, nine (5.1%) periplasmic proteins, six (3.4%) outer membrane proteins, two (1.1%) extracellular proteins, and one (0.6%) other protein detected in the vesicles. MdtQ was detected as the only multidrug resistance outer membrane protein. Further experiments confirmed that MdtQ included the 1440 BP sequence and had a unique three-dimensional structure. To superimpose MdtQ with KPC-2 resistant proteins, I7ACB1, I7AKP2, and Q93LQ9, the root mean square deviation (RMSD) values were calculated (0.379, 0.671, and 1.35, respectively). I7ACB1 had the lowest RMSD value, indicating that it had the best superimposition effect. Furthermore, MdtQ had 20 biological pocket structures, and the four most important pockets were evenly distributed around the inner perimeter of its three-dimensional structure. These findings may provide a theoretical basis for controlling the spread of bacterial resistance in the future.

First Report of Alternaria alternata Causing White Leaf Spot on Allium tuberosum in China.

Puding County is the major Allium tuberosum growing area in Guizhou Province of China. In 2019, white leaf spots were observed on Allium tuberosum in Puding County (26.31°N, 105.64°E). The white spots, ranging from elliptic to irregular in shape, first appeared on leaf tips. With disease aggravation, spots gradually coalesced, forming necrotic patches with yellow margins causing leaf necrosis; sometimes there was gray mold on dead leaves. The incidence of the diseased leaf rate was estimated to be 27-48%. To identify the pathogenic agent, 150 leaf tissues (5 mm × 5 mm) were obtained from disease-healthy junctions of 50 diseased leaves. Leaf tissues were disinfected in 75% ethanol for 30 s, soaked in 0.5% sodium hypochlorite for 5 min, and flushed three times with sterile water, before being placed on potato dextrose agar (PDA) in the dark at 25 °C. When colonies appeared, the mycelial tips were picked and placed on new PDA. Purified fungus was obtained after repeating this last step several times. The colonies were grayish-green with white round margins. Conidiophores (2.7-4.5 μm × 27-81 μm) were brown, straight, or flexuous with branches and septa. Conidia (8-34 µm × 5-16 µm) were brown, with 0-5 transverse septa and 0-4 longitudinal septa. The 18S nuclear ribosomal DNA (nrDNA; SSU), 28S nrDNA (LSU), RNA polymerase II second largest subunit (RPB2), internal transcribed spacer (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and translation elongation factor 1-alpha (TEF-α) (Woudenberg et al. 2013) were amplified and sequenced. The sequences were deposited in GenBank (ITS: OP703616, LSU: OP860684, SSU: OP860685, GAPDH: OP902372, RPB2: OP902373, TEF1-α: OP902374). According to BLAST analysis, the ITS, LSU, GAPDH, RPB2, SSU, and TEF1-α of the straishowed 100% (689 of 731 base pairs; bp), 100% (916 of 938 bp), 100% (579 of 600 bp), 100% (946 of 985 bp), 100% (1093 of 1134 bp), and 100% (240 of 240 bp) sequence identity to those of Alternaria alternata (ITS: LC440581.1, LSU: KX609781.1, GAPDH: MT109295.1, RPB2: MK605900.1, SSU: ON055699.1 and TEF1-α: OM220081.1). A phylogenetic tree was constructed using PAUP4 and the maximum parsimony method with 1000 replicas of bootstrapping for all datasets. According to morphological characteristics and phylogenetic analysis, FJ-1 was identified as Alternaria alternata (Simmons 2007, Woudenberg et al. 2015). The strain was preserved in the Agricultural Culture Collection of China (preservation number: ACC39969). To determine the pathogenicity of Alternaria alternata against Allium tuberosum, wounded healthy leaves were inoculated with a conidial suspension (106 conidial/mL) and round mycelial plugs (4mm). Sterile agar PDA plugs with no mycelium or sterile water were inoculated as negative controls. Three days later, white spots appeared on the wounded leaves inoculated with mycelial plugs or conidial suspension. However, the symptoms caused by conidial suspensions were weaker than those caused by mycelial plugs. No symptoms were observed in the control group. The experimental symptoms were consistent with the phenomena observed in the field. The same fungus was reisolated from necrotic lesions and identified as Alternaria alternata using the method described above. To our knowledge, this is the first report of Alternaria alternata causing white leaf spots on Allium tuberosum in China, a disease seriously affected the yield and quality of Allium tuberosum and caused economic losses to farmers. Reference: Simmons EG (2007) Alternaria: an identification manual. CBS Fungal Biodiversity Centre, Utrecht, the Netherlands. Woudenberg JHC, Groenewald JZ, Binder M, Crous PW ( 2013) Alternaria redefined. Stud Mycol, 75: 171-212. https://doi.org/10.3114/sim0015. Woudenberg JHC, Seidl MF, Groenewald JZ, Vries M de, Stielow JB, Thomma BPHJ, Crous PW (2015) Alternaria section Alternaria: Species, formae speciales or pathotypes? Stud Mycol, 82:1-21. https://doi.org/10.1016/j.simyco.2015.07.001.

Genetic Diversity Analysis and Breeding of Geese Based on the Mitochondrial ND6 Gene.

To explore the differences in body-weight traits of five goose breeds and analyze their genetic diversity and historical dynamics, we collected body-weight data statistics and used Sanger sequencing to determine the mitochondrial DNA of 100 samples of five typical goose breeds in China and abroad. The results indicated that Lion-Head, Hortobagy, and Yangzhou geese have great breeding potential for body weight. Thirteen polymorphic sites were detected in the corrected 505 bp sequence of the mitochondrial DNA (mtDNA) ND6 gene, accounting for approximately 2.57% of the total number of sites. The guanine-cytosine (GC) content (51.7%) of the whole sequence was higher than the adenine-thymine (AT) content (48.3%), showing a certain GC base preference. There were 11 haplotypes among the five breeds, including one shared haplotype. We analyzed the differences in the distribution of base mismatches among the five breeds and conducted Tajima's D and Fu's Fs neutral tests on the historical dynamics of the populations. The distribution of the mismatch difference presented an unsmooth single peak and the Tajima's D value of the neutral test was negative (D < 0) and reached a significant level, which proves that the population of the three species had expanded; the Lion-Head goose population tends to be stable. The genetic diversity of Lion-Head, Zhedong White, Yangzhou, and Taihu geese was equal to the average diversity of Chinese goose breeds. The Hortobagy goose is a foreign breed with differences in mating line breeding and hybrid advantage utilization.

Invasion success of a Lessepsian symbiont-bearing foraminifera linked to high dispersal ability, preadaptation and suppression of sexual reproduction

Among the most successful Lessepsian invaders is the symbiont-bearing benthic foraminifera Amphistegina lobifera. In its newly conquered habitat, this prolific calcifier and ecosystem engineer is exposed to environmental conditions that exceed the range of its native habitat. To disentangle which processes facilitated the invasion success of A. lobifera into the Mediterranean Sea we analyzed a ~ 1400 bp sequence fragment covering the SSU and ITS gene markers to compare the populations from its native regions and along the invasion gradient. The genetic variability was studied at four levels: intra-genomic, population, regional and geographical. We observed that the invasion is not associated with genetic differentiation, but the invasive populations show a distinct suppression of intra-genomic variability among the multiple copies of the rRNA gene. A reduced genetic diversity compared to the Indopacific is observed already in the Red Sea populations and their high dispersal potential into the Mediterranean appears consistent with a bridgehead effect resulting from the postglacial expansion from the Indian Ocean into the Red Sea. We conclude that the genetic structure of the invasive populations reflects two processes: high dispersal ability of the Red Sea source population pre-adapted to Mediterranean conditions and a likely suppression of sexual reproduction in the invader. This discovery provides a new perspective on the cost of invasion in marine protists: The success of the invasive A. lobifera in the Mediterranean Sea comes at the cost of abandonment of sexual reproduction.

Molecular Detection and Epidemiology of Potentially Zoonotic Cryptosporidium spp. and Giardia duodenalis in Wild Boar (Sus scrofa) from Eastern Spain.

The protozoans Giardia duodenalis and Cryptosporidium spp. are common causes of gastrointestinal disease in humans and animals. While both are commonly documented in domestic animals, few studies have analysed their presence in wildlife. To assess the prevalence of both parasites in wild boar (Sus scrofa) in the Valencian Community (eastern Spain), 498 wild boar faecal samples were collected from 2018 to 2022. Cryptosporidium spp. was detected by performing a nested PCR targeting a 578 bp sequence of the small subunit ribosomal RNA gene (SSU rRNA), followed by sequencing and phylogenetic analysis. For G. duodenalis, a qPCR amplifying a fragment of 62 bp from the SSU rRNA was employed. Positive samples were genotyped for glutamate dehydrogenase and β-giardin genes. Different epidemiological factors were considered potential modulating variables in the transmission of both parasites. G. duodenalis prevalence was 1.20%, while Cryptosporidium spp. prevalence reached 21.7%. Coinfection was observed in 0.2%. Genotyping of G. duodenalis isolates only detected genotype E. Two species of Cryptosporidium spp. were identified: Cryptosporidium scrofarum and Cryptosporidium suis. The results of this study demonstrate that the exposure to Cryptosporidium spp. in wild boars is high, particularly among young individuals belonging to the Typical Mediterranean climate. Moreover, the probability of infection is dependent on both the season and the density of wild boars. On the other side, exposure to G. duodenalis seems scarce and is influenced, in turn, by the climate. Both Cryptosporidium species detected in the present study have been reported in humans. Due to wild boar increasing in number and their colonisation of urban and peri-urban areas, this could represent an inherent health risk for the human population.