Comparative genomics of the Neodiprion sertifer nucleopolyhedrovirus from Turkey with the fewest ORFs among baculoviruses.

The complete genome of a European pine sawfly Neodiprion sertifer nucleopolyhedrovirus (NeseNPV-TR) was sequenced and characterized from next-generation sequencing data of N. sertifer larva from Türkiye. This genome was analyzed and compared to previously reported genomes of baculoviruses. The baculovirus phylogeny was reconstructed and the species identity of the NeseNPV-TR was delineated using K2P distance. The length of the genome was 82,052 bp, with a G + C content of 33.28%. It contained 83 putative ORFs, including 38 baculovirus core genes, three lepidopteran baculovirus core genes, and three non-conserved genes. It had five hrs with 20.6% overall mean distance on average. The pairwise K2P distances of lef-8, lef-9, and polh genes and combinations of three genes and 38 genes between NeseNPV-TR and NeseNPV were slightly higher than the specified threshold values for species demarcation. The most variable genes were lef-2, helicase, p40, desmoplakin, pif7, p6.9, vp91, and vp39, while the most conserved were lef-8, lef-9, odv-e18, pif2, and lef-5 among baculoviruses. The genome of NeseNPV-TR is smaller and contains the fewest ORFs among baculoviruses. Some of unassigned ORFs had conserved domains and hence, we suggest further investigation to determine their structural and functional roles. Phylogenetic analyses confirmed its position within genus Gammabaculovirus. Taking into account the phylogenetic position, K2P distances, and NJ tree, the NeseNPV-TR can be classified in the same species (Gammabaculovirus nesertiferis) with NeseNPV. The different divergence rates in the baculovirus core genes may be related with different selection pressures acting on the genes. The lower genetic diversity of Group I alphabaculoviruses is most probably due to recent emergence.

microRNAs in Syrista parreyssi (Hymenoptera) and Lepisma saccharina (Zygentoma) possibly involved in the mitochondrial function.

Mitochondria are essential organelles for maintaining vital cellular functions, and microRNAs (miRNAs) regulate gene expression posttranscriptionally. miRNAs exhibit tissue and time-specific patterns in mitochondria and specifically mitochondrial miRNAs (mitomiRs) can regulate the mRNA expression both originating from mitochondrial and nuclear transcription which affect mitochondrial metabolic activity and cell homeostasis. In this study, miRNAs of two insect species, Syrista parreyssi (Hymenoptera) and Lepisma saccharina (Zygentoma), were investigated for the first time. The known and possible novel miRNAs were predicted and characterized and their potential effects on mitochondrial transcription were investigated in these insect species using deep sequencing. The previously reported mitomiRs were also investigated and housekeeping miRNAs were characterized. miRNAs that are involved in mitochondrial processes such as apoptosis and signaling and that affect genes encoding the subunits of OXPHOS complexes have been identified in each species. Here, 81 and 161 novel mature miRNA candidates were bioinformatically predicted and 9 and 24 of those were aligned with reference mitogenomes of S. parreyssi and L. saccharina, respectively. As a result of RNAHybrid analysis, 51 and 69 potential targets of miRNAs were found in the mitogenome of S. parreyssi and L. saccharina, respectively. cox1 gene was the most targeted gene and cytB, rrnS, and rrnL genes were highly targeted in both of the species by novel miRNAs, hypothetically. We speculate that these novel miRNAs, originating from or targeting mitochondria, influence on rRNA genes or positively selected mitochondrial protein-coding genes. These findings may provide a new perspective in evaluating miRNAs for maintaining mitochondrial function and transcription.

Differential sense and antisense expression profiles of Syrista parreyssi (Hymenoptera: Cephidae) mitochondrial transcripts.

The transcription of the mitogenome shows a unique pattern that is both similar to and different from the nuclear and bacterial patterns. Mitochondrial transcription generates five polycistronic units from three promoters in Drosophila melanogaster, and different expression levels of genes were observed in both different and, interestingly, the same polycistronic units in D. melanogaster. This study was conducted to test this phenomenon in the mitogenome of Syrista parreyssi (Hymenoptera: Cephidae). RNA isolation and DNase digestion were performed using only one whole individual, and real-time polymerase chain reaction analyses were performed with complementary DNAs of 11 gene regions using gene-specific primers. It was found that the expression level of each gene exhibited differences from each other, and some genes (e.g., cox genes, and rrnS) were interestingly expressed at significant levels in the corresponding antisense chain. Additionally, the mitogenome of S. parreyssi was found to have the capacity to encode 169 additional peptides from 13 known protein-coding genes, most of which were encoded in antisense transcript units. One of the unique findings was a potential open reading frame sequence that was potentially encoded in the antisense rrnL gene and included a conserved cox3 domain.

A novel, conserved and possibly functional motif "WHWGHTW" in mitochondrial transcription across Bilateria.

The animal mitogenomes which undergone a reductive evolution has an obvious loss of coding capacity compared to their known closest relatives, but it has not yet been fully investigated why and how the intergenic regions do not encode protein and have no known functions, are stably maintained, replicated, and transmitted by the genome. These relatively small intergenic regions may not be under neutral evolution and they may have functional and/or regulatory roles that have yet to be identified. Here, the distribution pattern, sequence content and location of a novel sequence motif of 'WWWGHTW' were bioinformatically investigated and characterised by constructing a sampling mitogenome dataset of 1889 species from 14 phyla representing the clade of Bilateria. This motif is reverse complementary of the previously described DmTTF binding sequence and found in the nd4L- (X) -trnT gene cluster. This cluster commonly exhibits a strand displacement region and an intergenic region among the bilaterian superphylums, particularly in Ecdysozoa. This motif may be accepted as a substrate providing binding sites for the specific interaction with transcription factors because of (i) its reverse complementarity of previously described DmTTF binding sequence, and (ii) the possession of G and T nucleotides in the fourth and sixth positions, (iii) the bias on T and G nucleotides instead of C and A in the degenerated positions. This suggestion is also supported by the presence of a strand displacement region in the nd4L- (X) -trnT gene cluster, particularly in Ecdysozoa consisting of the most rearranged mitogenomes among the bilaterian superphylums.

Phylogenomic Analyses of the Tenthredinoidea Support the Familial Rank of Athaliidae (Insecta, Tenthredinoidea).

The systematic status of the genus Athalia and related genera is a perennial controversy in sawfly taxonomy. Several authors have hypothesized that the placement of Athalia within the Tenthredinidae is artificial, but no studies have focused on this topic. If the hypothesis that Athalia does not belong to Tenthredinidae can be supported, the taxonomic framework of Tenthredinoidea needs revision. We present a comprehensive phylogenomic study of Tenthredinoidae, focusing on the positions of Athalia and related genera by sampling 80 representatives mainly of the Tenthredinoidea, including Heptamelinae and Blasticotomidae. Our phylogenetic reconstructions based on nuclear genes and mitochondrial (mt) sequences support Athalia and related genera as a distinct clade sister to Tenthredinidae + (Cimbicidae + Diprionidae). A comparison of symphytan mitochondrial genomes reveals an innovative gene rearrangement pattern in Athaliidae, in which Dentathalia demonstrates a more ancestral pattern than Athalia and Hypsathalia. The lineage specificity of mt rRNA secondary structures also provides sufficient support to consider Athaliidae as a separate family. In summary, the phylogeny and genomic structural changes unanimously support the taxonomic treatment of Athaliidae as a family and the re-establishment of Dentathalia as a valid genus.

Mitochondrial Phylogenomics of Tenthredinidae (Hymenoptera: Tenthredinoidea) Supports the Monophyly of Megabelesesinae as a Subfamily.

Tenthredinidae represents one of the external feeders of the most diverse superfamily, Tenthredinoidea, with diverse host plant utilization. In this study, four complete mitochondrial genomes (mitogenomes), those of Cladiucha punctata, Cladiucha magnoliae, Megabeleses magnoliae, and Megabeleses liriodendrovorax, are newly sequenced and comparatively analyzed with previously reported tenthredinid mitogenomes. The close investigation of mitogenomes and the phylogeny of Tenthredinidae leads us to the following conclusions: The subfamilial relationships and phylogenetic placements within Tenthredinidae are mostly found to be similar to the previously suggested phylogenies. However, the present phylogeny supports the monophyly of Megabelesesinae as a subfamily, with the sister-group placement of Cladiucha and Megabeleses outside of Allantinae. The occurrence of the same type of tRNA rearrangements (MQI and ANS1ERF) in the mitogenomes of Megabelesesinae species and the presence of apomorphic morphological characters also provide robust evidence for this new subfamily. The divergence and diversification times of the subfamilies appear to be directly related to colonization of the flowering plants following the Early Cretaceous. The origin time and diversification patterns of Megabelesesinae were also well matched with the divergence times of their host plants from Magnoliaceae.

Computationally predicted SARS-COV-2 encoded microRNAs target NFKB, JAK/STAT and TGFB signaling pathways.

Recently an outbreak that emerged in Wuhan, China in December 2019, spread to the whole world in a short time and killed >1,410,000 people. It was determined that a new type of beta coronavirus called severe acute respiratory disease coronavirus type 2 (SARS-CoV-2) was causative agent of this outbreak and the disease caused by the virus was named as coronavirus disease 19 (COVID19). Despite the information obtained from the viral genome structure, many aspects of the virus-host interactions during infection is still unknown. In this study we aimed to identify SARS-CoV-2 encoded microRNAs and their cellular targets. We applied a computational method to predict miRNAs encoded by SARS-CoV-2 along with their putative targets in humans. Targets of predicted miRNAs were clustered into groups based on their biological processes, molecular function, and cellular compartments using GO and PANTHER. By using KEGG pathway enrichment analysis top pathways were identified. Finally, we have constructed an integrative pathway network analysis with target genes. We identified 40 SARS-CoV-2 miRNAs and their regulated targets. Our analysis showed that targeted genes including NFKB1, NFKBIE, JAK1-2, STAT3-4, STAT5B, STAT6, SOCS1-6, IL2, IL8, IL10, IL17, TGFBR1-2, SMAD2-4, HDAC1-6 and JARID1A-C, JARID2 play important roles in NFKB, JAK/STAT and TGFB signaling pathways as well as cells' epigenetic regulation pathways. Our results may help to understand virus-host interaction and the role of viral miRNAs during SARS-CoV-2 infection. As there is no current drug and effective treatment available for COVID19, it may also help to develop new treatment strategies.

The regulation of trophoblast invasion and decidual reaction by matrix metalloproteinase-2, metalloproteinase-7, and metalloproteinase-9 expressions in the rat endometrium.

PURPOSE: We aimed to evaluate how matrix metalloproteinases (MMPs) regulate the trophoblast invasion and placentation. METHODS: Female rats were divided into the estrous cycle and early pregnancy day groups. Obtained uterine tissues and implantation sites were processed for immunofluorescence and real-time PCR examinations. RESULTS: The mRNA expression of MMP-7 was higher than MMP-2 and MMP-9. Immunofluorescence findings confirmed that MMP-2, MMP-7, and MMP-9 were localized in the endometrial stroma, while MMP-7 was high in glandular and lining epithelial cells throughout the entire estrous cycle. However, their immunolocalizations and mRNA expressions were dramatically changed with the early pregnancy days. The MMP-7 reached very strong immunostaining in the giant trophoblast cells (GTCs), and the cytoplasm of mature and differentiating decidual cells, whereas MMP-2 and MMP-9 were mostly seen in the primary decidual zone (PDZ), GTCs, and the endothelium of blood vessels. CONCLUSIONS: All three MMPs seemed likely to be a key mediator of trophoblast invasion into the decidual region as well as angiogenesis during the placentation process. Due to the strong and wide expression of MMP-7 in the mature decidua, it could be suggested that MMP-7 is important for decidual ECM remodeling and it might be used as a new marker of decidual reaction.

Comparative mitogenomics of Hymenoptera reveals evolutionary differences in structure and composition.

The rapidly growing number of mitogenomes in Hymenoptera have mostly been used to explain higher level phylogeny, however, there are inadequate studies that focused on the shared and distinctive patterns of mitogenome evolution. Here, the complete mitogenome of Neodiprion sertifer (Symphyta: Diprionidae) was reported for the first time and it was found to be the most rearranged mitogenome in Symphyta, with five rearrangement events. The mitogenome architectures and features were also investigated in 73 hymenopteran species. The observation of positive GC skews may be related with selective forces acting on mitogenomes with the high number of transversions than transitions. The number of rearrangements exhibited negative correlation with T% and positive with C% content, indicating a tight relation between the number of rearrangements and deamination mutations. The rearrangements also displayed a significant increment from Symphyta to Aculeate and transpositions were found to be the most common type. The rrnS-nd2 was the most rearranged gene cluster, revealing the frequent occurrence of illegitimate recombination via duplications. The nucleotide bias was more important in the codon and anticodon interactions than the expected "exact-match" pattern. The conservation rate of tRNAs seems to be unrelated to that of strand location, amino acid composition, codon family degeneracy.

The first mitogenomes of the superfamily Pamphilioidea (Hymenoptera: Symphyta): Mitogenome architecture and phylogenetic inference.

The Pamphilioidea represents a small superfamily of the phytophagous suborder Symphyta (Hymenoptera). Here, nearly complete mitochondrial genomes (mitogenomes) of three pamphilioid species: Chinolyda flagellicornis (Pamphiliidae), Megalodontes spiraeae and M. cephalotes (Megalodontesidae) were newly sequenced using next generation sequencing and comparatively analysed with the previously reported symphytan mitogenomes. A positive AT skew (0.013) and a negative GC skew (-0.194) were found in pamphilioid mitogenome, and a deviation from strand asymmetry was also observed in the PCGs encoded on both strands. Several gene rearrangement events were observed in four tRNA gene clusters (WCY, IQM, ARNS1EF and TP clusters), which have not been reported from symphytan mitogenomes to date. As the most parsimonious explanation, compared with the inferred insect ancestral mitogenome architecture, the occurrence of gene rearrangements in pamphilioid mitogenomes requires totally five evolutionary steps, including four transpositions and one inversion. The predicted secondary structures of tRNAs, rrnS and rrnL genes are mostly consistent with reported hymenopteran species. Phylogenetic analyses recovered the monophyly of superfamily Pamphilioidea and indicated the relationship Tenthredinoidea + (Pamphilioidea + (Cephoidea + (Orussoidea + Apocrita))) with strong nodal supports.

The effects of IL-10 gene polymorphism on serum, and gingival crevicular fluid levels of IL-6 and IL-10 in chronic periodontitis.

OBJECTIVE: Anti-inflammatory cytokines play a crucial role in periodontitis by inhibiting synthesis of pro-inflammatory cytokines. The purpose of this study was to evaluate the effect of interleukin-10 (-597) gene polymorphism and genotype distributions on chronic periodontitis (CP) development and IL-6 and IL-10 levels in gingival crevicular fluid (GCF) and serum before and after non-surgical periodontal treatment. MATERIAL AND METHODS: The study population consisted of 55 severe generalized CP patients as CP group and 50 healthy individuals as control group. Plaque index, gingival index, probing depth and clinical attachment level were recorded and GCF and blood samples were taken at both the baseline and the sixth week after non-surgical periodontal treatment. PCR-RFLP procedure was used for gene analyses and cytokine levels were measured via ELISA. RESULTS: IL-10 genotype distribution was significantly different between CP and control groups (p=0.000, OR:7, 95%CI, 2.83-60.25). Clinical measurements significantly improved in the CP group after periodontal treatment (p<0.05). Periodontal treatment significantly decreased GCF IL-6 and IL-10 levels. No significant difference was found in clinical parameters between IL-10 AA and AC+CC genotypes at both the baseline and the sixth week (p>0.05). Sixth week GCF IL-10 levels were significantly lower in patients carrying IL-10 AC+CC genotype compared to the patients carrying IL-10 AA genotype (p<0.05). Serum IL-6 and IL-10 levels were lower in patients carrying the IL-10 AA genotype compared to patients with IL-10 AC+CC genotype, but the difference was not significant (p>0.05). CONCLUSION: IL-10 AA genotype carriers had lower IL-6 and IL-6/10 levels in serum; however, GCF IL-6/10 levels were similar in both genotypes. Within the limitations of our study, a possible association between IL-10(-597) gene polymorphism and CP might be considered.

The effects of IL-10 gene polymorphism on serum, and gingival crevicular fluid levels of IL-6 and IL-10 in chronic periodontitis

Abstract Objective Anti-inflammatory cytokines play a crucial role in periodontitis by inhibiting synthesis of pro-inflammatory cytokines. The purpose of this study was to evaluate the effect of interleukin-10 (-597) gene polymorphism and genotype distributions on chronic periodontitis (CP) development and IL-6 and IL-10 levels in gingival crevicular fluid (GCF) and serum before and after non-surgical periodontal treatment. Material and Methods The study population consisted of 55 severe generalized CP patients as CP group and 50 healthy individuals as control group. Plaque index, gingival index, probing depth and clinical attachment level were recorded and GCF and blood samples were taken at both the baseline and the sixth week after non-surgical periodontal treatment. PCR-RFLP procedure was used for gene analyses and cytokine levels were measured via ELISA. Results IL-10 genotype distribution was significantly different between CP and control groups (p=0.000, OR:7, 95%CI, 2.83-60.25). Clinical measurements significantly improved in the CP group after periodontal treatment (p<0.05). Periodontal treatment significantly decreased GCF IL-6 and IL-10 levels. No significant difference was found in clinical parameters between IL-10 AA and AC+CC genotypes at both the baseline and the sixth week (p>0.05). Sixth week GCF IL-10 levels were significantly lower in patients carrying IL-10 AC+CC genotype compared to the patients carrying IL-10 AA genotype (p<0.05). Serum IL-6 and IL-10 levels were lower in patients carrying the IL-10 AA genotype compared to patients with IL-10 AC+CC genotype, but the difference was not significant (p>0.05). Conclusion IL-10 AA genotype carriers had lower IL-6 and IL-6/10 levels in serum; however, GCF IL-6/10 levels were similar in both genotypes. Within the limitations of our study, a possible association between IL-10(-597) gene polymorphism and CP might be considered.

Analysis of IL-6, IL-10 and NF-κB Gene Polymorphisms in Aggressive and Chronic Periodontitis.

OBJECTIVE: Pro-inflammatory cytokines, interleukin-6 (IL-6), demonstrated to be suppressed by interleukin-10 (IL-10) are known to be regulated by the transcription factor nuclear factor-κB(NF-κB). The aim of this study was to ascertain the association between genetic polymorphism of these genes (IL-6(-174), IL-10(-597) and NF-κB1-94ins/del)) and chronic/aggressive periodontitis. METHODS: Forty-five patients with chronic periodontitis (CP), 58 patients with aggressive periodontitis (AP) and 38 periodontally healthy subjects were included in this study. Genomic DNA was isolated from whole blood samples. The NF-κB, IL-6, and IL-10 polymorphisms were determined by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. RESULTS: Among subjects for the ins/ins genotypes of NF-κB1 gene, the AA genotypes of IL-10 presented a higher frequency in chronic periodontitis group than in healthy controls (p=0.023). A statistically significant difference in genotyping frequencies between AP group and healthy controls was observed for the IL-6 gene. The AA genotype of IL-10 was overrepresented in CP and AP groups compared to healthy controls (OR=9.93, 95% CI: 2.11-46.7, OR=5.7, 95% CI: 1.22-26.89, respectively). CONCLUSIONS: Within the limits of this study, it can be concluded that the IL-10 (-597) AA genotype is associated with susceptibility to chronic/aggressive periodontitis and IL-6 (-174) GG genotypes and G allele seems to be associated with aggressive periodontitis. Clinical relevance: The results of the current study indicate that IL-6 and IL-10 genotypes seem to be associated with aggressive periodontitis. Also, the AA genotypes of IL-10 presented a higher frequency in chronic periodontitis subjects with carrying NF-κB1 ins/ins genotypes.

IL-6 and IL-10 gene polymorphisms in patients with aggressive periodontitis: effects on GCF, serum and clinic parameters.

Genetic variations observed in cytokines affect periodontitis susceptibility. The aim of this study was to investigate interleukin(IL)-6(-174) and IL-10(-597) gene polymorphisms in generalized aggressive periodontitis (GAgP) patients. Also, we aimed to evaluate the effects of IL-6 and IL-10 gene polymorphisms on the clinical outcomes of non-surgical periodontal therapy and cytokine levels in gingival crevicular fluid(GCF) and serum. Fifty-three patients with GAgP and 50 periodontally healthy individuals were included in this study. Clinical parameters, GCF and blood samples were collected at baseline and at 6-week. Non-surgical periodontal therapy was performed in patients with GAgP. Gene analysis were determined by PCR-RFLP(polymerase chain reaction-restriction fragment length polymorphism) and cytokine levels were determined by enzyme-linked immunosorbent assay(ELISA).GAgP patients showed significant improvement on clinical parameters after periodontal therapy(p<0.05). In the GAgP group, IL-6 GG genotype and G allele frequency were higher than in the control group. GCF IL-6 level was also significantly lower at 6-week in the GAgP group. Higher GCF IL-10 levelswere observed in patients carrying the IL-6 GG genotype than in those carrying the GC+CC genotype at baseline. In conclusion, IL-6(-174) and IL-10(-597) gene polymorphisms were found to be associated with GAgP and genotype distribution did not affect the outcome of non-surgical periodontal therapy, while patients with IL-6(-174) GG genotype had higher levels of GCF IL-10 levels.

IL-6 and IL-10 gene polymorphisms in patients with aggressive periodontitis: effects on GCF, serum and clinic parameters

Abstract Genetic variations observed in cytokines affect periodontitis susceptibility. The aim of this study was to investigate interleukin(IL)-6(-174) and IL-10(-597) gene polymorphisms in generalized aggressive periodontitis (GAgP) patients. Also, we aimed to evaluate the effects of IL-6 and IL-10 gene polymorphisms on the clinical outcomes of non-surgical periodontal therapy and cytokine levels in gingival crevicular fluid(GCF) and serum. Fifty-three patients with GAgP and 50 periodontally healthy individuals were included in this study. Clinical parameters, GCF and blood samples were collected at baseline and at 6-week. Non-surgical periodontal therapy was performed in patients with GAgP. Gene analysis were determined by PCR-RFLP(polymerase chain reaction-restriction fragment length polymorphism) and cytokine levels were determined by enzyme-linked immunosorbent assay(ELISA).GAgP patients showed significant improvement on clinical parameters after periodontal therapy(p<0.05). In the GAgP group, IL-6 GG genotype and G allele frequency were higher than in the control group. GCF IL-6 level was also significantly lower at 6-week in the GAgP group. Higher GCF IL-10 levelswere observed in patients carrying the IL-6 GG genotype than in those carrying the GC+CC genotype at baseline. In conclusion, IL-6(-174) and IL-10(-597) gene polymorphisms were found to be associated with GAgP and genotype distribution did not affect the outcome of non-surgical periodontal therapy, while patients with IL-6(-174) GG genotype had higher levels of GCF IL-10 levels.

Two nearly complete mitogenomes of wheat stem borers, Cephus pygmeus (L.) and Cephus sareptanus Dovnar-Zapolskij (Hymenoptera: Cephidae): an unusual elongation of rrnS gene.

Two nearly complete mitochondrial genomes (mitogenomes) of wheat stem borers, Cephus pygmeus and Cephus sareptanus (Hymenoptera: Cephidae), were sequenced, characterised and compared with the previously known mitogenome of Cephus cinctus. The gene orders are mostly conserved, except for translocation of trnM and swapped position of trnI and trnQ. An A+T bias was found, but a deviation from strand asymmetry was also detected on the J strand. All protein coding genes (PCGs) are initiated by ATN codons, except for nad1, nad2 and atp8, and all are terminated with TAA, TA- or T- as a stop codon. The predicted secondary structures of rrnS and rrnL genes are mostly consistent with reported hymenopteran species. However, an unusual elongation in rrnS, not know elsewhere in the order, was discovered in Cephus species. Three autonomous sequences detected in domains I and II are mainly responsible for the length expansions.