The Synechocystis ORF slr0201 product is involved in succinate dehydrogenase-mediated cyclic electron transfer around PSI

The Synechocystis sp. PCC 6803 open reading frame (ORF) slr0201 was originally annotated as heterodisulfide reductase B subunit (HdrB). The slr0201 encodes a 301-amino acid hypothetical protein with the predicted amino acid sequence significantly homologous to not only the HdrB from methanogenic bacteria, but also some novel succinate dehydrogenase C subunit (SdhC) found in Archaea and Campylobacter. Genetic manipulation via knocking-out approach created a Δslr0201 mutant showing a ΔsdhB-like phenotype that was characterized by impaired succinate-dependent DCPIP reduction activities, reduced SDH-mediated respiratory electron transports, lower cellular contents of succinate and fumarate, slower KCN-induced increases in Chl fluorescence yield in the dark, and weak state 2/strong state 1 transitions, being indicative of a more oxidized PQ pool. In addition, slower re-reductions of the photosystem (PS) I reaction center P700 upon light-off were also monitored in the Δslr0201, indicating functional involvements of Slr0201 in cyclic electron transfer around PSI. Both photoautptrophical and photomixotrophical growth rates of the Δslr0201 strain resembled to those of the wild type, but substantial growth deteriorations occurred when arginine (~25 mM) or other two urea-cycle relevant amino acids (citrulline and ornithine) were added, which were attributed to generations and accumulations of certain hazardous metabolites. Based on the ΔsdhB-resembling phenotype, in conjunction with its high sequence similarities to some archaeal SdhC, we proposed that the slr0201 encodes a SDH function-relevant protein and is most likely the SdhC, a membrane anchoring subunit, which, while being genetically distinct from those in traditional bacterial SDH, belongs to the C subunit of novel archaeal SDH.

A draft genome assembly for the eastern fox squirrel, Sciurus niger

The eastern fox squirrel, Sciurus niger, exhibits marked geographic variation in size and coat color, is a model organism for studies of behavior and ecology, and a potential model for investigating physiological solutions to human porphyrias. We assembled a genome using Illumina HiSeq, PacBio SMRT, and Oxford Nanopore MinION sequencing platforms. Together, the sequencing data resulted in a draft genome of 2.99 Gb, containing 32,830 scaffolds with an average size of 90.9 Kb and N50 of 183.8 Kb. Genome completeness was estimated to be 93.78%. A total of 24,443 protein-encoding genes were predicted from the assembly and 23,079 (94.42%) were annotated. Repeat elements comprised an estimated 38.49% of the genome, with the majority being LINEs (13.92%), SINEs (6.04%), and LTR elements. The topology of the species tree reconstructed using maximum-likelihood phylogenetic analysis was congruent with those of previous studies. This genome assembly can prove useful for comparative studies of genome structure and function in this rapidly diversifying lineage of mammals, for studies of population genomics and adaptation, and for biomedical research. Predicted amino acid sequence alignments for genes affecting heme biosynthesis, color vision, and hibernation showed point mutations and indels that may affect protein function and ecological adaptation.

Characterization of 1Sty13, a novel high-molecular-weight glutenin subunit from Elymus sibiricus L.

High-molecular-weight glutenin subunit (HMW-GS) is a key factor affecting dough-processing quality. 1Sty13 is a novel HMW-GS found in the tetraploid species, Elymus sibiricus L. 1Sty13 has faster electrophoretic mobility than the 1Dy12 subunit on sodium dodecyl sulphate (SDS)-polyacrylamide gel electrophoresis. The gene encoding the 1Sty13 subunit was composed of 1803 nucleotide base pairs with an open reading frame that was 599 amino acids in length. Analysis of the predicted amino acid sequence of 1Sty13 indicated that the N-terminal domain was similar to the y-type subunit, whereas the C-terminal domains were similar to the x-type subunit. Five cysteine residues were found in 1Sty13, which is one less than the published HMW-GS in the St genome. The 1Sty13 protein was purified at a scale sufficient for incorporation into flour for the SDS sedimentation test, which indicated that incorporating 1Sty13 improved dough quality.

Discovery of a Novel Member of the Carlavirus Genus from Soybean (Glycine max L. Merr.)

A novel member of the Carlavirus genus, provisionally named soybean carlavirus 1 (SCV1), was discovered by RNA-seq analysis of randomly collected soybean leaves in Illinois, USA. The SCV1 genome contains six open reading frames that encode a viral replicase, triple gene block proteins, a coat protein (CP) and a nucleic acid binding protein. The proteins showed highest amino acid sequence identities with the corresponding proteins of red clover carlavirus A (RCCVA). The predicted amino acid sequence of the SCV1 replicase was only 60.6% identical with the replicase of RCCVA, which is below the demarcation criteria for a new species in the family Betaflexiviridae. The predicted replicase and CP amino acid sequences of four SCV1 isolates grouped phylogenetically with those of members of the Carlavirus genus in the family Betaflexiviridae. The features of the encoded proteins, low nucleotide and amino acid sequence identities of the replicase with the closest member, and the phylogenetic grouping suggest SCV1 is a new member of the Carlavirus genus.

Diverse mosquito-specific flaviviruses in the Bolivian Amazon basin

The genus Flavivirus includes a range of mosquito-specific viruses in addition to well-known medically important arboviruses. Isolation and comprehensive genomic analyses of viruses in mosquitoes collected in Bolivia resulted in the identification of three novel flavivirus species. Psorophora flavivirus (PSFV) was isolated from Psorophora albigenu. The coding sequence of the PSFV polyprotein shares 60 % identity with that of the Aedes-associated lineage II insect-specific flavivirus (ISF), Marisma virus. Isolated PSFV replicates in both Aedes albopictus- and Aedes aegypti-derived cells, but not in mammalian Vero or BHK-21 cell lines. Two other flaviviruses, Ochlerotatus scapularis flavivirus (OSFV) and Mansonia flavivirus (MAFV), which were identified from Ochlerotatus scapularis and Mansonia titillans, respectively, group with the classical lineage I ISFs. The protein coding sequences of these viruses share only 60 and 40 % identity with the most closely related of known lineage I ISFs, including Xishuangbanna aedes flavivirus and Sabethes flavivirus, respectively. Phylogenetic analysis suggests that MAFV is clearly distinct from the groups of the current known Culicinae-associated lineage I ISFs. Interestingly, the predicted amino acid sequence of the MAFV capsid protein is approximately two times longer than that of any of the other known flaviviruses. Our results indicate that flaviviruses with distinct features can be found at the edge of the Bolivian Amazon basin at sites that are also home to dense populations of human-biting mosquitoes.

Exploring the Biological and Molecular Characteristics of resistance to Fludioxonil in Sclerotinia sclerotiorum from soybean in China

Sclerotinia sclerotiorum is one of the most damaging and economically important necrotrophic plant pathogens, infecting more than 400 plant species globally. Although the phenylpyrrole fungicide fludioxonil has high activity against S. sclerotiorum, recent reports have indicated that there is also a substantial potential for the development of fungicide resistance. However, the current study investigating five fludioxonil-resistant laboratory mutants found a significant fitness cost associated with fludioxonil resistance resulting in significantly (p < 0.005) reduced mycelial growth and sclerotia formation on PDA, as well as significantly (p < 0.05) lower pathogenicity on detached tomato leaves, with one mutant, LK-1R, completely losing the capacity to cause infection. In addition, all of the fludioxonil-resistant mutants had significantly (p < 0.05) increased sensitivity to osmotic stress (0.5 M KCl and 1.0 M Glucose), which is consistent with the proposed fludioxonil target sites within the High Osmolarity Glycerol (HOG1) stress response mitogen-activated protein kinase (MAPK) (HOG1-MAPK) signaling transduction pathway. Sequence analysis of six genes from this two-component pathway, including SsHk, SsYpd, SsSk1, SsSk2, SsPbs, and SsHog, revealed several mutations which maybe associated fludioxonil resistance. For example, six separate point mutations were found in the SsHk gene that lead to changes in the predicted amino acid sequence, including A136G, F249V, G353A, E560K, M610K, and K727R. Similarly, the SsPbs gene had three mutations (D34G, S46L, and L337E); the SsSk1 and SsYpd genes two (S53G and A795V, and E67G and Y141H, respectively) and the SsHog and SsSk2 genes one each (V220A and S763P, respectively). To the best of our knowledge, these constitute the first reports of amino acid changes in the proteins of the HOG1-MAPK pathway being associated with fludioxonil resistance in S. sclerotiorum. The study also found a positive cross-resistance between fludioxonil and dimethachlone and procymidone, but none with tebuconazole or carbendazim, indicating that the inclusion of tebuconazole within an integrated pest management program could reduce the risk of fludioxonil developing in field populations of S. sclerotiorum, and ensure the sustainable production of soybeans in China into the future.

Isolation of the Histone Lysine Methyltransferase Gene PhSDG8 and Characterization of Function in Shoot Branching

Petunia (Petunia ×hybrida) is an important ornamental plant, and its branch development has become a hot research topic. In this study, PhSDG8, an ortholog of SET domain group 8 (SDG8), was cloned from the petunia cultivar Mitchell Diploid. It had an open reading frame (ORF) of 5070 bp and encoded 1689 amino acids, with Suppressor variegation 3–9, Enhancer of zeste, Trithorax (SET), Zinc finger-cysteine and tryptophan conserved (Zf-CW), associated with SET (AWS) and Post SET domains. The predicted amino acid sequence of PhSDG8 was most closely related to Nicotiana sylvestris ASHH2 (NsASHH2). Expression analysis revealed that PhSDG8 expressed highest in the stems and lowest in the axil. Subcellular localization analysis showed that PhSDG8 was localized in the nucleus. Overexpression of PhSDG8 reduced the branch number of Arabidopsis thaliana sdg8-2. The silencing of PhSDG8 resulted in an increase in the number of branches of petunia and significant upregulation of PhUGT74E2. These results suggested that PhSDG8 may be a candidate gene for regulating the branching of petunia.

Functional activation of a novel R2R3-MYB protein gene, GmMYB68, confers salt-alkali resistance in soybean (Glycine max L.)

Soil salinity significantly reduces soybean (Glycine max L.) production worldwide. Plants resistance to stress conditions is a complex characteristic regulated by multiple signaling pathways. The v-Myb avian myeloblastosis viral oncogene homolog (MYB) transcription factor (TF) plays a crucial role in plant development, secondary metabolism, and abiotic stress responses. GmMYB68-overexpression and RNA interference (RNAi) lines were established for examining the function of G. max GmMYB68 in plant responses to abiotic stresses. The predicted amino acid sequence of GmMYB68 was similar to that of R2R3-MYB proteins. Quantitative real-time PCR analysis revealed that GmMYB68 expression varied in response to abiotic stresses. GmMYB68-overexpression lines showed enhanced resistance to salt and alkali stresses and their osmotic adjustment and photosynthetic rates were also stronger than that of GmMYB68-RNAi and wild type plants. Although wild type and transgenic plants showed no significant differences in agronomic traits under normal conditions, the overexpression of GmMYB68 increased grain number and 100-grain weights under salt stress. Our study identified a valuable TF associated with stress response in soybean, as its overexpression might help improve salt and alkali tolerance in soybean and other crops.

ANALYSIS OF GENETIC CHARACTERISTICS OF INFLUENZA VIRUS A/CHICKEN/CHELYABINSK/30/2019 H9N2 ISOLATED IN CHELYABINSK OBLAST

The paper presents data on the study of genetic characteristics of the infl uenza virus A/chicken/ Chelyabinsk/30/2019 H9N2 isolated from pathological material (chicken internal organs) in February 2019 and received from the poultry farm in the Chelyabinsk Oblast. The H9N2 subtype of the isolated virus was identifi ed based on virological analysis. Sequencing of the hemagglutinin gene segment revealed that the amino acid sequence at the cleavage site was RSSR/GLF, which is characteristic of a low virulent avian infl uenza virus. Phylogenetic analysis of the obtained nucleotide sequences of the hemagglutinin gene fragment (1–1539 bp open reading frame) showed that the A/chicken/Chelyabinsk/30/2019 H9N2 isolate belongs to the G1 genetic group of the low virulent infl uenza virus A/H9, the representatives of which are widely spread in the Middle Eastern and Central Asian countries. The complete nucleotide genome sequence of the studied pathogen was determined. The comparative analysis of all genomic segments using the GenBank database revealed a close relationship (over 99%) between the A/chicken/Chelyabinsk/30/2019 H9N2 virus and the A/H9 infl uenza virus isolates circulating in Israel in 2006–2012. According to the analysis of the predicted amino acid sequence of the studied isolate, the positions of some molecular markers that determine the biological properties of the virus have been identifi ed. Most amino acid positions of hemagglutinin (according to H3 subtype sequence numbering) suggest affi nity for the ACA2-3Gal-receptors of avian epithelial cells. Amino acid substitutions were detected at the site within the receptor-binding domain as compared to the A/H9N2 infl uenza virus isolates obtained in Russia in 2018. The primary structure of the A/chicken/Chelyabinsk/30/2019 H9N2 isolate demonstrates a very high level of genetic similarity to the infl uenza virus isolate A/chicken/ Israel/215/2007 H9N2 used as a vaccine strain.

Cloning and expression analysis of Serum Amyloid A (SAA) from Exopalaemon carinicauda (Holthuis, 1950) (Caridea, Palaemonidae)

Serum amyloid A (SAA), an acute-phase protein, has been demonstrated to play a critical role in the inflammatory response. However, data regarding its function in crustaceans are still scarce. In the present study, cDNA of SAA from Exopalaemon carinicauda (Holthuis, 1950) (designated as EcSAA) was cloned and characterized. The full-length cDNA was 683 bp, including an open reading frame (ORF) of 267 bp that encoded 88 amino acid residues. The predicted amino acid sequence of EcSAA contained characteristic motifs of the SAA family. The EcSAA was widely expressed in all tissues, with the highest expression in gill and hepatopancreas. In response to the Vibrio anguillarum Bergeman, 1909 challenge, EcSAA mRNA was up-regulated in gill, hepatopancreas, and haemolymph. These results suggest thatEcSAA may be a constitutive and inducible acute-phase protein involved in anti-pathogen responses in E. carinicauda.