Nucleotide Sequence Alignment Research Articles

Identification of a candidate gene underlying qKRN5b for kernel row number in Zea mays L.

A quantitative trait locus for kernel row number, qKRN5, was dissected into two tightly linked loci, qKRN5a and qKRN5b. Fine mapping, comparative analysis of nucleotide sequences and gene expression established the endonuclease/exonuclease/phosphatase family protein-encoding gene Zm00001d013603 as a causal gene of qKRN5b. Maize grain yield is determined by agronomically important traits that are controlled by interactions among and between genes and environmental factors. Considerable efforts have been made to identify major quantitative trait loci (QTLs) for yield-related traits; however, few were previously isolated and characterized in maize. In this study, we divided a QTL for kernel row number (KRN), qKRN5, into two tightly linked loci, qKRN5a and qKRN5b, using advanced backcross populations derived from near-isogenic lines. KRN was greater in individuals that were homozygous for the NX531 allele, which showed coupling-phase linkage. The major QTL qKRN5b had an additive effect of approximately one kernel row. Furthermore, fine mapping narrowed qKRN5b within a 147.2-kb region. The upstream sequence Zm00001d013603 and its expression in the ear inflorescence showed obvious differences between qKRN5b near-isogenic lines. In situ hybridization located Zm00001d013603 on the primordia of the spikelet pair meristems and spikelet meristems, but not in the inflorescence meristem, which indicates a role in regulating the initiation of reproductive axillary meristems of ear inflorescences. Expression analysis and nucleotide sequence alignment revealed that Zm00001d013603, which encodes an endonuclease/exonuclease/phosphatase family protein that hydrolyzes phosphatidyl inositol diphosphates, is the causal gene of qKRN5b. These results provide insight into the genetic basis of KRN and have potential value for enhancing maize grain yield.

Comparison of PCR-RFLP, API® 20 Strep and MALDI-TOF MS for identification of Streptococcus spp. collected from sheep and goat milk samples

Abstract In this study, a bank of 195 Streptococcus isolates collected in Sardinia (Italy) from sheep and goat milk samples was analysed. The purpose of this research was to compare the accuracy of different methods of identifying Streptococcus at the species level: API® 20 Strep, PCR-RFLP and MALDI-TOF MS. For PCR-RFLP analysis, the housekeeping gap gene was used as target gene. After alignment of nucleotide sequences of different Streptococcus species, a primer set was designed to amplify a 945-bp DNA fragment. Amplicons of gap gene were submitted to restriction fragment length polymorphism analysis with the enzyme AluI. When PCR-RFLP patterns were different from those of their reference strains, gap gene products were sequenced for definitive identification. Most of the isolates displayed the same PCR-RFLP profile of Streptococcus uberis type strain (124, corresponding to 63.6%), followed by S. dysgalactiae (18, corresponding to 9.2%) and S. suis (14, corresponding to 7.2%). Overall, in comparison with PCR-RFLP and sequence analysis results, 161 over 195 Streptococcus isolates were identified to the same species levels by means API® 20 Strep (82.6% agreement, CI95 = 77.2–87.9) versus 166/195 (85.1% agreement, CI95 = 80.1–90.1) using MALDI-TOF. In conclusion, the PCR-RFLP is the most accurate and reproducible method for the identification of streptococci collected from milk samples, although high cost and technical difficulty hinder its usage in routine diagnosis. In our study, the accuracy of MALDI-TOF MS in detecting streptococci at the species level has not been perfect; however we believe that MALDI-TOF has the advantage in terms of its rapidity, reliability and low cost.

Complete genomic sequence of Pseudomonas lactis bacteriophage HU1 isolated from raw cow's milk.

The lytic cold-active phage HU1, a member of the family Podoviridae, infects Pseudomonas lactis and was first isolated from raw cow's milk. In this study, we used deep sequencing to determine and analyze the DNA genome sequence of HU1. We identified a 42,551-base-pair genome comprising double-stranded DNA, with 69 predicted open reading frames and a GC content of 56.4%. A whole-genome comparison did not identify HU1 as a member of any previously reported cluster of Pseudomonas phages. By contrast, HU1 was most similar to AF, which infects P. putida, with nucleotide sequence alignment coverage of 24%. These results suggest that HU1 is a novel Pseudomonas phage.

DIVERSIFICATION INTO THE GENUS Badnavirus: PHYLOGENY AND POPULATION GENETIC VARIABILITY

Badnaviruses (family Caulimoviridae) have semicircular dsDNA genomes encapsidated into bacilliform particles. The genus Badnavirus is the most important due to its high number of species reported infecting cultivated plants worldwide. This study aimed to evaluate the phylogenetic positioning and population genetic variability into Badnavirus. Data sets comprising the badnavirus complete genome and partial sequences of the RT and RNaseH genes were obtained from the GenBank database. Multiple nucleotide sequence alignments from complete genome, ORFIII, complete genomic domain RT/RNaseH (1020pb) and partial (579pb) were performed. A total of 127 genomes were obtained, representing 53 species of badnavirus. Nucleotide sequence comparisons for the RT/RNaseH domain showed only a few isolates reported as distinct species shared ≥80% identity, the current threshold used for species demarcation into this genus. Phylogenetic trees for the complete genome and for ORFIII showed four well supported clusters (badnavirus groups 1-4), with clusters 1 and 3 being sister groups comprising predominantly sugarcane- and banana-infecting species. Non-tree-like evolution analysis evidenced putative recombination events among badnaviruses, and at least 23 independent events were detected. High levels of nucleotide diversity were observed for the partial RT/RNaseH region in isolates of 11 badnavirus species. These results showed that mutation and recombination are important mechanisms that acting on badnavirus diversification.

Increased cellulose production by heterologous expression of bcsA and B genes from Gluconacetobacterxylinus in E. coli Nissle 1917.

Based on cellulose biosynthesis pathway of Gluconacetobacterxylinus BPR2001 and E. coli Nissle 1917, bcsA and bcsB genes have been selected and bioinformatics studies done to the analyses of nucleotide and amino acid sequence alignment, stability of RNA, protein, and promotor power. We amplify and clone bcsA, bcsB, and bcsAB genes of G. xylinus BPR2001 in Escherichiacoli Nissle 1917 under the inducible tac promoter. Our results of bioinformatics predictions demonstrate similar active site and three-dimensional structure of BcsA and BcsB proteins in two different bacteria. In addition, our data reveal that BcsA and BcsB proteins of E. coli have weaker promotor power, RNA secondary structure, and protein stability than that of the same proteins in G. xylinus. Some of the reasons of BcsAB protein selection from G. xylinus and its heterologous expression in E. coli is the noted points. Production of the related proteins visualized using SDS-PAGE. We find out that Congo red absorbance at 490nm has no significant difference in wild-type strain (E. coli Nissle 1917) compared to recombinants bcsA+ or bcsB+, but recombinant bcsAB+ could produce more cellulose than that of the wild-type strain. Furthermore, the measurement of cellulose dry weights of all samples confirms bacterial cellulose production enhancement in recombinant bcsAB+ (1.94gl-1). The FTIR analysis reveals that the crystallinity indices do not change significantly after over expressing each of genes.

Morphological characterization of Chironomidae (Diptera) larvae in Anzali Wetland, Southwest Caspian Sea: First record of Chironomus plumosus

Chironomids (Diptera) include the most abundant group of macroinvertebrates. They are usually collected from aquatic environments for quality evaluation. Tolerant aquatic organisms such as Chironomids are more abundant in polluted sites. This note makes the Chironomids as an excellent bioindicators. This group is not characterized in Anzali Wetland as well. So that, the aim of this study was to recover and characterize chironomidlarvae in this wetland. Hence, Chironomidlarvae were collected on the seasonal basis from 13 stations in the wetland. The main characteristics for their identification were eye spot, mentum, ventromental plate, antenna, and ventral tubules. The mitochondrial cytochrome oxidase I (COI) gene was applied to simplify the identification of Chironomus species by polymerase chain reaction (PCR) and sequencing method. The nucleotide sequence alignments were used for construction of the phylogenetic trees based on maximum likelihood method. Six genera were identified in three subfamilies, including: Chironominae (1 genus), Orthocladinae (1 genus), and Tanypodinae (4 genera). Based on ventral tubules, the dominant population of Chironomus larvae found in this study, lie in thummi and plumosus types. Five genera were reported for the first time from Anzali Wetland. The dominant genus was Chironomus. These groups of larvae were ultimately identified as Chironomus plumosus reporting for the first time from the wetland. It was also found that the Chironomids diversity is higher than those described in few studies before, however, further studies are still needed.

Computational analysis of naturally occurring resistance-associated substitutions in genes NS3, NS5A, and NS5B among 86 subtypes of hepatitis C virus worldwide.

Background and objectiveDirect-acting antivirals (DAA) facing resistance continue to be used in some areas worldwide. Thus, identifying hepatitis C virus (HCV) genotypes/subtypes and loci with certain prevalent resistance-associated substitutions (RASs) deserves attention. We investigated the global and regional frequencies of naturally occurring RASs among all confirmed HCV subtypes (n=86) and explored co-occurring and mutually exclusive RAS pairs within and between genes NS3, NS5A, and NS5B.MethodsA total of 213,908 HCV sequences available as of July 10, 2019 were retrieved from the NCBI nucleotide database. After curation, 17,312 NS3, 8,478 NS5A, and 25,991 NS5B sequence fragments from DAA-naïve patients were screened for RASs. MEGA 6.0 was used to translate aligned nucleotide sequences into amino acid sequences, and RAS pairs were identified by hypergeometric analysis.ResultsRAS prevalence varied significantly among HCV subtypes. For example, D168E, highly resistanct to all protease inhibitors except voxilaprevir, was nearly absent in all subtypes except in 43.48% of GT5a sequences. RASs in NS3 exhibiting significantly different global distribution included Q80K in GT1a with the highest frequency in North America (54.49%), followed by in Europe (22.66%), Asia (6.98%), Oceania (6.62%), and South America (1.03%). The prevalence of NS3 S122G in GT1b was highest in Asia (26.6%) and lowest in Europe (2.64%). NS5A L28M, R30Q, and Y93H in GT1b, L31M in GT2b, and NS5B C316N in GT1b was most prevalent in Asia. A150V in GT3a, associated with sofosbuvir treatment failure, was most prevalent in Asia (44.09%), followed by Europe (31.19%), Oceania (24.29%), and North America (19.05%). Multiple mutually exclusive or co-occurring RAS pairs were identified, including Q80K+R155K and R155K+D168G in GT1a and L159F+C316N and R30Q (NS5A)+C316N (NS5B) in GT1b.ConclusionOur data may be of special relevance for those countries where highly effective antivirals might not be available. Considering the specific RASs prevalence will help the clinicians to make optimal treatment choices. The RASs pairs would benefit anti-HCV drug development.

Bioinformatic analysis of chickpea acetohydroxyacid synthase gene

Aim. Analysis of homologues of chickpea gene encoding acetohydroxyacid synthase, by bioinformatics methods. Methods. Alignment of nucleotide sequences, UPGMA method, Maximum Composite Likelihood method, homologous modeling of three-dimensional structure of enzyme. Results. Homologues of the acetohydroxyacid syntase gene (AHAS) of chickpea were found among representatives of different families. A certain level of conservativeness of mRNA homologues sequences of AHAS gene within the families was noted, including legumes. The distribution of clusters corresponds to the taxonomic position of the investigated plant species. The single nucleotide polymorphism C / T at position 581, potentially associated with herbicide resistance, was detected. Based on the homologous modeling results, two models of the enzyme AHAS were constructed. The replacement of C / T, which leads to the replacement of the amino acids of alanine with valine, leads to a change in the conformation in the A chain of protein. Conclusions. Marker screening of the source breeding material by «real-time» polymerase chain reaction with the developed primers and the TaqMan probe to the polymorphic region of the AHAS gene will allow differentiating the herbicide «resistant» and «tolerant» alleles of the gene for the selection of target genotypes.
 Keywords: chickpea, acetohydroxyacid syntase gene, single nucleotide polymorphism, resistance to herbicides.

Polymorphism of two wheat degydrines genes

Aim. The aim of this work is to study the nucleotide sequences variability of two genes encoding wheat dehydrins. One of them belong to K-2 group, the other refers to K-3 type (respectively, TaDHN18 and TaDHN19.3 according to the classification of Wang et al.). These loci sre interesting due to their's genes participation in protection of plants from the various adverse abioti ecffects. Methods. Polymorphism of two genes encoding dehydrins was investigated using 6 wheat varieties as examples, among which were spring and winter varieties with different cold resistance, using PCR-based cloning, sequencing, and data processing softwares. Results. An analysis of the obtained nucleotide and hypothetical protein sequences alignment showed that the locus under study in the genomes of different wheat varieties, both spring and winter, is characterized by a high identity degree. Conclusions. The high conservatism of two loci encoding K-2 and K-3 dehydrins was demonstrated.
 Keywords: wheat, dehydrins, polymorphism.

First report of megalocytivirus (iridoviridae) in cultured bluegill sunfish, Lepomis macrochirus, in China

The bluegill sunfish, Lepomis macrochirus, is an important aquacultural and recreational species in southern China because of its excellent taste, rapid growth rate, and good looks. At present, few pathogens are known to affect the bluegill sunfish. However, an iridovirus-like disease recently caused heavy losses to the bluegill sunfish aquaculture industry in Guangdong, China. We report that a virus, designated BSMIV-SD-20171020, was isolated from diseased bluegill sunfish in China. The isolate was efficiently propagated in a Chinese perch brain (CPB) cell line. The cytopathic effect was observed, the MCP gene PCR amplified, and the virus observed with electron microscopy. Its viral titer in CPB cells reached 104.13 TCID50 mL−1. The mortality rate was 100% when bluegill sunfish were challenged with BSMIV-SD-20171020 at a dose of 103.13 TCID50/fish. A histopathological examination revealed basophilic hypertrophied cells in the intestine, liver, and spleen. A nucleotide sequence alignment and phylogenetic analysis of the major capsid protein revealed that isolate BSMIV-SD-20171020 is the species Infectious spleen and kidney necrosis virus (ISKNV), in the genus Megalocytivirus.

Pairwise alignment of nucleotide sequences using maximal exact matches

BackgroundPairwise alignment of short DNA sequences with affine-gap scoring is a common processing step performed in a range of bioinformatics analyses. Dynamic programming (i.e. Smith-Waterman algorithm) is widely used for this purpose. Despite using data level parallelisation, pairwise alignment consumes much time. There are faster alignment algorithms but they suffer from the lack of accuracy.ResultsIn this paper, we present MEM-Align, a fast semi-global alignment algorithm for short DNA sequences that allows for affine-gap scoring and exploit sequence similarity. In contrast to traditional alignment method (such as Smith-Waterman) where individual symbols are aligned, MEM-Align extracts Maximal Exact Matches (MEMs) using a bit-level parallel method and then looks for a subset of MEMs that forms the alignment using a novel dynamic programming method. MEM-Align tries to mimic alignment produced by Smith-Waterman. As a result, for 99.9% of input sequence pair, the computed alignment score is identical to the alignment score computed by Smith-Waterman. Yet MEM-Align is up to 14.5 times faster than the Smith-Waterman algorithm. Fast run-time is achieved by: (a) using a bit-level parallel method to extract MEMs; (b) processing MEMs rather than individual symbols; and, (c) applying heuristics.ConclusionsMEM-Align is a potential candidate to replace other pairwise alignment algorithms used in processes such as DNA read-mapping and Variant-Calling.

English

This study characterized Cucumber mosaic virus (CMV) infecting pepper in Southwestern Nigeria with the aim of providing up-to-date information on the taxonomic subgroup(s) of the parading strains in the study area. Fifty pepper leaf samples with one or more symptoms of mottling, mosaic, necrosis, leaf distortion and stunting were collected from eight commercial farms across Southwestern Nigeria and screened for CMV using antigen coated plate enzyme linked immunosorbent assay (ACP-ELISA). From the seropositive samples, four representative samples were selected, labelled PSWN1-4 before subjected to reverse transcription polymerase chain reaction (RT-PCR) and nucleic acid sequencing using a pair of primers specific for the amplification of RNA 3 genomic fragment of CMV. These were followed by multiple nucleotide sequence alignment and phylogenetic estimations of the isolates alongside selected CMV strains that were reported in previous studies using the molecular evolutionary genetics analysis (MEGA) software. The result of the ACP-ELISA test revealed that 14 (28%) of the samples collected were positive for CMV infection. The resulting nucleotide sequences from RT-PCR revealed 98% nucleotide homologies with several corresponding sequences of CMV strains from the Genbank. Further analysis of the PSWN nucleotide sequences through multiple nucleotide sequence alignment revealed the absence of the EcoR1 restriction site found only within the examined genomic portion of RNA 3 of subgroup II strains. These features defined the detected isolates as subgroup I strains. Phylogenetic analysis and estimations of genetic distances, conclusively distinguished the pepper-infecting CMV isolates from Southwestern Nigeria as members of subgroups IA and IB, which are the most virulent subgroups. Key words: Cucumber mosaic virus (CMV), pepper, Southwestern Nigeria.

A gene based bacterial whole genome comparison toolkit

Most of the computational biology analysis is made comparing genomic features. The nucleotide and amino acid sequence alignments are frequently used in gene function identification and genome comparison. Despite its widespread use, there are limitations in their analysis capabilities that need to be considered but are often overlooked or unknown by many researchers. This paper presents a gene based whole genome comparison toolkit which can be used not only as an alternative and more robust way to compare a set of whole genomes, but, also, to understand the tradeoff of the use of sequence local alignment in this kind of comparison. A study case was performed considering fifteen whole genomes of the Xanthomonas genus. The results were compared with the 16S rRNA-processing protein RimM phylogeny and some thresholds for the use of sequence alignments in this kind of analysis were discussed.

First Report of North American Grapevine Yellows (NAGY) in Kansas: Detection of ‘Candidatus Phytoplasma pruni’- and ‘Ca. Phytoplasma asteris’-Related Strains in Diseased Plants

During surveillance for possible presence of exotic phytoplasma pathogens in the United States, plants of cultivated grapevine (Vitis vinifera L.) exhibiting symptoms suggestive of grapevine yellows disease were observed in vineyards in Kansas during the 2013 and 2014 growing seasons. Symptoms observed in <1% of plants examined consisted of leaf yellowing, downward rolling of leaf margins, and shriveling of fruit clusters. Symptomatic plants of cultivars Riesling (designated KS-JO48) and Chardonnay (designated KS-DG12) were selected for further work. To detect and identify the suspected phytoplasmal pathogen strain(s), DNA was extracted from veins excised from symptomatic leaves and used as template in polymerase chain reactions (PCRs) for amplification and cloning of phytoplasma rRNA (rDNA) and secY gene sequences as previously described (Davis et al. 2015; Lee et al. 2010). Nucleotide sequences of the PCR products were deposited in the GenBank database under accession numbers MH085064 and MH085065 (for cloned rrnA and rrnB gene sequences, respectively, reflecting interoperon heterogeneity) and MG992477 (secY) for KS-JO48; and MH085066 (rrnA), MH085067 (rrnB), and MG992478 (secY) for KS-DG12. In silico analysis of 16S rRNA gene sequences, using iPhyClassifier (Zhao et al. 2009), revealed that plant KS-JO48 was infected by a ‘Candidatus Phytoplasma asteris’-related phytoplasma belonging to subgroup 16SrI-A (I-A), and that plant KS-DG12 was infected by a ‘Ca. P. pruni’-related phytoplasma belonging to subgroup variant 16SrIII-A* (III-A*). Nucleotide sequence alignment of the strain KS-DG12 16S rRNA gene sequence with those of North American grapevine yellows (NAGY) strains previously reported (Davis et al. 2015) revealed that strain KS-DG12 is a NAGYIIIβ sequevar corresponding to sequevar NAGYIIIβ strains found in Maryland, Virginia, New York, and Pennsylvania (Davis et al. 2015). Alignments and phylogenetic analyses of secY gene sequences confirmed the close relatedness of the Kansas subgroup 16SrI-A strain KS-JO48 and subgroup 16SrIII-A* (NAGYIIIβ sequevar) strain KS-DG12 phytoplasmas with the reference strains of ‘Ca. P. asteris’ and ‘Ca. P. pruni’, respectively. The results provide the first evidence for the presence of NAGY in the state of Kansas, while revealing that the two NAGY phytoplasma strain lineages reported here are closely related to NAGY phytoplasma strains detected in other U.S. states. Although further work will be necessary to assess the impacts of NAGY in Kansas, the findings reported here expand the known geographic range of NAGY disease and support the concept that the geographic distribution of NAGY in the United States is greater than currently realized.

Characterisation of KiSS1R gene and Non genetic factors affecting reproductive traits in Indian goats

This study was undertaken to explore the genetic polymorphism in the KiSS1R (GPR54) gene from 80 Black Bengal, 50 Ganjam and 20 Raighar goat. Each of the sampled goats was recorded for its reproductive traits. The genomic DNA was isolated from the collected blood samples. The target 3’ UTR comprising of 246 bp fragment of KiSS1R gene was successfully amplified using the specific primer. Amplified samples were subjected for HRM analysis followed by sequencing. The nucleotide sequence alignment with the retrieved DNA sequence from NCBI BLAST confirmed absence of polymorphic pattern in KiSS1R gene in 3’ UTR. However, in the studied populations breed had significant effect on littersize, kidding interval and age at sexual maturity. It was found that age at sexual maturity and kidding interval were the highest in Ganjam goat population as compared to Raighar and Black Bengal goat population. Litter size was found highest in Black Bengal goat.

Nucleotide structure of prion protein gene in Egyptian camels

ABSTRACT The prion protein is coded by the PRP gene which is active in the brain and several other tissues. The functions of normal PrPs are related to energy production, protein degradation and DNA replication. Prions are the essential factor for the transmissible spongiform encephalopathies (TSEs) in different mammalian species. The present study aimed to identify the nucleotide characterization of the PRP gene in six camel breeds reared in Egypt. Genomic DNA which was extracted from 80 camels belonging to six breeds reared in Egypt was used to amplify fragments at 725-bp using a specific primer for PRP gene. Alignment of Egyptian camel PRP nucleotide sequences with those of other mammalian species declared the similarity 100% between PRP sequences of Egyptian and Iranian camels and 99.7% similarity with English, German and Chinese camel populations. The nucleotide sequence of Egyptian camel was submitted to GenBank under the accession no.: MF685344. The comparison between PRP amino acids of Camelus species with other mammalian species showed two missing amino acids in Camelus and Lama glama species; Glycine at position 83 and Leucine at position 229 whereas there is a unique amino acid addition – Glycine at position 89 – in Camelus species.

Genetic identification of bovine leukaemia virus

Molecular genetic research methods make it possible to evaluate the genetic diversity of bovine leukemia virus (BLV) and are the most informative approaches to its genetic identification. Molecular genetic research methods work well for the phylogenetic analysis of sequenced nucleotide DNA sequences of the provirus, as well as for the polymerase chain reaction-restriction fragment length polymorphism analysis (PCR-RFLP) according to the phylogenetic classification of the pathogen. The purpose of the research was to study the scientific and methodological approaches to the genetic identification of bovine leukemia virus, integrated into the molecular monitoring of infection of cattle with BLV genotypes. The authors used PCR-RFLP-genotyping and comparative phylogenetic analysis of aligned nucleotide sequences of the env gene fragment of the BLV provirus isolates to detect the genotypic affiliation of the cattle from twenty-one livestock farms of the Republic of Tatarstan. As a result, isolates of four out of ten BLV genotypes were found in the Tatarstani cattle, namely genotypes 1, 4, 7, and 8. The research involved a comparative analysis of 505 nucleotide sequences of a fragment of the BLV env gene, including those deposited in GenBank NCBI. The analysis confirms the inconsistency of several earlier PCR-RFLP typing strategies with the current approach in assessing the genotypic diversity by phylogenetic analysis. The improved strategy of PCR-RFLP genotyping of BLV corresponds with its modern phylogenetic classification. The strategy makes it possible to identify all the known genotypes of the viral pathogen. Its validity has been proved by in silico modelling of restrictogrammes and a phylogenetic analysis of the env gene fragment of 57 reference isolates of ten BLV genotypes that generate 57 genotype-associated combinations of diagnostically significant PCR-RFLP profiles.

Коитальная экзантема лошадей: диагностика и идентификация возбудителя

Comprehensive studies were performed during an acute outbreak of horses with symptoms of exanthematous lesions of the external genitalia, observed in 2018. The lesion of the external genital organs was observed in the form of puffiness of the vestibule of the vagina and vulva in mares and prepuce in stallions, formation on the mucous membrane and skin of papules, vesicles and pustules, in the last stage - ulceration and crusts on the affected areas. A fragment of the genome of equine herpesvirus type 3, the causative agent of coital exanthema, was found in scrapings from the affected areas using the methods of molecular genetic analysis. The results of the determination of nucleotide sequences showed a high degree of phylogenetic relationship with the strain «YS-1» isolated from sick horses in Japan in 2017. The homology of alignment of nucleotide sequences within the studied region of the genome ― a fragment of the gpG gene (813…1292 bp) ― was 100 %. In 90 % of the samples containing the DNA of the coital exanthema virus, DNA of the virus of rhinopneumonia-viral abortion (equine herpesvirus type 1) was also found, and only in 10 % of cases monoinfection of EHV-3 was observed. Participation in the EHV-1 infectious process was confirmed by a retrospective serological study. In NT, antibodies to EHV-1 were detected in a titer of 1: 16…1: 32. A comparative analysis of retrospective data showed that a similar outbreak of coital exanthema observed in 1980–81 was due to EHV-3 monoinfection.

A benchmark study of sequence alignment methods for protein clustering

BackgroundProtein sequence alignment analyses have become a crucial step for many bioinformatics studies during the past decades. Multiple sequence alignment (MSA) and pair-wise sequence alignment (PSA) are two major approaches in sequence alignment. Former benchmark studies revealed drawbacks of MSA methods on nucleotide sequence alignments. To test whether similar drawbacks also influence protein sequence alignment analyses, we propose a new benchmark framework for protein clustering based on cluster validity. This new framework directly reflects the biological ground truth of the application scenarios that adopt sequence alignments, and evaluates the alignment quality according to the achievement of the biological goal, rather than the comparison on sequence level only, which averts the biases introduced by alignment scores or manual alignment templates. Compared with former studies, we calculate the cluster validity score based on sequence distances instead of clustering results. This strategy could avoid the influence brought by different clustering methods thus make results more dependable.ResultsResults showed that PSA methods performed better than MSA methods on most of the BAliBASE benchmark datasets. Analyses on the 80 re-sampled benchmark datasets constructed by randomly choosing 90% of each dataset 10 times showed similar results.ConclusionsThese results validated that the drawbacks of MSA methods revealed in nucleotide level also existed in protein sequence alignment analyses and affect the accuracy of results.

Genomic characterization and pathogenicity of porcine deltacoronavirus strain CHN-HG-2017 from China.

Porcine deltacoronavirus (PDCoV) was first detected in Hong Kong and has recently spread to many countries around the world. PDCoV causes acute diarrhea and vomiting in pigs, resulting in significant economic losses in the global pork industry. In this study, a Chinese PDCoV strain, designated CHN-HG-2017, was isolated from feces of a suckling piglet with severe watery diarrhea on a farm located in central China. Subsequently, the virus was identified by an indirect immunofluorescence assay and electron microscopy. A nucleotide sequence alignment showed that the whole genome of CHN-HG-2017 is 97.6%-99.1% identical to other PDCoV strains. Analysis of potential recombination sites showed that CHN-HG-2017 is a possible recombinant originating from the strains CH/SXD1/2015 and Vietnam/HaNoi6/2015. Furthermore, the pathogenicity of this recombinant PDCoV strain was investigated in 5-day-old piglets by oral inoculation. The challenged piglets developed typical symptoms, such as vomiting, anorexia, diarrhea and lethargy, from 1 to 7 days post-inoculation (DPI). Viral shedding was detected in rectal swabs until 14 DPI in the challenged piglets. Interestingly, high titers of virus-neutralizing antibodies in sera were detected at 21 DPI. Tissues of small intestines from CHN-HG-2017-infected piglets at 4 DPI displayed significant macroscopic and microscopic lesions with clear viral antigen expression. Our analysis of the full genome sequence of a recombinant PDCoV and its virulence in suckling piglets might provide new insights into the pathogenesis of PDCoV and facilitate further investigation of this newly emerged pathogen.