• Mycobiology
• /
• v.48 no.6
• /
• pp.464-475
• /
• 2020

Acervus (Pyronemataceae, Pezizales) is a saprobic genus in Pezizomycetes, characterized by colored apothecia, subcylindrical to cylindrical asci and guttulate ascospores. We collected four Acervus samples from China and Thailand. Descriptions and illustrations are introduced for all fresh samples. One new record of A. globulosus from Thailand, one new species, A. rufus, two known species, A. epispartius and A. stipitatus from China are reported. Phylogenetic analysis based on five genes, the large subunit rRNA (LSU), the translation elongation factor-1 alpha (tef1-α), the second largest subunit of RNA polymerase II (rpb2), the largest subunit of RNA polymerase II (rpb1), and the small subunit rRNA (SSU), revealed the distinct position of the new species. The new species is set apart by its red apothecia. A key to Acervus species is also given.

• The Plant Pathology Journal
• /
• v.37 no.3
• /
• pp.280-290
• /
• 2021

Population genetic studies of Hemileia vastatrix have been conducted in order to describe the evolutionary dynamics of the pathogen and the disease epidemiology as consequence of changes in disease management and host distribution occurred in Peru after the 2013 epidemic. These analyses were performed by sequencing the internal transcribed spacers of the nuclear ribosomal DNA (rDNA-ITS) of H. vastatrix collected from two coffee growing areas in 2014 and 2018. H. vastatrix population showed high haplotype diversity (Hd = 0.9373 ± 0.0115) with a low nucleotide diversity (π = 0.00322 ± 0.00018). Likewise, AMOVA indicated that fungus population has behaved as a large population without structuring by geographical origin and sampling years (F_ST = 0.00180, P = 0.20053 and F_ST = 0.00241, P = 0.19693, respectively). Additionally, the haplotype network based on intraspecific phylogenetic analysis of H. vastatrix using Peruvian and NCBI sequences revealed that Peruvian ancestral haplotypes, which were maintained in time and space, would correspond to the reported sequences of the races II and XXII. This result suggests that no substantial changes have occurred through time in Peruvian Hemileia vastatrix population.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2020.06a
• /
• pp.120-120
• /
• 2020

Based on the simple sequence repeat (SSR) marker, a Korean wheat core collection were established with 616 wheat accessions. Among them, the SNP genotyping for the entire genome was performed using DNA chip array to clarify the whole genome SNP profiles. Consequently, a total of 35,143 SNPs were found and we re-established a mini-core collection with 247 accessions. Population diversity and phylogenetic analysis revealed genetic diversity and relationships from the mini core set. In addition, genome-wide association study (GWAS) was performed on 19 phenotypic traits; ear type, awn length, culm length, ear length, awn color, seed coat color, culm color, ear color, loading, leaf length, leaf width, seeding stand, cold damage, weight, auricle, plant type, heading stage, maturation period, upright habit, and degree of flag leaf. The GWAS was performed using the fixed and random model circulating probability unification (FarmCPU), which identified 14 to 258 SNP loci related to 19 phenotypic traits. Our study indicates that this Korean wheat mini-core collection is a set of germplasm useful for basic and applied research with the aim of understanding and exploiting the genetic diversity of Korean wheat varieties.

• Korean Journal of Environmental Biology
• /
• v.29 no.3
• /
• pp.225-235
• /
• 2011

The change of microbial communities during cyanobacterial bloom was comparatively analyzed by 16S rDNA PCR-DGGE in Daechung Reservoir during 2003~2005. Morphological analysis showed that Cyanophyceae dominated algal community in the bloom. Dominant cyanobacteria were Microcystis, Planktothrix (Oscillatoria), Phormidium and Anabaena. We used 16S rDNA-denaturing gradient gel electrophoresis (DGGE) profiles and phylogenetic affiliations of the DGGE bands to analyze the community structure and diversity of the predominant microbial community. The DGGE band patterns demonstrated that the most frequent bands were identified as Microcystis during the monitoring periods, Planktothrix also dominated on September 2003 and 2004, whereas Anabaena was showed a peak on September 2005 and Aphanizomenon on August 2003. DGGE and phylogenetic analysis provided us new information that could not be obtained by traditional, morphological analysis. The relationship between cyanobacteria and other aquatic bacteria can be traced and their genetic diversity also identified in detail.

• ALGAE
• /
• v.34 no.4
• /
• pp.277-288
• /
• 2019

Freshwater red algae of the order Batrachospermales are poorly studied in India and Nepal, especially on a molecular basis. During a survey in northeast India and east Nepal, six populations of the genus Sheathia were found and analyzed using molecular and morphological evidence. Phylogenetic analyses based on the rbcL gene sequences grouped all populations in a large clade including our S. arcuata specimens and others from several regions. Sheathia arcuata represents a species complex with a high sequence divergence and several smaller clades. Samples from India and Nepal were grouped in three distinct clades with high support and representing new cryptic species: a clade formed by two samples from India, which was named Sheathia assamica sp. nov.; one sample from India and one from Nepal formed another clade, named Sheathia indonepalensis sp. nov.; two samples from Nepal grouped with sequences from Hawaii and Indonesia (only 'Chantransia' stages) and gametophytes from Taiwan, named Sheathia dispersa sp. nov. Morphological characters of the specimens from these three species overlap one another and with the general circumscription of S. arcuata, which lacks the heterocortication (presence of bulbous cells in the cortical filaments) present in other species of the genus Sheathia. Although the region sampled is relatively restricted, the genetic diversity among specimens of these three groups was high and not closely related in the phylogenetic relationship with the other clades of S. arcuata. These data corroborate information from other groups of organisms (e.g., land and aquatic plants) that indicates this region (Eastern Himalaya) as a hotspot of biodiversity.

• BMB Reports
• /
• v.40 no.4
• /
• pp.577-587
• /
• 2007

Single-copy chloroplast loci are used widely to infer phylogenetic relationship at different taxonomic levels among various groups of plants. To test the utility of chloroplast loci and to provide additional data applicable to hybrid evolution in Musa, we sequenced two introns, rpl16 and ndhA, and two intergenic spacers, psaA-ycf3 and petA-psbJ-psbL-psbF and combined these data. Using these four regions, Musa acuminata Cola(A)- and M. balbisiana Colla (B)-containing genomes were clearly distinguished. Some triploid interspecific hybrids contain A-type chloroplasts (the AAB/ABB) while others contain B-type chloroplasts (the BBA/BBB). The chloroplasts of all cultivars in 'Namwa' (BBA) group came from the same wild maternal origin, but the specific parents are still unrevealed. Though, average sequence divergences in each region were little (less than 2%), we propose that petA-psbJ intergenic spacer could be developed for diversity assessment within each genome. This segment contains three single nucleotide polymorphisms (SNPs) and two indels which could distinguish diversity within A genome whereas this same region also contains one SNP and an indel which could categorize B genome. However, an inverted repeat region which could form hairpin structure was detected in this spacer and thus was omitted from the analyses due to their incongruence to other regions. Until thoroughly identified in other members of Musaceae and Zingiberales clade, utility of this inverted repeat as phylogenetic marker in these taxa are cautioned.

• Journal of Microbiology and Biotechnology
• /
• v.21 no.4
• /
• pp.333-340
• /
• 2011

Herbicide-tolerant Zoysia grass has been previously developed through Agrobacterium-mediated transformation. We investigated the effects of genetically modified (GM) Zoysia grass and the associated herbicide application on bacterial community structure by using culture-independent approaches. To assess the possible horizontal gene transfer (HGT) of transgenic DNA to soil microorganisms, total soil DNAs were amplified by PCR with two primer sets for the bar and hpt genes, which were introduced into the GM Zoysia grass by a callus-type transformation. The transgenic genes were not detected from the total genomic DNAs extracted from 1.5 g of each rhizosphere soils of GM and non-GM Zoysia grasses. The structures and diversities of the bacterial communities in rhizosphere soils of GM and non-GM Zoysia grasses were investigated by constructing 16S rDNA clone libraries. Classifier, provided in the RDP II, assigned 100 clones in the 16S rRNA gene sequences library into 11 bacterial phyla. The most abundant phyla in both clone libraries were Acidobacteria and Proteobacteria. The bacterial diversity of the GM clone library was lower than that of the non- GM library. The former contained four phyla, whereas the latter had seven phyla. Phylogenetic trees were constructed to confirm these results. Phylogenetic analyses of the two clone libraries revealed considerable difference from each other. The significance of difference between clone libraries was examined with LIBSHUFF statistics. LIBSHUFF analysis revealed that the two clone libraries differed significantly (P<0.025), suggesting alterations in the composition of the microbial community associated with GM Zoysia grass.

• Journal of Veterinary Science
• /
• v.22 no.5
• /
• pp.73.1-73.11
• /
• 2021

Background: Feline calicivirus (FCV) is a common pathogen of felids, and FCV vaccination is regularly practiced. The genetic variability and antigenic diversity of FCV hinder the effective control and prevention of infection by vaccination. Improved knowledge of the epidemiological characteristics of FCV should assist in the development of more effective vaccines. Objectives: This study aims to determine the prevalence of FCV in a population of cats with FCV-suspected clinical signs in Hangzhou and to demonstrate the antigenic and genetic relationships between vaccine status and representative isolated FCV strains. Methods: Cats (n = 516) from Hangzhou were investigated between 2018 and 2020. The association between risk factors and FCV infection was assessed. Phylogenetic analyses based on a capsid coding sequence were performed to identify the genetic relationships between strains. In vitro virus neutralization tests were used to assess antibody levels against isolated FCV strains in client-owned cats. Results: The FCV-positive rate of the examined cats was 43.0%. Risk factors significantly associated with FCV infection were vaccination status and oral symptoms. Phylogenetic analysis revealed a radial phylogeny with no evidence of temporal or countrywide clusters. There was a significant difference in the distribution of serum antibody titers between vaccinated and unvaccinated cats. Conclusions: This study revealed a high prevalence and genetic diversity of FCV in Hangzhou. The results indicate that the efficacy of FCV vaccination is unsatisfactory. More comprehensive and refined vaccination protocols are an urgent and unmet need.

• Parasites, Hosts and Diseases
• /
• v.60 no.4
• /
• pp.289-293
• /
• 2022

Blastocystis is a genus of unicellular heterokont parasites belonging to a group of organisms known as Stramenopiles, which includes algae, diatoms, and water molds. Blastocystis includes several species that habitat in the gastrointestinal tracts of organisms as diverse as humans, farm animals, birds, rodents, reptiles, amphibians, fish, and cockroaches. It is important to public health and distributed globally, but its prevalence in dogs in Korea has not been reported to date. Here, we collected 787 canine fecal samples and assessed Blastocystis infection by age, sex, region, season, and diarrhea symptoms. We determined Blastocystis subtypes using phylogenetic analyses based on 18S rRNA gene sequences. We identified, 10 Blastocystis positive samples (1.3%). A higher proportion of infected dogs was asymptomatic; however, infection rates did not significantly differ according to region, age, sex, and season. Phylogenetic analysis showed that the Blastocystis sp. identified belonged to 4 subtypes (STs), ST1, ST5, ST10, and ST14, thus revealed the genetic diversity of Blastocystis sp. in dogs Korean. This is first report on the presence of Blastocystis sp. in dogs Korean. This study revealed a lower infection rate than expected and differed from previous studies in STs. Further studies are warranted to observe the national infection status of Blastocystis in dogs and the genetic characteristics of this genus.

• Animal Bioscience
• /
• v.35 no.4
• /
• pp.517-526
• /
• 2022

Objective: The growth differentiation factor 8 (GDF8) gene plays a key role in bone formation, resorption, and skeletal muscle development in mammals. Here, we studied the genetic variants of GDF8 and their contribution to body conformation traits in Chinese Dabieshan cattle. Methods: Single nucleotide polymorphisms (SNPs) were identified in the bovine GDF8 gene by DNA sequencing. Phylogenetic analysis, motif analysis, and genetic diversity analysis were conducted using bioinformatics software. Association analysis between five SNPs, haplotype combinations, and body conformation traits was conducted in 380 individuals. Results: The GDF8 was highly conserved in seven species, and the GDF8 sequence of cattle was most similar to the sequences of sheep and goat based on the phylogenetic analysis. The motif analysis showed that there were 12 significant motifs in GDF8. Genetic diversity analysis indicated that the polymorphism information content of the five studied SNPs was within 0.25 to 0.5. Haplotype analysis revealed a total of 12 different haplotypes and those with a frequency of <0.05 were excluded. Linkage disequilibrium analysis showed a strong linkage (r²>0.330) between the following SNPs: g.5070C>A, g.5076T>C, and g.5148A>C. Association analysis indicated these five SNPs were associated with some of the body conformation traits (p<0.05), and the animals with haplotype combination H1H1 (-GGGG CCTTAA-) had greater wither height, hip height, heart girth, abdominal girth, and pin bone width than the other (p<0.05) Dabieshan cattle. Conclusion: Overall, our results indicate that the genetic variants of GDF8 affected the body conformation traits of Chinese Dabieshan cattle, and the GDF8 gene could make a strong candidate gene in Dabieshan cattle breeding programs.