• Journal of Microbiology and Biotechnology
• /
• 제34권6호
• /
• pp.1249-1259
• /
• 2024

It remains to be determined whether there is a geographical distribution pattern and phylogenetic signals for the Mycena strains with seed germination of the orchid plant Gastrodia elata. This study analyzed the community composition and phylogenetics of 72 Mycena strains associated with G. elata varieties (G. elata. f. glauca and G. elata. f. viridis) using multiple gene fragments (ITS+nLSU+SSU). We found that (1) these diverse Mycena phylogenetically belong to the Basidiospore amyloid group. (2) There is a phylogenetic signal of Mycena for germination of G. elata. Those strains phylogenetically close to M. abramsii, M. polygramma, and an unclassified Mycena had significantly higher germination rates than those to M. citrinomarginata. (3) The Mycena distribution depends on geographic site and G. elata variety. Both unclassified Mycena group 1 and the M. abramsii group were dominant for the two varieties of G. elata; in contrast, the M. citrinomarginata group was dominant in G. elata f. glauca but absent in G. elata f. viridis. Our results indicate that the community composition of numerous Mycena resources in the Zhaotong area varies by geographical location and G. elata variety. Importantly, our results also indicate that Mycena's phylogenetic status is correlated with its germination rate.

• Animal cells and systems
• /
• 제15권2호
• /
• pp.161-168
• /
• 2011

Siberian chipmunks, Tamias sibiricus, are one of several popular companion animals found in the pet shops of South Korea. At present, however, there have been no studies done in South Korea examining their origin even though they could be potential carriers of zoonotic diseases, and are a species of concern for efficient conservation and management strategies. Sequences of the mitochondrial cytochrome b gene (1140 bp) were determined to investigate the origin of Siberian chipmunks sold in four South Korean pet shops through comparison with sequence data from animals of known locality. Nine Siberian chipmunks were collected from pet shops in South Korea, which resulted in nine haplotypes. One (AR) of these coincided with the haplotype previously described. Phylogenetic and network analyses using 53 haplotypes including 45 haplotypes from GenBank showed three phylogenetic groups in South Korea, almost concordant to locality, designated as northern, central, and southern parts as described in a previous study. Of the nine individuals examined from the pet shops, eight were clustered into the northern phylogroup but one (cgrb9153) was grouped with the southern phylogroup, implying that at least the Siberian chipmunks examined in this study did not originate from other countries. It is likely that most individuals sold in the pet shops of Seoul were caught in the wild in Gyeonggi-do and Gangwon-do, or are maternal descendants of captive-bred individuals originating from the northern part of South Korea. It is recommended that conservation and management units of Korean chipmunks should be examined in further detail.

• Journal of Microbiology and Biotechnology
• /
• 제18권1호
• /
• pp.15-22
• /
• 2008

Four series (S, M, R, and W) of Alternaria longipes isolates were obtained based on consecutive selection with Dimethachlon (Dim) and ultraviolet irradiation. These isolates were then characterized according to their tolerance to Dim, sensitivity to osmotic stress, and phenotypic properties. All the selected Dim-resistant isolates showed a higher osmosensitivity than the parental strains, and the last generation was more resistant than the first generation in the M, R, and W series. In addition, the changes in the Dim resistance and osmotic sensitivity were not found to be directly correlated, and no distinct morphologic characteristics were found among the resistant and sensitive isolates, with the exception of the resistant isolate K-11. Thus, to investigate the molecular basis of the fungicide resistance, a group III two-component histidine kinase (HK) gene, AlHK1, was cloned from nineteen A. longipes isolates. AlHK1p was found to be comprised of a six 92-amino-acid repeat domain (AARD), HK domain, and response regulator domain, similar to the Os-1p from Neurospora crassa. A comparison of the nucleotide sequences of the AlHK1 gene from the Dim-sensitive and -resistant isolates revealed that all the resistant isolates contained a single-point mutation in the AARD of AlHK1p, with the exception of isolate K-11, where the AlHK1p contained a deletion of 107 amino acids. Moreover, the AlHK1p mutations in the isolates of each respective series involved the same amino acid substitution at the same site, although the resistance levels differed significantly in each series. Therefore, these findings suggested that a mutation in the AARD of AlHK1p was not the sole factor responsible for A. longipes resistance to dicarboximide fungicides.

• Mycobiology
• /
• 제51권1호
• /
• pp.36-48
• /
• 2023

Xanthoria elegans is a lichen symbiosis, that inhabits extreme environments and can absorb UV-B. We reported the de novo sequencing and assembly of X. elegans genome. The whole genome was approximately 44.63 Mb, with a GC content of 40.69%. Genome assembly generated 207 scaffolds with an N50 length of 563,100 bp, N90 length of 122,672 bp. The genome comprised 9,581 genes, some encoded enzymes involved in the secondary metabolism such as terpene, polyketides. To further understand the UV-B absorbing and adaptability to extreme environments mechanisms of X. elegans, we searched the secondary metabolites genes and gene-cluster from the genome using genome-mining and bioinformatics analysis. The results revealed that 7 NR-PKSs, 12 HR-PKSs and 2 hybrid PKS-PKSs from X. elegans were isolated, they belong to Type I PKS (T1PKS) according to the domain architecture; phylogenetic analysis and BGCs comparison linked the putative products to two NR-PKSs and three HR-PKSs, the putative products of two NR-PKSs were emodin xanthrone (most likely parietin) and mycophelonic acid, the putative products of three HR-PKSs were soppilines, (+)-asperlin and macrolactone brefeldin A, respectively. 5 PKSs from X. elegans build a correlation between the SMs carbon skeleton and PKS genes based on the domain architecture, phylogenetic and BGC comparison. Although the function of 16 PKSs remains unclear, the findings emphasize that the genes from X. elegans represent an unexploited source of novel polyketide and utilization of lichen gene resources.

• Animal Systematics, Evolution and Diversity
• /
• 제33권3호
• /
• pp.169-175
• /
• 2017

In the northwestern Pacific region, the pen shell (Atrina pectinata) is a widely distributed bivalve and economically important in fisheries. Recently, stock of this species has been greatly reduced due to overexploitation and marine pollution, which arouses interest in conservation. Studies on genetic and taxonomic entities of pen shells have not been tried in Korea, which makes difficult to take measures for effective conservation of this marine resource. In this study, we investigated mitochondrial genetic polymorphism of pen shells collected from 4 locations in Korea and Japan using cytochrome c oxidase I (COI) gene sequences. A total of 39 haplotypes were identified among 86 individuals of pen shell. Although only 5 haplotypes were shared, no significant genetic differentiation was observed between Korean and Japanese populations. These results suggest that pen shell populations of these regions share an ancestral population which might have experienced expansion during the Pleistocene, but gene flow must have been highly restricted after expansion.

• 한국작물학회:학술대회논문집
• /
• 한국작물학회 2017년도 9th Asian Crop Science Association conference
• /
• pp.68-68
• /
• 2017

The status of corn genetic diversity in the uplands of Sarangani in Southern Philippines was investigated using 12 morphological traits subjected to multivariate statistical analyses. Information about traditional farming, post-harvest and storage practices were also elicited especially in relation to losses of traditional varieties, a phenomenon known as genetic erosion. While a handful of farmers still plant traditional corn varieties in the remotest areas, a significant number had already shifted to genetically modified corn. Furthermore, principal component analysis (PCA) reduced the 12 morphological traits into 5 principal components and identified ear length and ear weight to be major contributors to variation. Cluster Analysis, on the other hand, formed two distinct groups but failed to give information about intra-cluster variability among the 32 collected corn accessions. These results warrant that more informative morphological traits and that molecular markers will be used to obtain a better picture of genetic diversity in Sarangani upland corn. Molecular analysis is also needed to establish genetic identities of these cultivars and to detect gene introgression from GM varieties into the gene pool of farmers' corn varieties. These analyses are imperative for the conservation of traditional corn varieties before they disappear in the Sarangani uplands because of shifting priorities of upland farmers.

• Asian-Australasian Journal of Animal Sciences
• /
• 제31권11호
• /
• pp.1729-1737
• /
• 2018

Objective: The aim of the current study is to investigate the relationship between prohibitin (PHB), capping actin protein of muscle Z-line beta subunit (CAPZB), and tektin-2 (TEKT2) and sperm motility in Murrah buffalo. Methods: We collected the high-motility and low-motility semen samples, testis, ovary, muscle, kidney, liver, brain and pituitary from Murrah buffalo, and analysed the expression of PHB, CAPZB, and TEKT2 in mRNA (message RNA) and protein level. Results: Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) result showed that the expression of PHB was higher and CAPZB, TEKT2 were specifically expressed in testis as compared to the other 6 tissues, and that in testis, the expression of TEKT2 was higher than that of CAPZB and PHB. Immunohistochemistry test revealed that all three genes were located on the convoluted seminiferous tubule and enriched in spermatogenic cells. Both qRT-PCR and Western Blot results showed that the expression levels of PHB, CAPZB, and TEKT2 were significantly lower in the low-motility semen group compared to the high-motility semen group (p<0.05). Conclusion: The expression levels of PHB, CAPZB, and TEKT2 in Murrah buffalo sperm have a high positive correlation with sperm motility. And the three genes may be potential molecular markers for the decline of buffalo sperm motility.

• International Journal of Industrial Entomology and Biomaterials
• /
• 제15권1호
• /
• pp.47-58
• /
• 2007

The tiny dragonfly, Nannophya pygmaea(Odonata: Libellulidae) is one the smallest dragonflies in the world and listed as a second-degree endangered wild animal and plant in Korea. For the long-term conservation of such endangered species, an investigation on nation-wide genetic magnitude and nature of genetic diversity is required as a part of conservation strategy. We, thus, sequenced a portion of mitochondrial COI gene, corresponding to "DNA Barcode" region(658 bp) from 68 N. pygmaea individuals collected over six habitats in Korea. The sequence data were used to investigate genetic diversity within populations and species, geographic variation within species, phylogeographic relationship among populations, and phylogenetic relationship among haplotypes. Phylogenetic analysis and uncorrected pairwise distance estimate showed overall low genetic diversity within species. Regionally, populations in southern localities such as Gangjin and Gokseong in Jeollanamdo Province showed somewhat higher genetic diversity estimates than those of remaining regions in Korean peninsula. Although geographic populations of N. pygmaea were subdivided into two groups, distance- or region-based geographic partition was not observed.

• BMB Reports
• /
• 제42권6호
• /
• pp.356-360
• /
• 2009

In the present study we have examined human-mouse homologous intronless disease and non-disease genes alongside their extent of sequence conservation, tissue expression, domain and gene ontology composition to get an idea regarding evolutionary and functional attributes. We show that selection has significantly discriminated between the two groups and the disease associated genes in particular exhibit lower $K_{a}$ and $K_{a}/K_{s}$ while $K_{s}$ although smaller is not significantly different. Our analyses suggest that majority of disease related intronless human genes have homology limited to eukaryotic genomes and their expression is localized. Also we observed that different classes of intronless disease related genes have experienced diverse selective pressures and are enriched for higher level functionality that is essentially needed for developmental processes in complex organisms. It is expected that these insights will enhance our understanding of the nature of these genes and also improve our ability to identify disease related intronless genes.

• Journal of Life Science
• /
• 제10권1호
• /
• pp.40-44
• /
• 2000

The SNF2/SW ATPase/helicase family comprises proteins form a variety of species with in vivo functions, such as transcriptional regulation, maintenance of chromosome stability during mitosis, and various types of DNA repair. Here, we reported the characterization of h게2+gene which was iolated by PCR amplification using the conserved domain of SNF2 motifs. Sequence analysis of PCR product showed striking evolutionary conservation among the SNF2 family of proteins. Two transcripts of 6.7 and 3.4 Lb were detected by Northern blot analysis. furthermore, the intensities of these two bands were increased by ultraviolet(UV) irradiation. These results indicate that the hrp2+ is a novel member of the SNF2 family of proteins and is one of the UV-inducible genes in S. pombe. To determine the level of transcripts of hrp2+ gene during cellular growth, Northern blot analysis were performed. This result indicates that the level of hrp2+transcript reached its maximum before cells entered the exponential growth phase. This suggests that hrp2+ gene is experssed mainly at the early stage of cell growth.