• The Plant Pathology Journal
• /
• v.40 no.2
• /
• pp.171-191
• /
• 2024

Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.

• Journal of the Korea Academia-Industrial cooperation Society
• /
• v.18 no.1
• /
• pp.141-147
• /
• 2017

In this study, a meta-analysis of fecal bacteria in dogs was conducted using 16S rRNA gene sequences that have been recovered from cloning and Sanger sequencing. For this meta-analysis, we retrieved all 16S rRNA gene sequences recovered from fecal bacteria in dogs in the RDP database (Release 11, Update 3). A total of 420 sequences were identified from the RDP database, 42 of which were also recovered from cultured isolates. The 420 sequences were assigned to five phyla, of which Firmicutes was the most predominant phylum, accounting for 55.2% of all 420 sequences. Bacteroidetes was the second most predominant phylum, accounting for 32.1% of the 420 sequences, followed by Actinobacteria (6.4%), Fusobacteria (3.8%), and Proteobacteria (2.4%). The genus Bacteroides within Bacteroidetes was the largest, representing 30.0% of all 420 sequences, while the putative genus Clostridium XI within Firmicutes was the second largest, representing 27.4% of all 420 sequences. A total of 82 operational taxonomic units (OTUs) that are putative species were identified from the retrieved sequences. The results of this study will improve understanding of the diversity of fecal bacteria in dogs and guide future studies on the health and well-being of dogs.

• Animal Systematics, Evolution and Diversity
• /
• v.28 no.3
• /
• pp.215-219
• /
• 2012

To examine genetic divergences of two endemic Sorex caecutiens subspecies from Korea (S. c. hallamontanus in Korean Jeju Island and S. c. annexus in the mainland Korean Peninsula), we obtained partial cytochrome oxidase I (COI) sequences (429 bp) and complete cytochrome b sequences (1,140 bp) from the two Korean subspecies, and we compared these sequences to the corresponding sequences of S. caecutiens, obtained from GenBank. We found that Jeju S. c. hallamontanus is one of three clades within S. caecutiens, with an average Jukes-Cantor distance of 1.57% in the COI sequences and the distance of 2.07% and 11 fixed site differences in the cytochrome b sequences, indicating that Jeju S. c. hallamontanus is one endemic subspecies with concordant genetic distinctness, although further analyses with nuclear DNA sequences are necessary to confirm these findings. However, S. c. annexus from the mainland Korean Peninsula was not divergent from S. c. macropygmaeus from northeastern China and adjacent Russia, indicating that S. c. annexus from the mainland Korean Peninsula is another endemic subspecies with only morphological differences, although it is necessary to reexamine the subspecies status of S. c. annexus.

• Journal of the Korea Academia-Industrial cooperation Society
• /
• v.18 no.12
• /
• pp.466-472
• /
• 2017

This study was designed to examine the diversity census of fungi in rumen microbiome via meta-analysis of fungal 28S rDNA sequences. Both terms, "rumen" and "ruminal," were searched to retrieve the sequences of rumen fungi. As of September 2016, these sequences (n=165) of ruminal origin were retrieved from the Ribosomal Database Project (RDP; http://rdp.cme.msu.edu), an archive of all 28S rDNA sequences and were assigned to the phyla Ascomycota, Neocallimastigomycota, and Basidiomycota, which accounted for 109, 48, and 8 of the 165 sequences, respectively. Ascomycota sequences were assigned to the genera Pseudonectria, Magnaporthe, Alternaria, Cochliobolus, Cladosporium, and Davidiella, including fungal plant pathogens or mycotoxigenic species. Moreover, Basidiomycota sequences were assigned to the genera Thanatephorus and Cryptococcus, including fungal plant pathogens. Furthermore, Neocallimastigomycota sequences were assigned to the genera Cyllamyces, Neocallimastix, Anaeromyces, Caecomyces, Orpinomyces, and Piromyces, which may degrade the major structural carbohydrates of the ingested plant material. This study provided a collective view of the rumen fungal diversity using a meta-analysis of 28S rDNA sequences. The present results will provide a direction for further studies on ruminal fungi and be applicable to the development of new analytic tools.

• Journal of applied mathematics & informatics
• /
• v.9 no.1
• /
• pp.239-252
• /
• 2002

A sort sequence $S_n$ is sequence of all unordered pairs of indices in $I_n$={1,2,…n}. With a sort sequence $S_n$ = ($s_1,S_2,...,S_{\frac{n}{2}}$),one can associate a predictive sorting algorithm A($S_n$). An execution of the a1gorithm performs pairwise comparisons of elements in the input set X in the order defined by the sort sequence $S_n$ except that the comparisons whose outcomes can be inferred from the results of the preceding comparisons are not performed. A sort sequence is said to be extremal if it maximizes a given objective function. First we consider the extremal sort sequences with respect to the objective function $\omega$($S_n$) - the expected number of tractive predictions in $S_n$. We study $\omega$-extremal sort sequences in terms of their prediction vectors. Then we consider the objective function $\Omega$($S_n$) - the minimum number of active predictions in $S_n$ over all input orderings.

• Molecules and Cells
• /
• v.19 no.2
• /
• pp.283-288
• /
• 2005

Complete 18S rDNA sequences were determined for 10 vetigastropods in order to investigate the phylogeny of Vetigastropoda, which is controversial. These sequences were analyzed together with published sequences for nine other vetigastropods and two nerites. With the two nerites as outgroups, the phylogeny was inferred by three analytical methods, neighbor-joining, maximum likelihood, and maximum parsimony. The 18S rDNA sequence data support the monophyly of four vetigastropod superfamilies, the Pleurotomarioidea, the Fissurelloidea, the Haliotoidea, and the Trochoidea. The present results yield the new branching order: (Pleurotomarioidea (Fissurelloidea ((Scissurelloidea, Lepetodriloidea) (Haliotoidea, Trochoidea)))) within the vetigastropod clade.

• Communications of the Korean Mathematical Society
• /
• v.19 no.1
• /
• pp.75-92
• /
• 2004

A generalised integration by parts formula for sequences of absolutely continuous functions that satisfy the ${\omega}-Appell$ condition and different estimates for the remainder are provided. Applications for particular instances of such sequences are pointed out as well.

• Bulletin of the Korean Mathematical Society
• /
• v.42 no.1
• /
• pp.149-155
• /
• 2005

The notion of U-exact sequence (or quasi-exact sequence) of modules was introduced by Davvaz and Parnian-Garamaleky as a generalization of exact sequences. In this paper, we prove further results about quasi-exact sequences. In particular, we give a generalization of Schanuel's Lemma. Also we obtain some relation-ship between quasi-exact sequences and superfluous (or essential) submodules.

• The Plant Pathology Journal
• /
• v.18 no.2
• /
• pp.98-101
• /
• 2002

Using phytoplasma universal primer pair Pl and P7, a fragment of about 1.8 kb nucleotide sequences of 16S rRNA gene and 16S-23S rRNA intergenic spacer region, and a portion of 23S rRNA gene of jujube witches'broom (JWB) and mulberry dwarf(MD) phytoplasmas were determined. The nucleotide sequences of JWB and MD were 1,850 bp and 1,831 bp long, respectively. The JWB phytoplasma sequence was aligned with the homologous sequence of MD phytoplasma. Twenty-eight base insertions and nine base deletions were found in the JWB phytoplasma sequence compared with that of MD phytoplasma. The similarity of the aligned sequences of JWB and MD was 84.8%. The near-complete 16S rRNA gene DNA sequences of JWB and MD were 1,529 bp and 1,530 bp in length, respectively, and revealed 89.0% homology. The 16S-23S rRNA intergenic spacer region DNA sequences were 263 bp and 243 bp in lengths respectively, while homology was only 70% and the conserved tRNA-lle gene of JWB and MD was located into the intergenic space region between 16S-23S rRNA gene. The nucleotide sequences were 77 bp long in both JWB and MD, and showed 97.4% sequence homology. Based on the phylogenetic analysis of the two phytoplasmas, the JWB phytoplasma belongs to the Elm yellow phytoplasma group (16S rV), whereas, the MD phytoplasma belongs to the Aster yellow group (16S rI).

• The KIPS Transactions:PartD
• /
• v.14D no.7
• /
• pp.727-732
• /
• 2007

Most of previous work on indexing and searching time series focused on the similarity matching and retrieval of one-attribute time series. However, multimedia databases such as music, video need to handle the similarity search in multi-attribute time series. The limitation of the current similarity models for multi-attribute sequences is that there is no consideration for attributes' sequences. The multi-attribute sequences are composed of several attributes' sequences. Since the users may want to find the similar patterns considering attributes's sequences, it is more appropriate to consider the similarity between two multi-attribute sequences in the viewpoint of attributes' sequences. In this paper, we propose the similarity search method based on attributes's sequences in multi-attribute time series databases. The proposed method can efficiently reduce the search space and guarantees no false dismissals. In addition, we give preliminary experimental results to show the effectiveness of the proposed method.