• Genomics & Informatics
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• v.21 no.1
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• pp.10.1-10.6
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• 2023

The fishes of the Chiasmodontidae family, known as swallower fishes, are species adapted to live in deep seas. Several studies have shown the proximity of this family to Tetragonuridae and Amarsipidae. However, the phylogenetic position of this clade related to other Pelagiaria groups remains uncertain even when phylogenomic studies are employed. Since the low number of published mitogenomes, our study aimed to assemble six new mitochondrial genomes of Chiasmodontidae from database libraries to expand the discussion regarding the phylogeny of this group within Scombriformes. As expected, the composition and organization of mitogenomes were stable among the analyzed species, although we detected repetitive sequences in the D-loop of species of the genus Kali not seen in Chiasmodon, Dysalotus, and Pseudoscopelus. Our phylogeny incorporating 51 mitogenomes from several families of Scombriformes, including nine chiasmodontids, recovered interfamilial relationships well established in previous studies, including a clade containing Chiasmodontidae, Amarsipidae, and Tetragonuridae. However, phylogenetic relationships between larger clades remain unclear, with disagreements between different phylogenomic studies. We argue that such inconsistencies are not only due to biases and limitations in the data but mainly to complex biological events in the adaptive irradiation of Scombriformes after the Cretaceous-Paleogene extinction event.

• Genomics & Informatics
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• v.21 no.4
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• pp.51.1-51.5
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• 2023

The genus Neoarius, known as marine catfish, is a group of the family Ariidae, composed of 10 species found in Oceania. None of the species in this genus have their mitochondrial genome described, which is highly valuable in phylogenetic and molecular evolution studies. For the present work, eight species from the Neoarius genus were selected: Neoarius utarus, Neoarius midgleyi, Neoarius graeffei, Neoarius leptaspis, Neoarius berenyi, Neoarius paucus, Neoarius pectoralis, and Neoarius aff. graeffei. DNA sequences of the eight species were obtained through the NCBI Sequence Read Archive (SRA) database, and the mitochondrial genomes were assembled using the NOVOplasty tool on the Galaxy platform, subsequently annotated with the MitoAnnotator tool. We then utilized the protein-coding genes from the mitogenomes to estimate the phylogenetic relationships within the group, including seven additional mitogenomes available in the NCBI. In all species, the mitochondrial genomes presented 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 D-loop.

• Parasites, Hosts and Diseases
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• v.54 no.6
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• pp.751-758
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• 2016

This study aimed at constructing a draft genome of the adult female worm Toxocara canis using next-generation sequencing (NGS) and de novo assembly, as well as to find new genes after annotation using functional genomics tools. Using an NGS machine, we produced DNA read data of T. canis. The de novo assembly of the read data was performed using SOAPdenovo. RNA read data were assembled using Trinity. Structural annotation, homology search, functional annotation, classification of protein domains, and KEGG pathway analysis were carried out. Besides them, recently developed tools such as MAKER, PASA, Evidence Modeler, and Blast2GO were used. The scaffold DNA was obtained, the N50 was 108,950 bp, and the overall length was 341,776,187 bp. The N50 of the transcriptome was 940 bp, and its length was 53,046,952 bp. The GC content of the entire genome was 39.3%. The total number of genes was 20,178, and the total number of protein sequences was 22,358. Of the 22,358 protein sequences, 4,992 were newly observed in T. canis. Following proteins previously unknown were found: E3 ubiquitin-protein ligase cbl-b and antigen T-cell receptor, zeta chain for T-cell and B-cell regulation; endoprotease bli-4 for cuticle metabolism; mucin 12Ea and polymorphic mucin variant C6/1/40r2.1 for mucin production; tropomodulin-family protein and ryanodine receptor calcium release channels for muscle movement. We were able to find new hypothetical polypeptides sequences unique to T. canis, and the findings of this study are capable of serving as a basis for extending our biological understanding of T. canis.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.3
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• pp.881-887
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• 2015

Purpose: To analyze treatment modalities and prognostic factors in patients with Stage I-II endometrial stromal sarcoma (ESS). Materials and Methods: Twenty four patients (nineteen with low-grade ESS [LGESS] and five with high-grade ESS [HGESS]) were assessed retrospectively in terms of general characteristics, prognostic factors, treatment methods and survival. Results: Twenty patients were at Stage I and three were at Stage II. The stage of one patient could not be determined. With respect to age and comorbidity, no statistically significant difference was found among disease-free survival (DFS) (p=0.990; p=0.995). However, DFS was significantly shorter in Stage II than Stage I patients (p=0.002). It was also significantly shorter in HGESS patients than in LGESS patients (p=0.000). There was no statistically significant differences among the overall survival (OVS) times of patients with respect to age at diagnosis and comorbid disease (p=0.905; p=0.979) but OVS was significantly shorter in patients with HGESS (p=0.00) and Stage II disease (p=0.001). No statistically significant difference was found with respect to OVS between patients who received radiotherapy (RT) and those who did not receive RT (p=0.055). It was not statistically possible to include other treatment modalities in the analysis because of the small sample size. Conclusions: Grade and stage of a tumour were found to be the most important prognostic factors. It was not possible to determine the optimal surgical method and the effect of adjuvant treatment since the number of cases was insufficient.

• The Plant Pathology Journal
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• v.35 no.1
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• pp.71-76
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• 2019

$SdhB^{P225F}$ and $SdhB^{H272R}$ mutations have been found associated with boscalid resistance in Botrytis cinerea from strawberry in Shanghai, China. For rapid detection of two mutations, tetra-primers were designed and optimized to gain the relatively high accuracy and specificity based on the ARMS-PCR technique, by which resistance can be identified with different lengths of products on agarose gels. The tetra-primer ARMS-PCR systems for $SdhB^{P225F}$ and $SdhB^{H272R}$ were validated by 9 SdhB-squenced strains repeatedly. Then, sensitivity of 30 more strains were also tested by the methods, which were accordant with genotypes by sequencing and the sensitivity of conidial germination to boscalid by 100%. Thus, the methods developed in this study are proved to be rapid, inexpensive, accurate and practical for resistance detection of Botrytis cinerea caused by $SdhB^{P225F}$ and $SdhB^{H272R}$ mutations.

• Korean journal of applied entomology
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• v.53 no.2
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• pp.149-156
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• 2014

The resistance levels of the green peach aphid, Myzus persicae (Sulzer), against 10 insecticides was checked and selected the applicable insecticide resistance markers. We conducted our study in 5 cabbage cultivation regions (Pyeongchang, Hongcheon, Bongwha, Muju, and Jeju) of Korea, over 3 successive years (2009-2011). We selected a multi-resistant (MR) strain from among the 5 field-collected populations. We analyzed esterase over-expression and mutation(s) in the target sites, by using native isoelectric focusing (IEF) and quantitative sequencing (QS). We detected esterase over-expression and StoF mutation in the acetylcholinesterase 1 gene (ace1) in all of the field-collected populations, including the MR strain. We did not detect the LtoF mutation, which is a well-known knockdown resistance (kdr) mutation in the para-type sodium channel gene (para), in the MR strain; however, the value of the MR strain for bifenthrin was 3,461-fold higher than that of the susceptible strain. Our results indicate that insecticide resistance is more effectively evaluated using molecular markers than by conducting a bioassay. The molecular markers StoF in ace1 and MtoL in para can easily be applied in diagnostic methods such as QS or PCR amplification of specific alleles (PASA). These methods may be extended to management of M. persicae resistance in the field.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.8
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• pp.3117-3120
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• 2015

Objective: Interferon-${\gamma}$ (IFN-${\gamma}$) and signal transducers and activators of transcription (STATs) each play an important role in carcinogenesis associated with viral infection. Cervical cancer is almost invariably associated with infection by human papillomavirus (HPV), and previous studies suggested that dysregulation of the signal pathway involved in IFN-${\gamma}$ and STATs is associated. Our objective was to evaluate the association of SNPs in STAT2, STAT3, and IFN-${\gamma}$ with cervical cancer susceptibility in Chinese Han women in Hunan province. Materials and Methods: Genomic DNA was extracted from peripheral blood samples of 234 cervical cancer patients and 216 healthy female controls. STAT2 and STAT3 genotyping was performed using polymerase chain reaction-restriction enzyme (PCR-RE) analysis. IFN-${\gamma}$ genotyping was detected by PCR-amplification of specific allele (PASA). Results: For STAT2 rs2066807 polymorphisms, there was no significant difference of genotype distribution (P=0.827) and allele frequencies (P=0.830, OR=1.09, 95% CI: 0.51-2.31) between cases and controls. For STAT3 rs957970 polymorphisms, there was no significant difference of genotype distribution (P=0.455) and allele frequencies (P=0.560, OR=0.92, 95% CI: 0.71-1.20) between cases and controls. For IFN-${\gamma}$ +874A/T polymorphisms, there was no significant difference of genotype distribution (P=0.652) and allele frequencies (P=0.527, OR=1.12, 95% CI: 0.79-1.59) between cases and controls. Conclusion: These results suggest that polymorphisms in STAT2, STAT3 and IFN-${\gamma}$ genes are not likely to be strong predictors of cervical cancer in Han women in southern China.