• Asian-Australasian Journal of Animal Sciences
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• v.33 no.10
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• pp.1566-1572
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• 2020

Objective: The extensive breeding of commercial chickens has led to a sharp decrease in the resources of many indigenous chickens, especially the indigenous chickens in the southeastern coastal region, which are on the verge of extinction, and the indigenous chickens in the northwestern region of China, which are also at risk. However, there are few reports on the evaluation of genetic diversity and conservation of genetic resources of indigenous chickens in remote areas in the Northwest of China. Methods: In the present study, the genetic diversity and phylogenetic relationship of six indigenous chickens from different regions were studied based on variation in mitochondrial DNA control region (D-loop), and the degree of introgression from commercial breeds into these chickens was determined by the amount of haplotype sharing between indigenous and commercial breeds. Results: Twenty-five polymorphic sites and 25 haplotypes were detected in 206 individuals. Principal component analysis showed that the Jingning chicken had the highest genetic diversity among the six indigenous chickens. According to the degree of introgression, the six indigenous breeds may be involved in haplotype sharing with commercial breeds, and the introgression from commercial chickens into the Haidong chicken is the most serious. Conclusion: The genetic uniqueness of indigenous chickens has been eroded, so it is necessary to consider the protection of their genetic resources. Phylogenetic analysis suggests that the six indigenous chickens have two major matrilineal origins: one from Yunnan or its surrounding areas in China and the other from the Indian subcontinent.

• Journal of Microbiology
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• v.44 no.1
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• pp.77-82
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• 2006

The tea looper caterpillar, Ectropis obliqua, is one of the major pests of tea bushes. E. obliqua single-nucleocapsid nucleopolyhedrovirus (EcobSNPV) has been used as a commercial pesticide for biocontrol of this insect. However only limited genetic analysis for this important virus has been done up to now. EcobSNPV was characterized in this study. Electron microscopy analysis of the occlusion body showed polyhedra of 0.7 to $1.7\;{\mu}m$ in diameter containing a single nucleocapsid per envelope of the virion. A 15.5 kb genomic fragment containing EcoRI-L, EcoRI-N and HindIII-F fragments, was sequenced. Analysis of the sequence revealed that the fragment contained eleven potential open reading frames (ORFs): lef-1, egt, 38.7k, rrl, polyhedrin, orfl629, pk-1, hoar and homologues to Spodoptera exigua multicapsid NPV (SeMNPV) ORFs 15, 28, and 29. Gene arrangement and phylogeny analysis suggest that EcobSNPV is closely related to the previously described Group II NPV. Bioassays on lethal concentration $(LC_{50}\;and\;LC_{90})$ and lethal time $(LT_{50}\;and\;LT({90})$ were conducted to test the susceptibility of E. obliqua larvae to the virus.

• Journal of Microbiology and Biotechnology
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• v.12 no.3
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• pp.508-513
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• 2002

Human endogenous retroviral long terminal repeats (LTRs) have been found to be coexpressed with sequences of genes located nearby. It has been suggested that the LTR elements have contributed to the structural change or genetic variation of human genome connected to various diseases. The HERV-W family has been identified in the cerebrospinal fluids and brains of individuals with schizophrenia. Using a cDNA library derived from a human brain, the HERV-W LTR elements were examined and five new LTR elements were identified. These elements were examined using a YAC clone panel from the Xq21.3 region linked to psychosis that was replicated on the Y chromosome after the separation of the chimpanzee and human lineages. Fourteen elements of the HERV-W LTR were identified in that region. Those LTR elements showed a high degree of sequence similarity ($91.8-99.5\%$) with previously reported HERV-W LTR. A phylogenetic tree obtained from the neighbor-joining method revealed that new HERV-W LTR elements were closely related to the AXt000960, AF072504, and AF072506 from the GenBank database. The data indicates that several copy numbers of the HERV-W LTR elements exist on the Xq21.3 region and are also expressed in the human brain. These LTR elements need to be further investigated as potential leads to neuropsychiatric diseases.

• Environmental Engineering Research
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• v.19 no.4
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• pp.317-329
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• 2014

The diversity of cyanobacteria in Sri Lanka was studied in different water reservoirs, paddy fields, brackish water and tsunami affected areas using light microcopy, 16S rRNA sequences, followed by phylogenetic analysis. Based on light microscopy, 24 genera were identified from environmental samples belonging to the orders Chroococcales, Oscillatoriales, Pleurocapsales and Nostocales. In cultures, 33 genera were identified from all five cyanobacterial orders, including Stigonematales. Based on 16S rRNA gene sequences and their morphology, two isolates were identified up to species level, 72 to genus level, one isolate up to family and 11 up to order level. Twelve isolates couldn't be assigned to any taxonomic level. The results of 16S rRNA gene sequences along with the phylogenetic analysis indicated that some cyanobacterial isolates could be accommodated to genus or order level. The 16S rRNA sequence analysis data in this study confirmed that order Nostocales and order Pleurocapsales cyanobacteria are monophyletic while orders Chroococcales, Oscillatoriales and Stigonematales cyanobacteria are polyphyletic. Polyphasic approach including the combination of light microscopy, cultures and the analysis of 16S rRNA gene sequences provide a promising approach to ascertain the diversity of cyanobacteria in different habitats.

• Fisheries and Aquatic Sciences
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• v.7 no.3
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• pp.122-129
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• 2004

Harmful Cochlodinium polykrikoides is a notorious harmful algal bloom (HAB) species that is causing mass mortality of farmed fish along the Korean coast with increasing frequency. We analyzed the sequence of the large subunit (LSD) rDNA D1-D3 region of C. polykrikoides and conducted phylogenetic analyses using Bayesian inference of phylogeny and the maximum likelihood method. The molecular phylogeny showed that C. polykrikoides had the genetic relationship to Amphidinium and Gymnodinium species supported only by the relatively high posterior probabilities of Bayesian inference. Based on the LSU rDNA sequence data of diverse dinoflagellate taxa, we designed the C. polykrikoides-specific PCR primer set, CPOLY01 and CPOLY02 and developed PCR detection assays for its sensitive, accurate HAB monitoring. CPOLY01 and CPOLY02 specifically amplified C. polykrikoides and did not cross-react with any dinoflagellates tested in this study or environmental water samples. The effective annealing temperature $(T_{p})$ of CPOLY01 and CPOLY02 was $67^{\circ}C$. At this temperature, the conventional and nested PCR assays were sensitive over a wide range of C. polykrikoides cell numbers with detection limits of 0.05 and 0.0001 cells/reaction, respectively.

• Parasites, Hosts and Diseases
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• v.45 no.3
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• pp.181-190
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• 2007

The phylogenie relationships existing among 14 parasitic Platyhelminthes in the Republic of Korea were investigated via the use of the partial 28S ribosomal DNA (rDNA) D1 region and the partial mitochondrial cytochrome c oxidase subunit 1 (mCOI) DNA sequences. The nucleotide sequences were analyzed by length, G + C %, nucleotide differences and gaps in order to determine the analyzed phylogenie relationships. The phylogenie patterns of the 28S rDNA D1 and mCOI regions were closely related within the same class and order as analyzed by the PAUP 4.0 program, with the exception of a few species. These findings indicate that the 28S rDNA gene sequence is more highly conserved than are the mCOI gene sequences. The 28S rDNA gene may prove useful in studies of the systematics and population genetic structures of parasitic Platyhelminthes.

• Animal Systematics, Evolution and Diversity
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• v.28 no.4
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• pp.269-278
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• 2012

Gobiids are hyperdiverse compared with other teleost groups, with about 2,000 species occurring in marine, freshwater, and blackish habitats, and they show a remarkable variety of morphologies and ecology. Testing the effectiveness of DNA barcodes on species that have emerged as a result of radiation remains a major challenge in evolutionary biology. Here, we used the cytochrome c oxidase subunit 1 (COI) sequences from 144 species of gobies and related species to evaluate the performance of distance-based DNA barcoding and to conduct a phylogenetic analysis. The average intra-genus genetic distance was considerably higher than that obtained in previous studies. Additionally, the interspecific divergence at higher taxonomic levels was not significantly different from that at the intragenus level, suggesting that congeneric gobies possess substantial interspecific sequence divergence in their COI gene. However, levels of intragenus divergence varied greatly among genera, and we do not provide sufficient evidence for using COI for cryptic species delimitation. Significantly more nucleotide changes were observed at the third codon position than that at the first and the second codons, revealing that extensive variation in COI reflects synonymous changes and little protein level variation. Despite clear signatures in several genera, the COI sequences did resolve genealogical relationships in the phylogenetic analysis well. Our results support the validity of COI barcoding for gobiid species identification, but the utilization of more gene regions will assist to offer a more robust gobiid species phylogeny.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.6
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• pp.789-793
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• 2008

The gayal (Bos frontalis) in China is a very rare semi-wild and semi-domestic bovine species. There still exist remarkable divergences on the gayal's origin and taxonomic status. In the present study, the cytochrome b (Cyt b) gene entire sequences (1,140 bp) of 11 gayals in Yunnan China were analyzed. Combined with other bovine Cyt b sequences cited in GenBank, the phylogenetic trees of genus Bos were reconstructed by neighbor-joining (NJ) and maximum parsimony (MP) methods with Bubalus bubalis as outgroup. Sequence analysis showed that, among 1,140 sites compared for 11 gayals, 95 variable sites (8.33% of all sites) and 6 different haplotypes were observed, showing abundant mitochondrial genetic diversity in gayals. Both NJ and MP trees demonstrated that gayals in this study were markedly divided into three embranchments: one embranchment clustering with Bos gaurus, another clustering with Bos taurus, and the third clustering with Bos indicus. The result of phylogenetic analysis suggested that the gayal might be the domesticated form of the gaur, and a great proportion of the gayal bloodline in China was invaded by other bovine species.

• Journal of Species Research
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• v.4 no.1
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• pp.49-56
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• 2015

Zeuzera is one of the most important wood borer pests in South East Asia. Like of most other genera of moths, the systematic of this genus is still in dispute, especially on the monophyly and the relationship within this genus due to the fact that genus is very varied. This genus was defined based on external characters only such as cross vein Sc-Rs present, humeral plate approximately triangular in shape and anal plate moderately long to moderately short. Therefore, the monophyly of this genus need to be evaluated based on more comprehensive data. To clarify the monophyly of the genus Zeuzera, to reveal the phylogenetic relationships among the Indonesian species, and to establish the genetic characters of Indonesian Zeuzera, we analyzed seven species of Indonesian Zeuzera including three other species distributed around the world based on nucleotide sequence variation across a 580-bp region in the CO I gene. The results showed that the monophyly of Zeuzera was supported by bootstrap tests at the MP and ML tree building methods (>95%). Genus Zeuzera was divided into two groups (A and B) with Z. borneana was excluded from the two groups and occupied at the basal node. Indonesian species was distributed into two different clades. CO I gene alone was able to fully resolve the relationships among species within clade B. However, further investigations were needed by including more species and other genes that the more conserved to test the validity of the phylogenetic hypothesis proposed here.

• Korean Journal of Ecology and Environment
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• v.39 no.2 s.116
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• pp.265-270
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• 2006

The nucleotide sequence variations of mitochondrial DNA were investigated to understand genetic differentiation for five different Pungitius kaibarae populations at five study sites from selected four streams flowing into the East Sea. The complete sequences of mtDNA control regions of them were determined the constant sites 342 bp and variable sites 183 bp including parsimony infromative sites 122 bp. Based on the phylogenetic tree, five populations were monophyletic unit (97% MPand 100% NJ) and separated two groups (Myongpa-Songhuen stream group and others group). The population of Baebong stream (82nd bp, G-A) consistently formed them of the Jasan stream into a monophyletic unit even though it is closer then Myongpa stream (99th bp, T-C) from the Baebong stream. Further studies on the molecular phylogeny for the primary freshwater fish are needed to establish for the fish biodiversity conservation in mountainous and upland streams.