• International Journal of Industrial Entomology and Biomaterials
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• v.1 no.1
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• pp.9-17
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• 2000

Genetic variation in the domestic silkworm strains (Bombyx mori) and phylogenetic relationships between domestic silkworms and wild silkworms (B. mandarina) were investigated by using a portion of mitochondrial CGI gene sequences. Ten geographic strains of B. mori we sequenced were identical in the 410 bp-section of mitochondrial COI gene. This sequence was also identical to the homologous sequence of the four Gen-Bank-registered strains, but one strain of B. mori differed a single nucleotide (0.2%) from others. MtDNA homogeneity in the B. mori strains appears to be resulted from fixation into the mast frequent mtDNA type during the course of breeding for new strains, in which an extensive indoor rearing and removal of unwanted individuals were accompanied. In the comparisons between domestic and wild silkworms, some wild silkworms were closely related to domestic silkworms (0.2%-1.2% of divergence), but the others were not (2.7%-3.7% of sequence divergence). This result was also reflected in the phylogenetic analyses, showing two independent phylogenetic groups: one including all B. mandarina sequences and the other including both B. mandarina and B. mori sequences. Thus, domestic silkworms may have been derived from the ancestor of B. mandarina, which belongs to this group, alto-ough more extensive study will provide better understanding on this issue.

• The Plant Pathology Journal
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• v.35 no.1
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• pp.41-50
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• 2019

Sugarcane bacilliform viruses (SCBV), which belong to the genus Badnavirus, family Caulimoviridae, are an important DNA virus complex that infects sugarcane. To explore the genetic diversity of the sugarcane-infecting badnavirus complex in China, we tested 392 sugarcane leaf samples collected from Fujian, Yunnan, and Hainan provinces for the occurrence of SCBV by polymerase chain reaction (PCR) assays using published primers SCBV-F and SCBV-R that target the reverse transcriptase/ribonuclease H (RT/RNase H) regions of the viral genome. A total of 111 PCR-amplified fragments (726 bp) from 63 SCBV-positive samples were cloned and sequenced. A neighbor-joining phylogenetic tree was constructed based on the SCBV sequences from this study and 34 published sequences representing 18 different phylogroups or genotypes (SCBV-A to -R). All SCBV-tested isolates could be classified into 20 SCBV phylogenetic groups from SCBV-A to -T. Of nine SCBV phylogroups reported in this study, two novel phylogroups, SCBV-S and SCBV-T, that share 90.0-93.2% sequence identity and show 0.07-0.11 genetic distance with each other in the RT/RNase H region, are proposed. SCBV-S had 57.6-92.2% sequence identity and 0.09-0.66 genetic distance, while SCBV-T had 58.4-90.0% sequence identity and 0.11-0.63 genetic distance compared with the published SCBV phylogroups. Additionally, two other Badnavirus species, Sugarcane bacilliform MO virus (SCBMOV) and Sugarcane bacilliform IM virus (SCBIMV), which originally clustered in phylogenetic groups SCBV-E and SCBV-F, respectively, are first reported in China. Our findings will help to understand the level of genetic heterogeneity present in the complex of Badnavirus species that infect sugarcane.

• Mycobiology
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• v.50 no.1
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• pp.46-54
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• 2022

Although Apiospora Sacc. has previously been considered a sexual morph of Arthrinium species on the basis of phylogenetic, morphological, and ecological diagnoses, a recent study delimited these as different species. Recently, 14 species, including eight new species, of marine Arthrinium have been reported from Korea. Six known species have previously been renamed as species in the genus Apiospora (A. arundinis, A. marii, A. piptatheri, A. rasikravindrae, A. sacchari, and A. saccharicola). However, the eight new species of marine Arthrinium (Ar. agari, Ar. arctoscopi, Ar. fermenti, Ar. koreanum, Ar. marinum, Ar. pusillispermum, Ar. sargassi, and Ar. taeanense) are yet to be studied, and thus the taxonomic status of these species remains to be clarified. In this study, we conducted phylogenetic analyses using the internal transcribed spacer, 28S large subunit ribosomal RNA gene, translation elongation factor 1-alpha, and beta-tubulin regions to confirm the phylogenetic position of these eight species. Based on these analyses, we re-identified the eight Arthrinium species as new combinations in Apiospora. Additionally, among the six known Apiospora species, two (A. piptatheri and A. rasikravindrae) have not previously been recorded in Korea. On the basis of morphological and molecular analyses, we report these as new species in Korea. Herein, we present scanning electron micrographs detailing the morphologies of these species, along with phylogenetic trees and detailed descriptions.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.5
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• pp.603-607
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• 2001

This paper is based on the 36 wild Japanese quails which migrated to and settled in the Weishan Lake area. The gene frequency of 10 loci encoding the enzymes in viscera and muscle was detected. After collecting the same data about 20 quail colonies in China and other countries, it clusters the 21 quail populations by fuzzy cluster analysis. The study indicates that the wild Japanese quail in the Weishan Lake area is closer to domestic quail for phylogenetic system than wild Japanese quails in Japanese Islands. The paper supports the thesis that the quail domestication area should be further studied.

• ALGAE
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• v.34 no.4
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• pp.267-275
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• 2019

Three new species of the genus Micractinium were collected from five localities on the South Shetland Islands in maritime Antarctica, and their morphological and molecular characteristics were investigated. The vegetative cells are spherical to ellipsoidal and a single chloroplast is parietal with a pyrenoid. Because of their simple morphology, no conspicuous morphological characters of new species were recognized under light microscopy. However, molecular phylogenetic relationships were inferred from the concatenated small subunit rDNA, and internal transcribed spacer (ITS) sequence data indicated that the Antarctic microalgal strains are strongly allied to the well-supported genus Micractinium, including M. pusillum, the type species of the genus, and three other species in the genus. The secondary structure of ITS2 and compensatory base changes were used to identify and describe six Antarctic Micractinium strains. Based on their morphological and molecular characteristics, we characterized three new species of Micractinium: M. simplicissimum sp. nov., M. singularis sp. nov., and M. variabile sp. nov.

• Genomics & Informatics
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• v.10 no.1
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• pp.9-15
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• 2012

Horizontal gene transfer (HGT) is the movement of genetic material between kingdoms and is considered to play a positive role in adaptation. $Cryptosporidium$ $parvum$ is a parasitic protozoan that causes an infectious disease. Its genome sequencing reported 14 bacteria-like proteins in the nuclear genome. Among them, cgd2_1810, which has been annotated as CysQ, a sulfite synthesis pathway protein, is listed as one of the candidates of genes horizontally transferred from bacterial origin. In this report, we examined this issue using phylogenetic analysis. Our BLAST search showed that $C.$ $parvum$ CysQ protein had the highest similarity with that of proteobacteria. Analysis with NCBI's Conserved Domain Tree showed phylogenetic incongruence, in that $C.$ $parvum$ CysQ protein was located within a branch of proteobacteria in the cd01638 domain, a bacterial member of the inositol monophosphatase family. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, the sulfate assimilation pathway, where CysQ plays an important role, is well conserved in most eukaryotes as well as prokaryotes. However, the Apicomplexa, including $C.$ $parvum$, largely lack orthologous genes of the pathway, suggesting its loss in those protozoan lineages. Therefore, we conclude that $C.$ $parvum$ regained cysQ from proteobacteria by HGT, although its functional role is elusive.

• Parasites, Hosts and Diseases
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• v.55 no.1
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• pp.47-54
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• 2017

The prevalence of cercarial infection in freshwater snails and their evolutionary trends were studied in Nakhon Nayok province, Thailand. A total of 2,869 individual snails were examined for parasitic infections. The results showed that 12 snail species were found to host larval stages of trematodes with an overall prevalence of 4.7%. The infected specimens included 7 types at the cercarial stage; cercariae, megalurous cercariae, echinostome cercariae, furcocercous cercariae, parapleurolophocercous cercariae, virgulate cercariae, and xiphidiocercariae. Regarding molecular identification, ITS2 sequence data of each larval trematode were analyzed, and a dendrogram was constructed using the neighbor-joining method with 10,000 replicates. The dendrogram was separated into 6 clades (order/family), including Echinostomatida/Echinostomatidae, Echinostomatida/Philophthalmidae, Opisthorchiida/Heterophyidae, Plagiorchiida/Prosthogonimidae, Plagiorchiida/Lecithodendriidae, and Strigeatida/Cyathocotylidae. These findings were used to confirm morphological characteristics and evolutionary trends of each type of cercariae discovered in Nakhon Nayok province. Furthermore, this investigation confirmed that the ITS2 data of cercariae could be used to study on phylogenetic relationships or to determine classification of this species at order and/or family level when possible.

• Animal Systematics, Evolution and Diversity
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• v.19 no.2
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• pp.297-304
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• 2003

Phylogenetic analysis of 31 species representing 12 genera in the family Strigidae (Aves: Strigiformes) including 5 species (Bubo bubo, Otus sunia, O. semitorques, Ninox scutulato, Strix aluco) collected from Korea has been undertaken using nucleotide sequences of the mitochondrial cytochrome b gene. Maximum likelihood analysis was performed and pairwise genetic distances were calculated with Kimura's two-parameter and p-distance. Among well-aligned 959 bp used for this study, 459 sites were variable and 398 sites were informative for the phylogenetic analysis. The family Strigidae was divided into three subgroups, Clade I (Aegolius), Clade II (Athene, Micrathene, Glaucidium and Surnia) and Clade III (Bubo, Nycteo, Pulsatrix, Strix, Otus, Ptilopsis, and Ninox). Also, two separated subgroups in the genus Otus were confirmed by the geographical distribution.

• Journal of Microbiology
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• v.44 no.1
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• pp.83-91
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• 2006

The sudden appearance and potential lethality of severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV) in humans has resulted in a focusing of new attention on the determination of both its origins and evolution. The relationship existing between SARS-CoV and other groups of coronaviruses was determined via analyses of phylogenetic trees and comparative genomic analyses of the coronavirus genes: polymerase (Orflab), spike (S), envelope (E), membrane (M) and nucleocapsid (N). Although the coronaviruses are traditionally classed into 3 groups, with SARS-CoV forming a $4^{th}$ group, the phylogenetic position and origins of SARS-CoV remain a matter of some controversy. Thus, we conducted extensive phylogeneitc analyses of the genes common to all coronavirus groups, using the Neighbor-joining, Maximum-likelihood, and Bayesian methods. Our data evidenced largely identical topology for all of the obtained phylogenetic trees, thus supporting the hypothesis that the relationship existing between SARS-CoV and group 2 coronavirus is a monophyletic one. Additional comparative genomic studies, including sequence similarity and protein secondary structure analyses, suggested that SARS-Co V may bear a closer relationship with group 2 than with the other coronavirus groups. Although our data strongly suggest that group 2 coronaviruses are most closely related with SARS-CoV, further and more detailed analyses may provide us with an increased amount of information regarding the origins and evolution of the coronaviruses, most notably SARS-CoV.

• The Korean Journal of Mycology
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• v.32 no.2
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• pp.148-151
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• 2004

This study was carried out to elucidate phylogenetic relationship of a yellow lump, Phellinus linteus by comparing the nuclear ribosomal intergenic spacer (IGS) I region with that of other genera of basidiomycetes retrieved from Genbank. IGS I region of Phellinus linteus was 730 bp long and sequence homology was conserved in the 5' region, in particular $1{\sim}280\;bp$, and decreased in the direction toward the 3' end. ITS region was widely studied in phylogenies related to basidiomycetes, but IGS region was not well understood yet. Our study indicated that IGS region can be a good tool in phylogenetic study of basidiomycetes.