Mitochondrial genome of Euchirus longimanus (Coleoptera: Scarabaeidae) and phylogenetic relationship of Euchirini

Yu Yingying,Lee Seunghyun,Jin Lijie,Bai Ming 한국응용곤충학회 2023 Journal of Asia-Pacific Entomology Vol.26 No.4

The long-armed scarab beetles, a charismatic group within the small tribe Euchirini, are characterized by their large body sizes and distinctly elongated forelegs in males. While mitochondrial genomes have been sequenced for two of the included genera, Cheirotonus and Propomacrus, the type genus of the tribe, Euchirus, remains unexplored. It will provide valuable insights into the phylogenetic position and internal relationships of the Euchirini to investigate the mitochondrial genome of Euchirus and conduct phylogenetic analyses. In this study, it presents the first mitochondrial genome of Euchirus longimanus. The length of the mitochondrial genome of Euchirus longimanus is 16,591 bp. We analyzed its genes arrangement, base composition, codon usage frequency, and constructed phylogenetic trees based on the nucleic acid sequences of 13 protein-coding genes. The phylogenetic results are consistent with previous studies, confirming the phylogenetic position of Euchirini within the paraphyletic Melolonthinae. Notably, we firstly elucidate the phylogenetic relationship among all three genera: Propomacrus + (Cheirotonus + Euchirus), supported by robust values in Bayesian inference (BI) analysis. However, the maximum likelihood (ML) tree shows weaker support for the internal node of Euchirini and exhibits distinct topological variations compared to the BI tree, suggesting the potential paraphyly of Cheirotonus with the inclusion of Euchirus longimanus. These findings highlight the importance of including additional species of Euchirus and Cheirotonus in the future phylogenetic investigations to achieve a compre hensive understanding of their evolutionary relationships.

Phylogenetic Relationship among Several Korean Coastal Red Tide Dinoflagellates Based on their rDNA Internal Transcribed Spacer Sequences

Cho, Eun-Seob,Kim, Gi-Yong,Park, Hyung-Sik,Nam, Byung-Hyouk,Lee, Jae-Dong Korean Society of Life Science 2001 Journal of Life Science Vol.11 No.2

The nucleotide sequences of the internal transcribed spacer regions (ITS1 and ITS2) of ribosomal DNA (rDNA), and the 5.85 rRNA gene, have been determined for 13 strains of dinoflagellates in order to analyze the phylo-genetic relationship. The DNA sequences contained considerable variation in the ITS regions, but little in the 5.85 rDNA. In addition, the ITS1 was more variable than the ITS2 in all species examined. The nucleotide length of this region varied from 519 bp to 596 bp depending on the taxa. The investigated taxa were divided into three large groups based on the ITS length, i. e., a group with short ITS region (A. fraterculus and Alexandrium sp.), a with ITS region group (P. micans, P. minimum and P. triestinum) and a with ITS region group (G. impudicum, C. polykrikoides, G. sanguineum, G. catenatum and H. triquetra). The relationship between nucleotide length of ITS1 and that of ITS2 was negative, whereas G+C content and nucleotide length showed positive correlation. In phylogenetic analyses producing NJ trees, the topology was similar cluster and clearly divided the taxa into three groups based on 5.8S rDNA that were similar to those based on morphological characteristics. In particular, G. impudicum was more closely related to G. catenatum than to C. polykrikoides using phylogenetic analysis. From this study, we chew that the length of ITS region contributes to discriminate Korean harmful algal species and ITS analysis is a useful method for resolving the systematic relationships of dinoflagellates.

핵 리보솜 DNA ITS1 염기서열에 기초한 한국산 사철란속 식물의 계통유전학적 유연관계

김재환,정용환,한상현,오문유 濟州大學校 基礎科學硏究所 2001 基礎科學硏究 Vol.14 No.1

Phylogenetic relationships of Korean Goodyera ( G. schlechtendaliana, G. macrantha, G. maximowicziana and G. velutina) were analyzed by comparing the nucleotide sequences of the internal transcribed spacer 1 (ITS1) region of the nuclear ribosomal DNA (nrDNA). The ITSl region of the nrDNA was amplified with the universal ITS primers (ITS1-F and ITS-R) by polymerase chain reaction (PCR). The length of the nrDNA ITSl regions identically represented 238 base pairs (bp) among selected taxa. The G+C contents of the nrDNA ITSl region ranged from 45.3 (G. maximowicziana and G. macrantha) to 45.7% (G. schlechtendaliana and G. velutina). Comparing the nucleotide sequences among selected taxa, twenty one sites of point mutation (base substitution) were found. The pairwise distance between G. macrantha and G. maximowicziana was 0.0043 showing the lowest value among any other pairs. These results showed that ITSl sequences analysis in Korean Goodyera is a useful tool for elucidating phylogenetic relationship.

On Phylogenetic Relationships Among Native Goat Populations Along the Middle and Lower Yellow River Valley

Chang, H.,Nozawa, K.,Liu, X.L.,Geng, S.M.,Ren, Z.J.,Qin, G.Q.,Li, X.G.,Sun, J.M.,Zheng, H.L.,Song, J.Z.,Kurosawa, Y.,Sano, A.,Jia, Q.,Chen, G.H. Asian Australasian Association of Animal Productio 2000 Animal Bioscience Vol.13 No.2

This paper is based on the 9 goat colonies along the middle and lower Yellow River valley and 7 local goat colonies in the Northeast, Tibet and the Yangtze valley. After collecting the same data about the 22 goat colonies in China and other countries, it establishes and composes the matrix of fuzzy similarity relation describing the genetic similarities of different colonies. It also clusters 38 colonies according to their phylogenetic relationship. The establishment of the matrix and the cluster are effected in terms of the frequency of 18 loci and 43 allelomorphs in blood enzyme and other protein variations. The study proves that the middle Yellow River valley is one of the taming and disseminating centers of domestic goats in the South and East of Central Asia. Compared with other goat populations in this vast area, the native goat populations in the west of Mongolian Plateau, the Qinghai-Tibet Plateau and the middle Yellow River valley share the same origin. The colonies in the lower Yellow River valley and those in the middle valley, however, are relatively remote in their phylogenetic relationship. The native goat colonies in the southeast of Central Asia can be classified into two genetic groups: "East Asia" and "South Asia" and the colonies in Southeast Asia belong to either group.

Molecular phylogenetic analysis of key Jatropha species inferred from nrDNA ITS and chloroplast (trnL-F and rbcL) sequences

Fang Chen,Guo-ye Guo,Sheng-hua Wang,Ying Xu,Lin Tang,Mao-qun Yu 한국유전학회 2016 Genes & Genomics Vol.38 No.6

The genus Jatropha (Euphorbiaceae) contains species that are of significant economic and ornamental value. However, Jatropha breeding material is rather limited due to incomplete information regarding phylogenetic relationships among germplasm resources. Phylogenetic analyses were performed based on the internal transcribed spacer of nuclear ribosomal DNA (nrDNA ITS), two chloroplast regions (trnL-F and rbcL), and the combined (ITS?trnL-F?rbcL) dataset among twenty-five specimens representing six key Jatropha species. Phylogenetic relationships of Jatropha were well resolved between subgenus Curcas and subgenus Jatropha, and demonstrated the intermediate position of section Polymorphae among sections of both subgenera. Jatropha curcas and J. integerrima demonstrated a close phylogenetic relationship. The molecular data agreed with the morphological classification that recognized J. multifida and J. podagrica in sec. Peltatae. The distinct intraspecific divergence that occurred in J. curcas could be attributed to restricted gene flow caused by geographical isolation and different ecological conditions. Phylograms produced with trnL-F and rbcL sequence data suggested slow rates of sequence divergence among Jatropha spp., while the ITS gene tree had good resolution suggesting high genetic variation of ITS among Jatropha species.

Cultural characteristics and phylogenetic relationships based on RFLP analysis in Pleurotus species

Sun-Gyu Choi,Kab-Yeul Jang,Gyu-Hyun Kim,Won-Sik Kong,Jae-Sun Jo,Hae-Yeong Kim,Young-Bok Yoo 한국버섯학회 2014 한국버섯학회지 Vol.12 No.3

Pleurotus has increased rapidly production and consumption because of highly nutritional value, natural healthy food and so on. The basic studies for Pleurotus need for development of mushroom industry. This study was to investigate the cultural characteristics among 15 strains of 6 species and to analyze their phylogenetic relationships. The cultural characteristics were investigated by mycelial growth activity at different media, temperature and pH. The optimum media for mycelial growth were YM and MCM in most species. The optimum temperature for mycelial growth were 25oC and 30oC. The optimum pH for mycelial growth were widly range from pH 5.1 to 7.4. Through the RFLP (restriction fragment length polymorphism) of IGS (intergenic spacer) I region in ribosomal DNA, it was analyzed phylogeny of interspecies and intraspecies. Each species was discriminated well as isolates within each species formed clade to be distinguished other species. P. florida was highly similar to P. floridanus, and P. flabellatus was P. cornucopiae. P. fuscus var. ferulae was highly similar to P. eryngii but discriminated different species in analysis of RFLP of IGS I region and showed different characteristics in mycelial culture. RFLP of IGS I region was useful of studying phylogenetic relationships of species and population.

Cultural characteristics and phylogenetic relationships based on RFLP analysis in Pleurotus species

Choi, Sun-Gyu,Jang, Kab-Yeul,Kim, Gyu-Hyun,Kong, Won-Sik,Jo, Jae-Sun,Kim, Hae-Yeong,Yoo, Young-Bok The Korean Society of Mushroom Science 2014 한국버섯학회지 Vol.12 No.3

Pleurotus has increased rapidly production and consumption because of highly nutritional value, natural healthy food and so on. The basic studies for Pleurotus need for development of mushroom industry. This study was to investigate the cultural characteristics among 15 strains of 6 species and to analyze their phylogenetic relationships. The cultural characteristics were investigated by mycelial growth activity at different media, temperature and pH. The optimum media for mycelial growth were YM and MCM in most species. The optimum temperature for mycelial growth were $25^{\circ}C$ and $30^{\circ}C$. The optimum pH for mycelial growth were widly range from pH 5.1 to 7.4. Through the RFLP (restriction fragment length polymorphism) of IGS (intergenic spacer) I region in ribosomal DNA, it was analyzed phylogeny of interspecies and intraspecies. Each species was discriminated well as isolates within each species formed clade to be distinguished other species. P. florida was highly similar to P. floridanus, and P. flabellatus was P. cornucopiae. P. fuscus var. ferulae was highly similar to P. eryngii but discriminated different species in analysis of RFLP of IGS I region and showed different characteristics in mycelial culture. RFLP of IGS I region was useful of studying phylogenetic relationships of species and population.

Cultural characteristics and phylogenetic relationships based on RFLP analysis in Pleurotus species

Choi, Sun-Gyu,Jang, Kab-Yeul,Kim, Gyu-Hyun,Kong, Won-Sik,Jo, Jae-Sun,Kim, Hae-Yeong,Yoo, Young-Bok 한국버섯학회 2014 한국버섯학회지 Vol.12 No.3

Pleurotus has increased rapidly production and consumption because of highly nutritional value, natural healthy food and so on. The basic studies for Pleurotus need for development of mushroom industry. This study was to investigate the cultural characteristics among 15 strains of 6 species and to analyze their phylogenetic relationships. The cultural characteristics were investigated by mycelial growth activity at different media, temperature and pH. The optimum media for mycelial growth were YM and MCM in most species. The optimum temperature for mycelial growth were 25˚C and 30˚C. The optimum pH for mycelial growth were widly range from pH 5.1 to 7.4. Through the RFLP (restriction fragment length polymorphism) of IGS (intergenic spacer) I region in ribosomal DNA, it was analyzed phylogeny of interspecies and intraspecies. Each species was discriminated well as isolates within each species formed clade to be distinguished other species. P. florida was highly similar to P. floridanus, and P. flabellatus was P. cornucopiae. P. fuscus var. ferulae was highly similar to P. eryngii but discriminated different species in analysis of RFLP of IGS I region and showed different characteristics in mycelial culture. RFLP of IGS I region was useful of studying phylogenetic relationships of species and population.

Cultural characteristics and phylogenetic relationships based on RFLP analysis in Pleurotus species

최선규,장갑열,김규현,공원식,조재순,김혜영,유영복 한국버섯학회 2014 한국버섯학회지 Vol.12 No.3

Pleurotus has increased rapidly production and consumption because of highly nutritional value, natural healthy foodand so on. The basic studies for Pleurotus need for development of mushroom industry. This study was to investigate the culturalcharacteristics among 15 strains of 6 species and to analyze their phylogenetic relationships. The cultural characteristics wereinvestigated by mycelial growth activity at different media, temperature and pH. The optimum media for mycelial growth wereYM and MCM in most species. The optimum temperature for mycelial growth were 25oC and 30oC. The optimum pH formycelial growth were widly range from pH 5.1 to 7.4. Through the RFLP (restriction fragment length polymorphism) of IGS(intergenic spacer) I region in ribosomal DNA, it was analyzed phylogeny of interspecies and intraspecies. Each species wasdiscriminated well as isolates within each species formed clade to be distinguished other species. P. florida was highly similar to P. floridanus, and P. flabellatus was P. cornucopiae. P. fuscus var. ferulae was highly similar to P. eryngii but discriminated differentspecies in analysis of RFLP of IGS I region and showed different characteristics in mycelial culture. RFLP of IGS I region wasuseful of studying phylogenetic relationships of species and population.

Genetic Diversity and Phylogenetic Relationships between Chinese Cabbages [B. campestris (syn. rapa) L.] and Cabbages (B. oleracea L.) in Korea

Yan-Lin Sun,Shi-Lin Zheng,Kyong-Cheul Park,Ki-Young Choi,Ho-Min Kang,Soon-Kwan Hong 한국원예학회 2016 원예과학기술지 Vol.34 No.2

Members of the genus Brassica, which are known as oil crops or cruciferous vegetables, are widely cultivated in Canada, Australia, Asian and Europe. Because Brassica species have high yields, are well adapted to their environments, and are self-incompatible, the germplasm is abundant. Previous studies have reported abundant genetic diversity even within Brassica subspecies. In Korea, fresh cabbage leaves are eaten with roast meat, and to meet the current popular demand, new varieties are being increasingly bred. To determine the genetic diversity and relationships among the cabbage vegetables in Korea, we evaluated the genetic variation of 18 accessions based on 5S and 18S ribosomal RNA (rRNA) gene sequences. We detected many variable nucleotide sites, especially in the 5S rRNA gene sequences. Because the length of the 18S rRNA gene might influence the dissimilarity rate statistics, we used both the 5S and 18S sequences to analyze the phylogenetic relationships. S7 (B. oleracea) showed the most distant phylogenetic relationship with the other Brassica species. Interestingly, B2 (B. oleracea), B15, and B18 (B. campestris) have three different types of leaf profiles, and were divided into one group, and the other Brassica species formed another group. Statistical analysis of interspecies and intraspecies genetic distances revealed that B. campestris L. showed higher genetic diversity than B. oleracea L. This work provides additional data that facilitates the evaluation of the genetic variation and relationships among Brassica species. The results could be used in functional plant breeding programs to improve Brassica crops.