미토콘드리아 COI 유전자 서열의 다형성과 반수체형에 근거한 한국산 붉바리(Epinephelus akaara)의 유전적 구조와 계통 유연관계

한상현(Sang-Hyun Han),이영돈(Young-Don Lee),백혜자(Hae-Ja Baek),오홍식(Hong-Shik Oh),노충환(Choong Hwan Noh) 한국생명과학회 2014 생명과학회지 Vol.24 No.6

한국산 붉바리 집단에서 유전적 구조와 계통 유연관계를 mtDNA COI 유전자 서열의 다형성을 이용하여 조사하였다. COI 유전자 서열을 결정하였고 기존에 보고된 서열들과 비교하였다. 본 연구를 통해 결정된 COI 서열들은 기존에 보고된 EF607565에 대하여 99.1-99.8%의 동일성을 나타내었다. 전체 20가지의 haplotype들이 발견되었고, 한국산 붉바리 집단은 19가지의 haplotype을 나타내었다. 이들 중 Hap_03과 Hap_08은 각각 제주도와 중국-특이적인 COI 서열들을 보였다. 반면, Hap_07은 한국에서 채집된 시료들과 홍콩과 대만에서 보고된 기록 등 여러 COI 서열들을 포함하였다. COI haplotype들의 다형성에 근거한 계통 유전학적 분석을 통해 작성된 NJ tree는 Epinephelus 속 내에서 단계통적인 분지양상을 나타내었고, 이는 붉바리 집단들이 공통의 모계 선조에서 진화한 것임을 나타내었다. 또한 중국해에서 보고된 COI 서열만을 포함하였던 Hap_08은 NJ tree의 중앙부에서 위치하였고, Hap_07의 서열들과도 근연의 관계임을 보여주었다. 이 결과는 중국산 붉바리 역시 동아시아의 다른 집단들과 모계적으로 연관되어있음을 보여주었다. 결과적으로, 동아시아 붉바리 집단들은 모계적으로 연관되어있을 뿐만 아니라 공통의 진화 역사를 공유하고 있으며 여전히 동아시아 해류(Kuroshio 해류)에 의해 영향을 받는 집단이라고 할 수 있다. 본 연구는 붉바리의 유전적 구조와 계통 유연관계를 이해하는 데 도움을 줄 수 있으며, 인공증식과 산업화에 관련된 연구에 있어 중요한 역할을 담당할 것으로 기대된다. The genetic structure and phylogenetic relationship were investigated in Korean red spotted grouper populations using the nucleotide sequence polymorphisms of the mitochondrial DNA (mtDNA) cytochrome c oxidase subunit I (COI) gene. The COI gene was sequenced showed 99.1-99.8% identity with the EF607565 sequence previously reported. A total of twenty haplotypes were found, and the Korean population showed nineteen haplotypes. Among those, Hap_03 and Hap_08 showed Jeju-do and China-specific COI sequences, respectively. However, Hap_07 had twelve COI sequences from South Korea and records from Hong Kong and Taiwan. Neighbor-joining (NJ) trees constructed from the phylogenetic analyses based on the polymorphisms of the COI haplotypes showed a monophyletic branching pattern within the genus Epinephelus. This indicated that the red spotted grouper populations had evolved from common maternal ancestors. In addition, the Hap_08, which had the COI sequence recorded only from China Sea, was found in the middle of the NJ tree nearby Hap_07 and showed a close relationship with Hap_07. This indicates that Chinese red spotted grouper is also maternally related to other populations in East Asia. Consequently, East Asian red spotted grouper populations are maternally related, as well as sharing the same evolutionary history, and are still affected by the East Asian ocean current (Kuroshio). These findings help to explain the genetic structure and phylogenetic relationship of red spotted grouper and also contribute to research on artificial breeding and industrialization.

하플로타입을 이용한 연관성 분석

김명숙,이정형 한국자료분석학회 2012 Journal of the Korean Data Analysis Society Vol.14 No.2

Phylogenetic tree is extremely useful tools, not only for establishing genealogical relationships among a group of organisms or their genes, but also for a variety of research once the phylogeny is estimated. In this paper, we review SNP (single nucleotide polymorphism)-based and haplotype-based tests of association, haplotype frequencies, and linkage disequilibrium with adjacent genetic markers. We also analyzed the COI gene for 49 specimens of Gracilaria salicornia from Southeast Asia. Finally, it is shown that a total of 13 SNPs and 7 COI haplotypes were found for Gracilaria salicornia. As such, haplotype association analysis will provide an important shortcut to carry out candidate-gene and genome-wide association studies. 생물계통수(phylogenetic tree)는 생물유전자 집단 사이의 계통관계를 보여줄 뿐 아니라 계통발생의 추정과 같이 다양한 연구 분야에서 매우 유용한 도구로 사용되고 있다. 본 논문에서는 단일염기다형성(single nucleotide polymorphism, SNP)과 하플로타입(haplotype)에 기반을 둔 연관성 검정, 하플로타입빈도, 인접한 유전자마커(genetic marker)들과의 연관불균형 분석에 대해 알아보기 위하여 홍조류 Gracilaria salicornia에 대한 COI 염기서열을 이용하였다. 그 결과 13개의 SNP와 7개의 하플로타입이 관찰되었다. 하플로타입에 대한 연관성 분석은 유용한 후보유전자의 탐색과 유전체 수준의 연관연구 등에 중요한 방법론을 제공하게 될 것이다.

Haplotype diversity and distribution pattern of Oecophylla smaragdina (Fabricius) (Hymenoptera, Formicidae) in Bangladesh based on mitochondrial COI genes

Rahman Md Mamunur,Hosoishi Shingo,Kazuo Ogata 한국응용곤충학회 2021 Journal of Asia-Pacific Entomology Vol.24 No.1

Climatic oscillation often have influenced the present distribution and intraspecific genetic diversity Oecophylla smaragdina through its wide range of geographical distribution. Previous phylogeographic study of Asian weaver ant population denotes the evidence of distribution of Indian types in Indian, Sri Lanka and SE Asian types in South Asian countries including Bangladesh. However, recent phylogenetic analysis reveals the overlapping distribution of the Indian and South East Asian clades of O. smaragdina in Bangladesh. The present study aims to identify the haplotypes and it’s networking in Bangladesh based on extensive materials. Sampling was executed according to zonation of 5 areas, demarcated by 3 main rivers during the years 2013 to 2018. Adult O. smaragadina workers were collected from 71 colonies of 67 localities belonging to 47 districts of Bangladesh. A total of 25 haplotypes were identified in Bangladesh comprises 13 and 12 of Indian and SE Asian types, respectively from 93 sequences of Cytochrome c oxidase subunit I (COI) gene of 639 bp. The geographical distribution of this haplotype reveals that the Indian haplotypes are mostly located at the western part of Bangladesh while SE Asian haplotypes were dominated in the Eastern part of the country. Central part of Bangladesh has overlapped with the mixture of both Indian and SE Asian haplotypes. The results of the haplotype network give the evidence of recent expansion of O. smaragdina population in Bangladesh and clarify the evi dence of presence of many missing haplotypes in refugee.

COI-haplotype composition of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae), in Taiwan

Gwan-Seok Lee,Kyung San Choi,Jeong Joon Ahn,Shaw-Yhi Hwang,Wonhoon Lee 한국응용곤충학회 2021 한국응용곤충학회 학술대회논문집 Vol.2021 No.10

Haplotype Network Analyses of Two Fire ants Species in genus Solenopsis Based on Sequences of COI-COII

Sohee Kim,Hyojoong Kim,Heung-Sik Lee,Hyun-jik Lee,Seonwoo Lee,Soo-Jung Suh,Jong-Ho Lee 한국응용곤충학회 2022 한국응용곤충학회 학술대회논문집 Vol.2022 No.10

Genetic lineage of Thrips tabaci (Thysanoptera: Thripidae) and their haplotypes in South Korea, using mitochondrial COI gene sequences

Gwan-Seok Lee,In Hong Jeong,Wonhoon Lee 한국응용곤충학회 2023 한국응용곤충학회 학술대회논문집 Vol.2023 No.10

The onion thrips, Thrips tabaci, is a serious global pest attacking many agricultural crops such as onion and Welsh onion. The thrips, assumed to originate in the Mediterranean region, has been reported for a long time in South Korea. According to worldwide molecular works, the species composes of three genetic lineages (LI, L2 and T) which related to reproductive mode (arrhenotoky vs. thelotoky). To understand the genetic diversity of T. tabaci in South Korea, we investigated genetic lineage and haplotype composition, using about 80 mitochondrial COI gene sequences (369bp) along with foreign sequences from GenBank and BOLD. The COI gene analysis shows that both of thelotokous L1 and arrhenotokous L2 population distribute in South Korea. Among 97 COI-haplotypes worldwide, only six haplotypes are found and thelotokous H1 dominantly distributes.

Morphometric and genetic diversity of Rasbora several species from farmed and wild stocks

Bambang Retnoaji,Boby Muslimin,Arif Wibowo,Ike Trismawanti 한국수산과학회 2023 Fisheries and Aquatic Sciences Vol.26 No.9

The morphology and genetic identification of Rasbora lateristriata and Rasbora argyrotaenia between cultivated and wild populations has never been reported. This study compares morphology and cytochrome c oxidase (COI) genes between farmed and wild stock Rasbora spp. in Java and Sumatra island, Indonesia. We analyzed the truss network measurement (TNM) characters of 80 fish using discriminant function analysis statistical tests. DNA was extracted from muscle tissue of 24 fish specimens, which was then followed by polymerase chain reaction, sequencing, phylogenetic analysis, fixation index analysis, and statistical analysis of haplotype networks. Basic Local Alignment Search Tool analysis validated the following species: R. lateristriata and R. argyrotaenia from farming (Jogjakarta); Rasbora agryotaenia (Purworejo), R. lateristriata (Purworejo and Malang), Rasbora dusonensis (Palembang), and Rasbora einthovenii (Riau) from natural resources. Based on TNM characters, Rasbora spp. were divided into four groups, referring to four distinct characters in the middle of the body. The phylogenetic tree is divided into five clades. The genetic distance between R. argyrotaenia (Jogjakarta) and R. lateristriata (Malang) populations (0.66) was significantly different (p < 0.05). R. lateristriata (Purworejo) has the highest nucleotide diversity (0.43). R. argyrotaenia from Jogjakarta and Purworejo shared the same haplotype. The pattern of gene flow among them results from the two populations’ close geographic proximity and environmental effects. R. argyrotaenia had low genetic diversity, therefore, increasing heterozygosity in cultivated populations is necessary to avoid inbreeding. Otherwise, R. lateristriata (Purworejo) had a greater gene variety that could be used to develop breeding. In conclusion, the middle body parts are a distinguishing morphometric character of Rasbora spp., and the COI gene is more heterozygous in the wild population than in farmed fish, therefore, enrichment of genetic variation is required for sustainable Rasbora fish farming.

The Mitochondrial Genetic Population Structure of the Ant Species, Vollenhovia emeryi (Hymenoptera: Myrmicinae) in Korea

Seung-Yoon Oh,Jae Chun Choe,Gilsang Jeong 한국응용곤충학회 2012 한국응용곤충학회 학술대회논문집 Vol.2012 No.05

The ant species, Vollenhovia emeryi, is distributed in Far East. The species can be divided into two major groups by their wing morphology of reproductives: short-winged and long-winged. A nationwide survey of the species was conducted for analyzing the mitochondrial haplotype diversity and genetic population structure. We collected 91 samples from 40 locations. A total of the 1239 bp partial COI (cytochrome C oxidase 1) region was used for the analyses. We found the total of 21 haplotypes. The mitochondrial haplotypes may correspond to the wing morphology. The genetic population structure examined potential geographic barriers of gene flow such as distance, mountains, rivers and plains which are non-mountain areas to prevent dispersal through mountain range. The result implied that no barriers considered in this study affected differently gene flow. Therefore, the behavioral characteristics of the ant may be the causal constraint of its genetic exchange.

Preliminary study for COI-haplotypes of Solenopsis invicta Buren (Hymenoptera: Formicidae), including samples from China

Gwan-Seok Lee,Li-Hua Lu,Wonhoon Lee 한국응용곤충학회 2020 한국응용곤충학회 학술대회논문집 Vol.2020 No.10

Genetic diversity of Insect farm populations of Protaetia brevitarsis seulensis (Kolbe, 1886) (Coleoptera, Scarabaeidae) in South Korea inferred from COI gene sequences

Taeman Han(Taeman Han),Seung-Chul Park(Seung-Chul Park),Haechul Park(Haechul Park) 국립공원연구원 2022 국립공원연구지 Vol.13 No.1

A Korean indigenous species, Protaetia brevitarsis seulensis (PBS), is popularly reared at many insect farms as valuable industrial insect resources in South Korea. However, there is no comprehensive study on the genetic diversity within the Korean PBS population as well as between morphologically closed species. Employing the rapidly evolved genetic markers such as mitochondrial DNA is important in the detection of haplotype diversity and rapid species identification of larval stage and/or its processed goods. We here examined how many genetically different haplotypes distribute in the reared PBS collected from 14 insect farms and the interspecific genetic difference between congeners using mitochondrial COI gene sequences (DNA barcoding region). As a results, the PBS was clearly separated from two related species with large genetic distances (7.98%~8.86%). In the PBS, 57 haplotypes were detected from 223 specimens with low intraspecific genetic distance (~1.3%). Among them, the most dominant haplotypes are subsequently detected in H4 (25.6%), H38 (15.7%) and H26 (10.3%). From the haplotype network and distribution analyses, we consider that many haplotypes have been mixed by artificial collections from various local places and exchanged between insect farms within South Korea. We expect that this data will be helpful in rapid species identification for its processed goods, and understanding the exact population diversity and detection of the original habitats for each haplotype of the reared PBS throughout comparing with natural populations in the further study.