Comparative genomic and functional analysis of Akkermansia muciniphila and closely related species

Juyuan Xing,Xiaobo Li,Yingjiao Sun,Juanjuan Zhao,Shaohua Miao,Qin Xiong,Yonggang Zhang,Guishan Zhang 한국유전학회 2019 Genes & Genomics Vol.41 No.11

Background Akkermansia muciniphila is an important bacterium that resides on the mucus layer of the intestinal tract. Akkermansia muciniphila has a high abundance in human feces and plays an important role in human health. Objective In this article, 23 whole genome sequences of the Akkermansia genus were comparatively studied. Methods Phylogenetic trees were constructed with three methods: All amino acid sequences of each strain were used to construct the first phylogenetic tree using the web server of Composition Vector Tree Version 3. The matrix of Genome-to- Genome Distances which were obtained from GGDC 2.0 was used to construct the second phylogenetic tree using FastME. The concatenated single-copy core gene-based phylogenetic tree was generated through MEGA. The single-copy genes were obtained using OrthoMCL. Population structure was assessed by STRU CTU RE 2.3.4 using the SNPs in core genes. PROKKA and Roary were used to do pan-genome analyses. The biosynthetic gene clusters were predicted using antiSMASH 4.0. IalandViewer 4 was used to detect the genomic islands. Results The results of comparative genomic analysis revealed that: (1) The 23 Akkermansia strains formed 4 clades in phylogenetic trees. The A. muciniphila strains isolated from different geographic regions and ecological niches, formed a closely related clade. (2) The 23 Akkermansia strains were divided into 4 species based on digital DNA-DNA hybridization (dDDH) values. (3) Pan-genome of A. muciniphila is in an open state and increases with addition of new sequenced genomes. (4) SNPs were not evenly distributed throughout the A. muciniphila genomes. The genes in regions with high SNP density are related to metabolism and cell wall/membrane envelope biogenesis. (5) The thermostable outer-membrane protein, Amuc_1100, was conserved in the Akkermansia genus, except for Akkermansia glycaniphila PytT. Conclusion Overall, applying comparative genomic and pan-genomic analyses, we classified and illuminated the phylogenetic relationship of the 23 Akkermansia strains. Insights of the evolutionary, population structure, gene clusters and genome islands of Akkermansia provided more information about the possible physiological and probiotic mechanisms of the Akkermansia strains, and gave some instructions for the in-depth researches about the use of Akkermansia as a gut probiotic in the future.

경남지역 수달( Lutra lutra)의 mitochondrial DNA D-loop지역과 microsatellite marker를 이용한 계통유전학적 유연관계 분석

Moon-Sung Park(박문성),Hyun-Tae Lim(임현태),Ki-Cheol Oh(오기철),Young-Rok Moon(문영록),Jong-Gap Kim(김종갑),Jin-Tae Jeon(전진태) 한국생명과학회 2011 생명과학회지 Vol.21 No.3

국내에 서식하는 수달의 경우 멸종 위기Ⅰ급 종으로 지정되어 국가적인 차원에서 관리하고 있는 보호종이다. 수달의 유전자원 보호 및 체계적인 관리를 위한 기초자료로 활용하기 위해 경남지역에 서식하는 수달의 계통유전학적 유연관계를 mtDNA D-loop 지역의 염기서열분석과 MS marker 분석을 통하여 실시하였다. 그 결과 mtDNA D-loop 지역의 676 bp 부분만 보았을 때 5개의 SNP가 확인되었으며, 6개의 haplotype이 추정되었다. 진주 인근 지역과 거제도 인근 지역에서 수집한 시료는 지역 내 유전적 거리가 지역 간의 유전적 거리보다는 가까운 것을 확인 할 수 있었고, 진주와 거제도 지역 간의 유전적 거리는 확연히 구분이 되었다. MrBays의 Bayesian Markov chain Monte Carlo 분석법을 이용하여 추정한 phylogeny 분석결과 뚜렷한 2개 그룹(진주와 거제/창녕 그룹)으로 분류 되었다. Parsimonious median-joining network [5] 분석의 결과 또한 2개의 뚜렷한 그룹으로 분류되어 phylogeny 분석결과와 일치하는 결과를 보였다. MS marker를 이용하여 추정한 유전적 거리지수를 활용하여 추정한 consensus tree의 결과 또한 크게 2개의 그룹으로 분류 되며, 첫 번째 그룹에는 거제도지역시료, 진주인근지역 시료 일부 그리고 창녕 우포늪에서 채취한 시료가 하나의 그룹으로 나뉘어 졌으며, 두 번째 그룹에는 진주인근 지역에서 채취한 시료만이 포함되어 하나의 그룹을 형성하여, mtDNA를 이용하여 분석한 것과 일부 다른 결과를 보였다. 이러한 결과의 차이는 모계를 추정하는 mtDNA와 상염색체 상의 MS marker의 특성에 기인한 것으로 보이나, 경상남도에 서식하는 수달을 크게 진주와 거제지역의 수달로 구분하는 것에는 유사한 결과를 보여 서식지 별 유전적 고정현상이 있음을 확인할 수 있었다. 하지만 좀 더 정확한 검증을 위해서는 수달의 full mtDNA 분석 및 국내에서 서식하는 수달에 적합한 MS marker발굴을 통한 대립유전자형을 분석하는 추가 연구가 필요하며, 전국 단위의 수달 시료를 확보하여 유전적 유연관계 분석을 실시한다면 한국 내 수달의 보전 및 보호에 도움이 될 것으로 사료되어 진다. The otter (Lutra lutra) in Korea is classified as a first grade endangered species and is managed under state control. We performed a phylogenetic analysis of the otter that inhabits the Changnyeong, Jinju, and Geoje areas in Gyeongsangnamdo, Korea using mtDNA and microsatellite (MS) markers. As a result of the analysis using the 676-bp D-loop sequence of mtDNA, six haplotypes were estimated from five single nucleotide polymorphisms. The genetic distance between the Jinju and Geoje areas was greater than distances within the areas, and the distance between Jinju and Geoje was especially clear. From the phylogenetic tree estimated using the Bayesian Markov chain Monte Carlo analysis by the MrBays program, two subgroups, one containing samples from Jinju and the other containing samples from the Changnyeong and Geoje areas were clearly identified. The result of a parsimonious median-joining network analysis also showed two clear subgroups, supporting the result of the phylogenetic analysis. On the other hand, in the consensus tree estimated using the genetic distances estimated from the genotypes of 13 MS markers, there were clear two subgroups, one containing samples from the Jinju, Geoje and Changnyeong areas and the other containing samples from only the Jinju area. The samples were not identically classified into each subgroup defined by mtDNA and MS markers. It could be inferred that the differential classification of samples by the two different marker systems was because of the different characteristics of the marker systems used, that is, the mtDNA was for detecting maternal lineage and the MS markers were for estimating autosomal genetic distances. Nonetheless, the results from the two marker systems showed that there has been a progressive genetic fixation according to the habitats of the otters. Further analyses using not only newly developed MS markers that will possess more analytical power but also the whole mtDNA are needed. Expansion of the phylogenetic analysis using otter samples collected from the major habitats in Korea should be helpful in scientifically and efficiently maintaining and preserving them.

ITS 염기서열에 의한 한국산 담배풀속(Carpesium L.)의 계통분류학적 연구

유광필,박선주 한국자원식물학회 2012 한국자원식물학회지 Vol.25 No.1

Phylogenetic analyses were conducted to evaluate relationships of 7 taxa of Korean Carpesium including three outgroup (Inula britannica L., Inula germanica L., Rhanteriopsis lannginosa (DC.) Rauschert) by using ITS (internal transcribed spacer) sequences of nuclear ribosomal DNA. Phylogenetic studies used maximum parsimony, neighbor-joining and maximum likelihood methods analysis. The length of the ITS sequences was 731 bp, and the lengths of the ITS1, ITS2and 5.8S regions were 284~297 bp, 264~266 bp and 164 bp, respectively. The total number of variable sites was 111 for the entire sequences, and a parsimony informative sites of 64 are valid. Base change appeared variously in ITS1 rather than in ITS2. As the result, Korean Carpesium were formed monophyletic group and C. abrotanoides situated as the most basal clade. The results show that C. macrocephalum is closely related with C. triste. C. rosulatum has the closest relationship with C. glossophyllum. C. cernuum is close to C. divaricatum. These results suggest that the ITS data used in this study could be useful for the phylogenetic analysis of Korean Carpesium. 한국산 담배풀속(Carpesium L.) 7분류군과 3개의 외군(Inula britannica L., Inula germanica L., Rhanteriopsis lannginosa(DC.) Rauschert)을 대상으로 유연관계를 파악하기 위하여 nuclear ribosomal DNA(nrDNA) 중 ITS (internal transcribed spacer) 지역의 계통분류학적 분석을수행하였다. 계통분류학적 연구방법은 maximum parsimony,neighbor-joining와 maximum likelihood 방법을 사용하였다. 정렬된 계통분의 총 길이는 731 bp이며, ITS1, ITS2와 5.8S 부위의 길이는 각각 284~297 bp, 264~266 bp와164 bp로 나타났다. 계통분류학 변이를 보이는 site는 111개로 확인 되었으며, 그 중 64개의 site가 계통학적으로 유효한 것으로 나타났고, ITS1 지역이 ITS2 지역보다 염기 변이가다양하게 나타나는 것으로 확인되었다. 그 결과, 한국산 담배풀속은 단계통을 형성하였으며, 담배풀(C. abrotanoides L.)이 가장 기저부에 위치하였다. 여우오줌(C. macrocephalum Franch. & Sav.)와 두메담배풀(C. triste Maxim.)은 가까운 유연관계를 나타냈으며, 애기담배풀(C. rosulatum Miq.)와 천일담배풀(C. glossophyllum Maxim.) 그리고 좀담배풀(C. cernuum L.)와 긴담배풀(C. divaricatum Siebold & Zucc.)도 유연관계가 가깝게 나타났다. 이와 같은 결과로 담배풀속 nrDNA의 ITS 지역 염기서열에 기초한 분자계통학적 연구는 계통분류를 이해하는데 유용한 방법으로판단된다.

Phylogenetic Study on the Genus Pungitius (Pisces: Gasterosteidae) Populations by the RAPD analysis통 연구

Chae, Byung-Soo,Seo, Bo-Keun 한국어류학회 2003 韓國魚類學會誌 Vol.15 No.1

한국산 가시고기속(genus Pungitius) 어류의 분류학적 위치를 밝히기 위하여 RAPD(random amplified polymorphic DNAs) method를 이용하여 분석하였다. 가시고기속 어류 중 P. kaibarae와 P. sinensis의 분류학적 위치에 대해서는 학자들 간에 이견이 많지만, 이들 2종은 뚜렷한 형태적 차이와 지리적 분포 양상에 의해 P. sinensis 집단 및 P. kaibarae 내의 3개 집단으로 구분된다. 집단간의 이러한 형태의 차이는 본 조사의 RAPD 분석 및 기존의 isoenzyme 분석에 의해 밝혀진 유전적 차이와 일치하였다. P. sinensis 집단과 P.kaibarae 집단 사이의 유전적 차이는 D = 0.772였으며, P. kaibarae 집단 내의 강릉 이북 집단과 금호강-형산강 집단 사이의 유전적 차이는 D = 0.680이었다. 이들 두 유전적 차이의 값은 별종 혹은 그 이상 수준의 차이에 해당하였다. 이들 두 유전적 차이의 값은 별종 혹은 그 이상 수준의 차이에 해당하였다. 한편 금호강과 형신강의 집단 사이의 유전적 차이는 D = 0.370이었으며 이는 아종수준의 차이에 해당하였다. 따라서 저자들은 유전적 및 형태적 차이를 근거로 P. sinensis 집단, P.kaibarae 집단 중 강릉 이북 집단 및 금호강-형산강 집단을 각기 별종으로 하고, 금호강 집단과 형산강 집단은 서로 아종으로 분류하였다. RAPD 분석은 기존의 방법보다 단순하고 쉬운 technique이며 계통 연구에 있어서 적절한 방법으로 판단되었다. Taxonomic relationships of the fishes in the genus Pungitius from Korea were analyzed using RAPD (random amplified polymorphic DNAs) method. The taxonomic status of P. sinensis and P. kaibarae have been disputed among researchers, but these two species can be divided into a P. sinensis group and three groups within P. kaibarae by their distinct morphological differences and geographical distribution patterns. The morphological differences among the groups accord with the genetic differences as revealed by RAPD analysis in the present study and by isoenzyme analysis in previous reports. The genetic difference between the P. sinensis and P. kaibarae groups was D = 0.772, and that between P. kaibarae groups of Sacheon river and Geumho-Hyeongsan river was D = 0.680. These two values correspond to species level or above. The genetic difference between Geumho and Hyeongsan river groups was D = 0.370, which means that the two groups are distinguishable at the subspecies level. On the basis of genetic and morphological differences, we classify the P. sinensis group, the northern group of P. kaibarae above Gangneung, and the Geumho-Hyeongsan river group as distinct species respectively, and classify the Geumho river group and Hyeongsan river group as subspecies. RAPD analysis was more simple and an easier technique than previous methods, and proved to be a proper method for phylogenetic studies.

Phylogenetic Analysis of 16S rDNA Sequences Manifest Rumen Bacterial Diversity in Gayals (Bos frontalis) Fed Fresh Bamboo Leaves and Twigs (Sinarumdinaria)

Deng, Weidong,Wanapat, Metha,Ma, Songcheng,Chen, Jing,Xi, Dongmei,He, Tianbao,Yang, Zhifang,Mao, Huaming Asian Australasian Association of Animal Productio 2007 Animal Bioscience Vol.20 No.7

Six male Gayal (Bos frontalis), approximately two years of age and with a mean live weight of $203{\pm}17$ kg ($mean{\pm}standard\;deviation$), were housed indoors in metabolism cages and fed bamboo (Sinarundinaria) leaves and twigs. After an adjustment period of 24 days of feeding the diet, samples of rumen liquor were obtained for analyses of bacteria in the liquor. The diversity of rumen bacteria was investigated by constructing a 16S rDNA clone library. A total of 147 clones, comprising nearly full length sequences (with a mean length of 1.5 kb) were sequenced and submitted to an on-line similarity search and phylogenetic analysis. Using the criterion of 97% or greater similarity with the sequences of known bacteria, 17 clones were identified as Ruminococcus albus, Butyrivibrio fibrosolvens, Quinella ovalis, Clostridium symbiosium, Succiniclasticum ruminis, Selenomonas ruminantium and Allisonella histaminiformans, respectively. A further 22 clones shared similarity ranging from 90-97% with known bacteria but the similarity in sequences for the remaining 109 clones was less than 90% of those of known bacteria. Using a phylogenetic analysis it was found that the majority of the clones identified (57.1%) were located in the low G+C subdivision, with most of the remainder (42.2% of clones) located in the Cytophage-Flexibacter-Bacteroides (CFB) phylum and one clone (0.7%) was identified as a Spirochaete. It was apparent that Gayal have a large and diverse range of bacteria in the rumen liquor which differ from those of cattle and other ruminants. This may explain the greater live weights of Gayal, compared to cattle, grazing in the harsh natural environments in which Gayal are located naturally.

섬진강-광양만 하구 기수 재첩 (Corbicular japonica)의 분자 계통유전학적 분석

김지훈,김원석,박기연,곽인실 한국하천호수학회 2022 생태와 환경 Vol.55 No.3

An estuary is a water ecosystem with a high abundance of the species diversity, due to a variety of complex physicochemical factors of the area where freshwater and ocean mixed. The identification of Corbicula species in the estuary environments is difficult because of various morphological characteristics. In this study, we provide taxonomic information on Corbicula species with taxonomic difficulties using morphological and genetic analysis. This study was conducted on clams from the Seomjin River-Gwangyang Bay, one of the major production area of marsh clam in Korea. As a result, we characterized Cytocrome C Oxidase subunit I (COI) sequences of the Corbicula. The 636 bp nucleotide sequences of COI have 98% homology among Corbicula species collected from 2 sites of Seomjin River-Gwangyang Bay. The phylogenetic analysis with 17 species of Corbicula indicated that most of the species collected from Seomjin River-Gwangyang Bay were brackish water clam (Corbicula japonica), and only one Asian clam (Corbicula fluminea). The evolutionary distance between C. japonica and C. fluminea was less than 0.003. Therefore, it was confirmed that C. japonica is phylogenetically closely related to C. fluminea. In 9 species of Cyrenidae, phylogenetic tree was classified into three lineages. These results will be used as an important data for an identification of clam species by providing genetic information for Corbicula species with a morphological diversity.

Species Relationships among Allium Species by ISSR Analysis

손재한,박경철,이성일,김종화,김남수 한국원예학회 2012 Horticulture, Environment, and Biotechnology Vol.53 No.3

The genus Allium includes several important condiment and ornamental vegetable species. The botanical status of many more than 600 species in the genus Allium has not been clearly classified. We used inter simple sequence repeat (ISSR) technique to analyze the phylogenetic relationships among 24 individual accessions and species that represent cultivated Allium species and their ancestral species. Nucleotide sequence analysis was used to rule out homoplasy,the possibility that unrelated ISSR-bands migrated to the same positions during gel electrophoresis. To avoid spurious results, PCR reactions were conducted in duplicate on independent thermocyclers and only reproducible bands were used for analysis. We detected 153 polymorphic bands from 20 ISSR primers. The ISSR polymorphism profiles were used to group most of the Allium species and accessions according to previous classification. However, A. chinense,previously included in the Rhizirideum section, was distinct from other species in the phylogenetic dendrogram. A. wakegi,the Korean endemic ‘Jjokpa’ and hybrid between A. cepa and A. fistulosum, was grouped in the Cepa section. A. monanthum, another Korean endemic ‘Dalae,’ was grouped in the Rhizirideum section. Because phylogenetic analysis of these three Korean endemic species has not been reported previously, the current report may allow these species to be included in future phylogenetic studies.

Species Relationships among Allium Species by ISSR Analysis

Son, Jae-Han,Park, Kyong-Cheul,Lee, Sung-Il,Kim, Jong-Hwa,Kim, Nam-Soo 한국원예학회 2012 Horticulture, Environment, and Biotechnology Vol.53 No.3

The genus Allium includes several important condiment and ornamental vegetable species. The botanical status of many more than 600 species in the genus Allium has not been clearly classified. We used inter simple sequence repeat (ISSR) technique to analyze the phylogenetic relationships among 24 individual accessions and species that represent cultivated Allium species and their ancestral species. Nucleotide sequence analysis was used to rule out homoplasy, the possibility that unrelated ISSR-bands migrated to the same positions during gel electrophoresis. To avoid spurious results, PCR reactions were conducted in duplicate on independent thermocyclers and only reproducible bands were used for analysis. We detected 153 polymorphic bands from 20 ISSR primers. The ISSR polymorphism profiles were used to group most of the Allium species and accessions according to previous classification. However, A. chinense, previously included in the Rhizirideum section, was distinct from other species in the phylogenetic dendrogram. A. wakegi, the Korean endemic 'Jjokpa' and hybrid between A. cepa and A. fistulosum, was grouped in the Cepa section. A. monanthum, another Korean endemic 'Dalae,' was grouped in the Rhizirideum section. Because phylogenetic analysis of these three Korean endemic species has not been reported previously, the current report may allow these species to be included in future phylogenetic studies.

Comparative Analysis of the Amino Acid Composition and Phylogenetic Diversity of Five Seaweed Species

Seung Won Son(손승원),Hyeyoung Lee(이혜영) 한국생명과학회 2024 생명과학회지 Vol.34 No.3

해조류는 풍부한 필수 영양소 공급으로 인해 귀중한 해양 자원으로 여겨지며 특히 단백질과 아미노산이 풍부하게 함유되어 있다. 한국에서는 500종 이상의 해조류가 서식하며 그 중 50종 이상이 식품용으로 이용 되어 일상 식단의 중심 역할을 한다. 본 연구는 한국에서 가장 흔히 섭취되는 해조류 5종(매생이, 톳, 김, 다시마, 미역; Capsosiphon fulvescens, Hizikia fusiforme, Porphyra yezoensis, Saccharina japonica, Undaria pinnatifida)의 단백질 구성 아미노산을 분석하였다. 고성능 액체 크로마토그래피 분석 결과, 아스파르트산, 글루탐산, 알라닌, 류신이 가장 풍부한 아미노산 성분임을 알 수 있었다. 주성분 분석에서는 이 다섯 종류의 해조류가 아미노산 구성에 따라 세 개의 군집으로 분류될 수 있었고, 이는 부분적으로 계통 분류 결과와 일치하였다. 다양한 아미노산 중에서도 글루탐산, 아스파르트산, 알라닌이 구분을 주도하는 주요 아미노산이였다. 특히, 가까운 계통적 근접성을 보이는 Undaria pinnatifida와 Capsosiphon fulvescens는 뚜렷하게 유사한 아미노산 프로필을 나타내었다. 그에 비해 Porphyra yezoensis와 Saccharina japonica는 계통적 관계를 공유하더라도 다른 아미노산 구성을 보였다. Hizikia fusiforme는 두 분석 모두에서 독특한 군집으로 나타났다. Seaweeds represent a widely harnessed marine resource that are valued for their abundant supply of essential nutrients, particularly proteins and amino acids. In Korea, where over 500 species of seaweed thrive and more than 50 are utilized for culinary purposes, seaweed has become a staple in regular diets. In this study, we focused on five of the most commonly consumed seaweed species in Korea: Capsosiphon fulvescens, Hizikia fusiforme, Porphyra yezoensis, Saccharina japonica, and Undaria pinnatifida. We closely examined the amino acid compositions of these five species. High-performance liquid chromatography showed that aspartic acid, glutamic acid, alanine, and leucine were the most abundant amino acids in the seaweeds. Principal component analysis revealed that the five seaweed species could be classified into three clusters according to their amino acid composition, partially corroborating findings from the phylogenetic analysis. Among various amino acids, glutamic acid, aspartic acid, and alanine were the primary amino acids driving differentiation. Notably, U. pinnatifida and C. fulvescens, which demonstrated close phylogenetic proximity, exhibited remarkably similar amino acid profiles. Conversely, although P. yezoensis and S. japonica shared a phylogenetic relationship, they displayed distinctly different amino acid compositions. H. fusiforme emerged as a distinct group in both analyses.

Taxonomic and phylogenetic study of the subgenus Tricercandra in the genus Chloranthus (Chloranthaceae)

강종수,유기억 한국식물분류학회 2023 식물 분류학회지 Vol.53 No.4

The genus Chloranthus consists of 17 taxa with the two subgenera Chloranthus and Tricercandra. These two subgenera can be distinguished by the morphology of the androecium. In South Korea, C. japonicus and C. fortunei of the subgenus Tricercandra are distributed. Although C. fortunei is typically not branched, a variant that branches from the stem has recently been discovered. Here, we conducted morphological and molecular phy- logenetic analyses to elucidate the interspecific relationships within the subgenus Tricercan- dra and to evaluate the taxonomic position of the variant of C. fortunei. Morphological analyses revealed distinct differences among C. angustifolius, C. japonicus, C. fortunei, and the variant of C. fortunei. However, distinguishing between C. holostegius and C. nervosus was challenging. A principal component analysis also showed that while C. angustifolius, C. japonicus, C. fortunei, and the corresponding variant clustered independently, C. holoste- gius and C. nervosus overlapped, rendering them indistinguishable. Molecular phylogenetic studies using nuclear ribosomal internal transcribed spacer (nrITS) regions and three plastid regions, rbcL, rpl20-rps12, and trnL-F, revealed that the subgenus Tricercandra was mono- phyletic. Within the subgenus Tricercandra, C. angustifolius formed a sister clade with C. fortunei in the combined three plastid gene tree, while C. japonicus displayed different phy- logenetic relationships between the nrITS and plastid gene trees. In addition, neither C. holos- tegius nor C. nervosus was monophyletic, consistent with the morphological analyses. The variant of C. fortunei formed an independent subclade on the nrITS tree but was not distin- guished from other C. fortunei on the plastid gene tree. Our study elucidated clear species delim- itation among C. angustifolius, C. japonicus, and C. fortunei and suggested key morphological characters useful for distinguishing them. Furthermore, our findings highlighted the ambiguous species delimitation and phylogenetic uncertainty between C. holostegius and C. nervosus. While we demonstrated morphological differences between the typical C. fortunei and its variant, the limited molecular phylogenetic evidence implies a need for further study.