Comparative analysis of genome-based CAZyme cassette in Antarctic Microbacterium sp. PAMC28756 with 31 other Microbacterium species

Gupta Sushma,Han So-Ra,Kim Byeollee,Lee Chang-Muk,Oh Tae-Jin 한국유전학회 2022 Genes & Genomics Vol.44 No.6

Background: The genus Microbacterium belongs to the family Microbacteriaceae and phylum Actinobacteria. A detailed study on the complete genome and systematic comparative analysis of carbohydrate-active enzyme (CAZyme) among the Microbacterium species would add knowledge on metabolic and environmental adaptation. Here we present the comparative genomic analysis of CAZyme using the complete genome of Antarctic Microbacterium sp. PAMC28756 with other complete genomes of 31 Microbacterium species available. Objective: The genomic and CAZyme comparison of Microbacterium species and to rule out the specific features of CAZyme for the environmental and metabolic adaptation. Methods: Bacterial source were collected from NCBI database, CAZyme annotation of Microbacterium species was analyzed using dbCAN2 Meta server. Cluster of orthologous groups (COGs) analysis was performed using the eggNOG4.5 database. Whereas, KEGG database was used to compare and obtained the functional genome annotation information in carbohydrate metabolism and glyoxylate cycle. Results: Out of 32 complete genomes of Microbacterium species, strain No. 7 isolated from Activated Sludge showed the largest genomic size at 4.83 Mb. The genomic size of PAMC28756 isolated from Antarctic lichen species Stereocaulons was 3.54 Mb, the G + C content was 70.4% with 3,407 predicted genes, of which 3.36% were predicted CAZyme. In addition, while comparing the Glyoxylate cycle among 32 bacteria, except 10 strains, all other, including our strain have Glyoxylate pathway. PAMC28756 contained the genes that degrade cellulose, hemicellulose, amylase, pectinase, chitins and other exo-and endo glycosidases. Utilizing these polysaccharides can provides source of energy in an extreme environment. In addition, PAMC28756 assigned the (10.15%) genes in the carbohydrate transport and metabolism functional group closely related to the CAZyme for polysaccharides degradation. Conclusions: The genomic content and CAZymes distribution was varied in Microbacterium species. There was the presence of more than 10% genes in the carbohydrate transport and metabolism functional group closely related to the CAZyme for polysaccharides degradation. In addition, occurrence of glyoxylate cycle for alternative utilization of carbon sources suggest the adaptation of PAMC28756 in the harsh microenvironment.

mySyntenyPortal: an application package to construct websites for synteny block analysis

Lee, Jongin,Lee, Daehwan,Sim, Mikang,Kwon, Daehong,Kim, Juyeon,Ko, Younhee,Kim, Jaebum BioMed Central 2018 BMC bioinformatics Vol.19 No.-

<P><B>Background</B></P><P>Advances in sequencing technologies have facilitated large-scale comparative genomics based on whole genome sequencing. Constructing and investigating conserved genomic regions among multiple species (called synteny blocks) are essential in the comparative genomics. However, they require significant amounts of computational resources and time in addition to bioinformatics skills. Many web interfaces have been developed to make such tasks easier. However, these web interfaces cannot be customized for users who want to use their own set of genome sequences or definition of synteny blocks.</P><P><B>Results</B></P><P>To resolve this limitation, we present mySyntenyPortal, a stand-alone application package to construct websites for synteny block analyses by using users’ own genome data. mySyntenyPortal provides both command line and web-based interfaces to build and manage websites for large-scale comparative genomic analyses. The websites can be also easily published and accessed by other users. To demonstrate the usability of mySyntenyPortal, we present an example study for building websites to compare genomes of three mammalian species (human, mouse, and cow) and show how they can be easily utilized to identify potential genes affected by genome rearrangements.</P><P><B>Conclusions</B></P><P>mySyntenyPortal will contribute for extended comparative genomic analyses based on large-scale whole genome sequences by providing unique functionality to support the easy creation of interactive websites for synteny block analyses from user’s own genome data.</P>

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.

Comparative genomics of canine Lactobacillus reuteri reveals adaptation to a shared environment with humans

Seungwoo Son,오재돈,Sung Ho Lee,Donghyun Shin,Yangseon Kim 한국유전학회 2020 Genes & Genomics Vol.42 No.9

Background Lactobacillus reuteri is a gram-positive, non-motile bacterial species that has been used as a representative microorganism model to describe the ecology and evolution of vertebrate gut symbionts. Objective Because the genetic features and evolutionary strategies of L. reuteri from the gastrointestinal tract of canines remain unknown, we tried to construct draft genome canine L. reuteri and investigate modifed, acquired, or lost genetic features that have facilitated the evolution and adaptation of strains to specifc environmental niches by this study. Methods To examine canine L. reuteri, we sequenced an L. reuteri strain isolated from a dog in Korea. A comparative genomic approach was used to assess genetic diversity and gain insight into the distinguishing features related to diferent hosts based on 27 published genomic sequences. Results The pan-genome of 28 L. reuteri strains contained 7,369 gene families, and the core genome contained 1070 gene families. The ANI tree based on the core genes in the canine L. reuteri strain (C1) was very close to those for three strains (IRT, DSM20016, JCM1112) from humans. Evolutionarily, these four strains formed one clade, which we regarded as C1-clade in this study. We could investigate a total of 32,050 amino acid substitutions among the 28 L. reuteri strain genomes. In this comparison, 283 amino acid substitutions were specifc to strain C1 and four strains in C1-clade shared most of these 283 C1-strain specifc amino acid substitutions, suggesting strongly similar selective pressure. In accessory genes, we could identify 127 C1-clade host-specifc genes and found that several genes were closely related to replication, recombination, and repair. Conclusion This study provides new insights into the adaptation of L. reuteri to the canine intestinal habitat, and suggests that the genome of L. reuteri from canines is closely associated with their living and shared environment with humans.

Study of Modern Human Evolution via Comparative Analysis with the Neanderthal Genome

Musaddeque Ahmed,Ping Liang 한국유전체학회 2013 Genomics & informatics Vol.11 No.4

Many other human species appeared in evolution in the last 6 million years that have not been able to survive to moderntimes and are broadly known as archaic humans, as opposed to the extant modern humans. It has always been consideredfascinating to compare the modern human genome with that of archaic humans to identify modern human-specificsequence variants and figure out those that made modern humans different from their predecessors or cousin species. Neanderthals are the latest humans to become extinct, and many factors made them the best representatives of archaichumans. Even though a number of comparisons have been made sporadically between Neanderthals and modern humans,mostly following a candidate gene approach, the major breakthrough took place with the sequencing of the Neanderthalgenome. The initial genome-wide comparison, based on the first draft of the Neanderthal genome, has generated someinteresting inferences regarding variations in functional elements that are not shared by the two species and the debatedadmixture question. However, there are certain other genetic elements that were not included or included at a smaller scalein those studies, and they should be compared comprehensively to better understand the molecular make-up of modernhumans and their phenotypic characteristics. Besides briefly discussing the important outcomes of the comparative analysesmade so far between modern humans and Neanderthals, we propose that future comparative studies may includeretrotransposons, pseudogenes, and conserved non-coding regions, all of which might have played significant roles duringthe evolution of modern humans.

Study of Modern Human Evolution via Comparative Analysis with the Neanderthal Genome

Ahmed, Musaddeque,Liang, Ping Korea Genome Organization 2013 Genomics & informatics Vol.11 No.4

Many other human species appeared in evolution in the last 6 million years that have not been able to survive to modern times and are broadly known as archaic humans, as opposed to the extant modern humans. It has always been considered fascinating to compare the modern human genome with that of archaic humans to identify modern human-specific sequence variants and figure out those that made modern humans different from their predecessors or cousin species. Neanderthals are the latest humans to become extinct, and many factors made them the best representatives of archaic humans. Even though a number of comparisons have been made sporadically between Neanderthals and modern humans, mostly following a candidate gene approach, the major breakthrough took place with the sequencing of the Neanderthal genome. The initial genome-wide comparison, based on the first draft of the Neanderthal genome, has generated some interesting inferences regarding variations in functional elements that are not shared by the two species and the debated admixture question. However, there are certain other genetic elements that were not included or included at a smaller scale in those studies, and they should be compared comprehensively to better understand the molecular make-up of modern humans and their phenotypic characteristics. Besides briefly discussing the important outcomes of the comparative analyses made so far between modern humans and Neanderthals, we propose that future comparative studies may include retrotransposons, pseudogenes, and conserved non-coding regions, all of which might have played significant roles during the evolution of modern humans.

Comparative genomics of 151 plant-associated bacteria reveal putative mechanisms underlying specific interactions between bacteria and plant hosts

Hongsheng Cai,Yan Bai,Changhong Guo 한국유전학회 2018 Genes & Genomics Vol.40 No.8

Although much work has explored how microbes can benefit plant growth, the mechanisms underlying this intriguing process remain largely unknown, especially considering the diversity of bacteria that surrounds plants. The objective of the present study was to identify bacterial genes contributing to plant–microbe associations, beneficial effects, and host specificities. For this purpose, comparative genomics investigation of 151 plant-associated bacteria was performed. A principal component analysis of seven key genomic features revealed patterns in the specific properties of these bacteria: N2- fixing bacteria were more closely related to pathogenic ones than to beneficial bacteria. A common set of genes over-represented in these plant-associated bacteria were found to be remarkably similar in terms of (1) genetic information processing, (2) amino acid metabolism, (3) metabolism of cofactors and vitamins, (4) nucleotide metabolism, (5) human diseases, and (6) metabolism of terpenoids and polyketides. Although we did not detect a common genetic basis for these beneficial effects, further in-depth analysis revealed that each of five beneficial bacterial groups shared specific gene sets. Functional annotation showed that environmental information processing, genetic information processing and cellular processes predominated in these beneficial groups. Hypothesizing that plant-associated bacteria may have overlapping strategies to colonize their plant hosts, we successfully identified many putative genes that determine host specificities. Most of these genes were classified as transcription factors, enzymes, transporters, and chemotaxis regulators. Comparative genomics provides a powerful tool for helping to identify genes that are common among species. Genome-based views of plant-associated bacteria reveal specific interactions between bacteria and plant hosts.

Comparative Genomic Hybridization 기법을 이용한 한국인 원발성 간세포암에서의 염색체 변화에 대한 연구

박훤겸,정풍만,이광수,조율희 한양대학교 의과대학 2001 한양의대 학술지 Vol.21 No.1

Comparative genomic hybridization(CGH) technique is one of the screening tests for DNA sequence copy number changes(losses, deletions, gains, amplifications) in tumor genomes. DNA changes in 23 hepatocellular carcinomas(HCC) associated with hepatitis B virus(HBV) were analyzed by CGH technique. Eighteen of the 23 cases showed genetic alterations. The remaining 5 cases showed no detectagble aberration. The losses of chromosome regions 17p(74%), 4q (57%), 16p (52%), 16q (48%), 8p (43%) and 13q (43%) were detected in the order of decreasing frequency. In cases of multiple losses of chromosomes, a combination of 17p,16p,16q,4q, and 8p losses was found in 5 cases (30%). On the other hand, chromosomal gains occurred on 1q (65%), 8q (52%), 20p (48%) and 20q (43%) in the order of decreasing frequency. And the simultaneous genomic gains of these 4 chromosomes were found in 9 cases (40%). Moreover, the combination of 5 genomic losses (17p, 16p, 16q, 4q, & 8p) and 4 genomic gains (1q, 8q, 20p, & 20q) was observed in 4 case s(23%). The pattern of chromosomal gains and losses in HCC with hepatitis B in Korean patients is very complex and involves virtually every site in the genome. This indicated a high genomic instability. This could possibly be explained either as the result of random chromosomal changes during early development of tumor, or as the highly variable and random pattern of integration of HBV in the HCC. The hepatocarcinogenesis may be the result of cumulative effocts rather than those orders of occurrence of those genomic changes. The sites of cellular DNA at which HBV integrates frequently undergo rearrangements, resulting in translocations, inverted duplications, deletions, and possibly recombinational events. But, CGH only detects changes of chromosomal copy number but could not identify translocations, inversions, and other aberrations of chromosome. The chromosomal analysis of HCC with HBV in Korean patients by CGH technique confirms the presence of complex and sporadic, but nonrandom genetic changes in the chromosome. In the future, more detailed oncogenic study could be carried out on the chromosomes which showed abnormal aberrations through this study.

Nitrosomonadales 목의 핵심유전체(core genome)와 범유전체(pan-genome)의 비교유전체학적 연구

이진환,김경호,Lee, Jinhwan,Kim, Kyoung-Ho 한국미생물학회 2015 미생물학회지 Vol.51 No.4

Nitrosomonadales 목에서 속하는 균주 중 현재 유전체 서열이 알려진 모든 유전체(N=10)를 이용하여 범유전체 및 핵심유전체 분석을 수행한 결과, 각각 9,808개와 908개 유전자클러스터를 포함하는 것을 확인하였다. Betaproteobacteria의 다른 목의 참조군들과 비교를 통하여 범유전체와 핵심유전체의 크기에 유전체의 수와 집단 내의 유전체들의 차이가 영향을 미치는 것을 확인하였다. Nitrosomonas 속과 Nitrosospira 속의 범유전체는 7,180개와 4,586개, 핵심유전체는 1,092개와 1,600로로 각각 측정되어 Nitrosospira 속의 동질성이 더 높은 것을 확인하였다. Nitrosomonadales 목의 범유전체와 핵심유전체의 크기에 Nitrosomonas 속이 대부분의 영향을 미치는 것을 확인하였다. COG 분석을 통하여 핵심유전체의 크기에는 J (translation, ribosomal structure and biogenesis) 범주가 가장 큰 비율(9.7-21.0%)을 차지하며, 유전체 사이의 유전적 거리가 먼 집단일수록 그 비율이 높아지는 것을 확인하였다. 범유전체의 크기에는 "-" (unclassified) 범주가 34-51%의 높은 비율을 차지하고 있을 정도로 큰 영향을 미치는 것을 확인하였다. 총 97개의 유전자 클러스터가 참조군에는 없고 Nitrosomonadales에만 존재하는 것을 확인하였다. 이들 클러스터들은 Nitrosomonadales을 특징 지우는 유전자들인 ammonia monooxygenase의 유전자인 amoA와 amoB와 그와 관련 있는 amoE와 amoD들을 포함하는 반면에 unclassified 유전자들도 상당량(16-45%)을 포함하고 있다. 이러한 유전자 클러스터는 Nitrosomonadales의 유전적 특이성을 밝히는 데 중요한 역할을 할 것이다. All known genomes (N=10) in the order Nitrosomonadales were analyzed to contain 9,808 and 908 gene clusters in their pan-genome and core genome, respectively. Analyses with reference genomes belonging to other orders in Betaproteobacteria revealed that sizes of pan-genome and core genome were dependent on the number of genomes compared and the differences of genomes within a group. The sizes of pan-genomes of the genera Nitrosomonas and Nitrosospira were 7,180 and 4,586 and core genomes, 1,092 and 1,600, respectively, which implied that similarity of genomes in Nitrosospira were higher than Nitrosomonas. The genomes of Nitrosomonas contributed mostly to the size of the pan-genome and core genomes of Nitrosomonadales. COG analysis of gene clusters showed that the J (translation, ribosomal structure and biogenesis) category occupied the biggest proportions (9.7-21.0%) among COG categories in core genomes and its proportion increased in the group which genetic distances among members were high. The unclassified category (-) occupied very high proportions (34-51%) in pan-genomes. Ninety seven gene clusters existed only in Nitrosomonadales and not in reference genomes. The gene clusters contained ammonia monooxygenase (amoA and amoB) and -related genes (amoE and amoD) which were typical genes characterizing the order Nitrosomonadales while they contained significant amount (16-45%) of unclassified genes. Thus, these exclusively-conserved gene clusters might play an important role to reveal genetic specificity of the order Nitrosomonadales.

Pan-genome Analysis Reveals Comparative Genomic Features of Central Metabolic Pathways in Methylorubrum extorquens

이규민,Zoe K. Scott-Nevros,이상목,김동혁 한국생물공학회 2023 Biotechnology and Bioprocess Engineering Vol.28 No.6

Methylobacterium is a genus belonging to the pink-pigmented facultative methylotrophs, which can use C1 substrates as a sole carbon source. Methylorubrum extorquens (formerly Methylobacterium extorquens) is a potentially valuable bacteria in methanol-based bioindustry producing high-value-added chemicals. Thus, it is critical to understand the core metabolic pathways of M. extorquens strains for further advancement as a platform bacterium in the bioindustry. However, there are no reported systems biological approaches comparing different M. extorquens strains. This paper focuses on comparing the genomic properties of seven completely sequenced M. extorquens strains, including M. extorquens PA1, which was re-sequenced, and M. extorquens ATCC 55366, which was newly sequenced in this study. Pan-genome analysis indicated that a total of 10,431 ortholog clusters composed the pan-genome of these M. extorquens strains, including 3,507 core genome, 1,860 accessory genome, and 5,064 unique genome clusters. The functional annotation discovered that genes related to signal transduction were the most abundant in the pan-genome. Pan-genome analysis of two different habitat-specific groups revealed that the strains isolated from various soil environments had a higher percentage of genes involved in mobilome in their core genome. Subsequent exploration for secondary metabolite biosynthesis clusters denoted the unique ability of M. extorquens AM1 to produce various toblerols. M. extorquens PA1 could be a strong candidate for industrial strain development because of its minimal genome size with fully conserved central metabolism. This study provides the first inclusive insight into the differences in genomic characteristics of central metabolic networks of M. extorquens.