scholarly journals A pan-genome method to determine core regions of the Bacillus subtilis and Escherichia coli genomes

2020 ◽  
Author(s):  
Granger Sutton ◽  
Gary B. Fogel ◽  
Bradley Abramson ◽  
Lauren Brinkac ◽  
Todd Michael ◽  
...  
Keyword(s):  
Essential Genes ◽  
Considerable Time ◽  
Laboratory Methods ◽  
Pan Genome ◽  
Gene Acquisition ◽  
A Genome ◽  
Low Penetrance Genes ◽  
Almost All ◽  
Conserved Core ◽  
Core Genes

AbstractSynthetic engineering of bacteria to produce industrial products is a burgeoning field of research and application. In order to optimize genome design, designers need to understand which genes are essential, which are optimal for growth, and locations in the genome that will be tolerated by the organism when inserting engineered cassettes. We present a pan-genome based method for the identification of core regions in a genome that are strongly conserved at the species level. We show that these core regions are very likely to contain all or almost all essential genes. We assert that synthetic engineers should avoid deleting or inserting into these core regions unless they understand and are manipulating the function of the genes in that region. Similarly, if the designer wishes to streamline the genome, non-core regions and in particular low penetrance genes would be good targets for deletion. Care should be taken to remove entire cassettes with similar penetrance of the genes within cassettes as they may harbor toxin/antitoxin genes which need to be removed in tandem. The bioinformatic approach introduced here saves considerable time and effort relative to knockout studies on single isolates of a given species and captures a broad understanding of the conservation of genes that are core to a species.ImportanceThe pan-genome approach presented in this paper can be used to determine core regions of a genome and has many possible applications. Synthetic engineering design can be informed by which genes/regions are more conserved (core) versus less conserved. The level of conservation of adjacent non-core genes tends to define cassettes of genes which may be part of a pathway or system that can inform researchers about possible functional significance. The pattern of gene presence across the different genomes of a species can inform the understanding of evolution and horizontal gene acquisition. The approach saves considerable time and effort relative to laboratory methods used to identify essential genes in species.

scholarly journals A pan-genome method to determine core regions of the Bacillus subtilis and Escherichia coli genomes

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 286
Author(s):  
Granger Sutton ◽  
Gary B. Fogel ◽  
Bradley Abramson ◽  
Lauren Brinkac ◽  
Todd Michael ◽  
...  
Keyword(s):  
Essential Genes ◽  
Considerable Time ◽  
The Core ◽  
Pan Genome ◽  
A Genome ◽  
Low Penetrance Genes ◽  
Almost All ◽  
Bioinformatic Approach ◽  
Core Genes ◽  
Broad Understanding

Background: Synthetic engineering of bacteria to produce industrial products is a burgeoning field of research and application. In order to optimize genome design, designers need to understand which genes are essential, which are optimal for growth, and locations in the genome that will be tolerated by the organism when inserting engineered cassettes. Methods: We present a pan-genome based method for the identification of core regions in a genome that are strongly conserved at the species level. Results: We show that the core regions determined by our method contain all or almost all essential genes. This demonstrates the accuracy of our method as essential genes should be core genes. We show that we outperform previous methods by this measure. We also explain why there are exceptions to this rule for our method. Conclusions: We assert that synthetic engineers should avoid deleting or inserting into these core regions unless they understand and are manipulating the function of the genes in that region. Similarly, if the designer wishes to streamline the genome, non-core regions and in particular low penetrance genes would be good targets for deletion. Care should be taken to remove entire cassettes with similar penetrance of the genes within cassettes as they may harbor toxin/antitoxin genes which need to be removed in tandem. The bioinformatic approach introduced here saves considerable time and effort relative to knockout studies on single isolates of a given species and captures a broad understanding of the conservation of genes that are core to a species.

scholarly journals A pan-genome method to determine core regions of the Bacillus subtilis and Escherichia coli genomes

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 286
Author(s):  
Granger Sutton ◽  
Gary B. Fogel ◽  
Bradley Abramson ◽  
Lauren Brinkac ◽  
Todd Michael ◽  
...  
Keyword(s):  
Essential Genes ◽  
Considerable Time ◽  
The Core ◽  
Pan Genome ◽  
A Genome ◽  
Low Penetrance Genes ◽  
Almost All ◽  
Bioinformatic Approach ◽  
Core Genes ◽  
Broad Understanding

Background: Synthetic engineering of bacteria to produce industrial products is a burgeoning field of research and application. In order to optimize genome design, designers need to understand which genes are essential, which are optimal for growth, and locations in the genome that will be tolerated by the organism when inserting engineered cassettes. Methods: We present a pan-genome based method for the identification of core regions in a genome that are strongly conserved at the species level. Results: We show that the core regions determined by our method contain all or almost all essential genes. This demonstrates the accuracy of our method as essential genes should be core genes. We show that we outperform previous methods by this measure. We also explain why there are exceptions to this rule for our method. Conclusions: We assert that synthetic engineers should avoid deleting or inserting into these core regions unless they understand and are manipulating the function of the genes in that region. Similarly, if the designer wishes to streamline the genome, non-core regions and in particular low penetrance genes would be good targets for deletion. Care should be taken to remove entire cassettes with similar penetrance of the genes within cassettes as they may harbor toxin/antitoxin genes which need to be removed in tandem. The bioinformatic approach introduced here saves considerable time and effort relative to knockout studies on single isolates of a given species and captures a broad understanding of the conservation of genes that are core to a species.

Analysis of pan-genome to identify the core genes and essential genes of Brucella spp.

2016 ◽  
Vol 291 (2) ◽  
pp. 905-912 ◽  
Author(s):  
Xiaowen Yang ◽  
Yajie Li ◽  
Juan Zang ◽  
Yexia Li ◽  
Pengfei Bie ◽  
...  
Keyword(s):  
Essential Genes ◽  
The Core ◽  
Pan Genome ◽  
Core Genes

scholarly journals Genome-wide mapping of unexplored essential regions in the Saccharomyces cerevisiae genome: evidence for hidden synthetic lethal combinations in a genetic interaction network

2014 ◽  
Vol 42 (15) ◽  
pp. 9838-9853 ◽  
Author(s):  
Saeed Kaboli ◽  
Takuya Yamakawa ◽  
Keisuke Sunada ◽  
Tao Takagaki ◽  
Yu Sasano ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genetic Interaction ◽  
Interaction Network ◽  
Essential Genes ◽  
Genetic Interactions ◽  
Lethal Gene ◽  
Synthetic Lethal ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale

Abstract Despite systematic approaches to mapping networks of genetic interactions in Saccharomyces cerevisiae, exploration of genetic interactions on a genome-wide scale has been limited. The S. cerevisiae haploid genome has 110 regions that are longer than 10 kb but harbor only non-essential genes. Here, we attempted to delete these regions by PCR-mediated chromosomal deletion technology (PCD), which enables chromosomal segments to be deleted by a one-step transformation. Thirty-three of the 110 regions could be deleted, but the remaining 77 regions could not. To determine whether the 77 undeletable regions are essential, we successfully converted 67 of them to mini-chromosomes marked with URA3 using PCR-mediated chromosome splitting technology and conducted a mitotic loss assay of the mini-chromosomes. Fifty-six of the 67 regions were found to be essential for cell growth, and 49 of these carried co-lethal gene pair(s) that were not previously been detected by synthetic genetic array analysis. This result implies that regions harboring only non-essential genes contain unidentified synthetic lethal combinations at an unexpectedly high frequency, revealing a novel landscape of genetic interactions in the S. cerevisiae genome. Furthermore, this study indicates that segmental deletion might be exploited for not only revealing genome function but also breeding stress-tolerant strains.

scholarly journals Pan-Genome Analysis of Mycobacterium Africanum: Insights to Dynamics and Evolution.

2020 ◽  
Author(s):  
Idowu Olawoye ◽  
Simon D.W. Frost ◽  
Christian T. Happi
Keyword(s):  
West Africa ◽  
Genome Analysis ◽  
West African ◽  
Multiple Copy ◽  
Genome Sequences ◽  
Animal Reservoir ◽  
Pan Genome ◽  
Lineage Specificity ◽  
Mycobacterium Africanum ◽  
Core Genes

Abstract Background: Mycobacterium tuberculosis complex (MTBC) consists of seven major lineages with three of them reported to circulate within West Africa: lineage 5 (West African 1) and lineage 6 (West African 2) which are geographically restricted to West Africa and lineage 4 (Euro-American lineage) which is found globally. It is unclear why the West African lineages are not found elsewhere; some hypotheses suggest that it could either be harboured by an animal reservoir which is restricted to West Africa, or strain preference for hosts of West African ethnicity, or inability to compete with other lineages in other locations.We tested the hypothesis that M. africanum West African 2 (lineage 6) might have emigrated out of West Africa but was outcompeted by more virulent modern strains of M. tuberculosis (MTB).Whole genome sequences of M. tuberculosis from Nigeria (n=21), South Africa (n=24) and M. africanum West African 2 from Mali (n=22) were retrieved, and a pan-genome analysis was performed after fully annotating these genomes. Results: The outcome of this analysis shows that Lineages 2, 4 and 6 all have a close pan-genome. We also see a correlation in numbers of some multiple copy core genes and amino acid substitution with lineage specificity that may have contributed to geographical distribution of these lineages.Conclusions: The findings in this study provides a perspective to one of the hypotheses that M. africanum West African 2 might find it difficult to compete against the more modern lineages outside West Africa hence its localization to the geographical region.

scholarly journals Pan-Genome of Novel Pantoea stewartii subsp. indologenes Reveals Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer

2021 ◽  
Vol 9 (8) ◽  
pp. 1761
Author(s):  
Gaurav Agarwal ◽  
Ronald D. Gitaitis ◽  
Bhabesh Dutta
Keyword(s):  
Gene Transfer ◽  
Core Genome ◽  
Foxtail Millet ◽  
Gene Clusters ◽  
Evaluation Study ◽  
Full Spectrum ◽  
Pan Genome ◽  
Pantoea Stewartii ◽  
Comparative Phylogenetic Analysis ◽  
Core Genes

Pantoea stewartii subsp. indologenes (Psi) is a causative agent of leafspot on foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onions. Our recent host range evaluation study identified two pathovars; P. stewartii subsp. indologenes pv. cepacicola pv. nov. and P. stewartii subsp. indologenes pv. setariae pv. nov. that are pathogenic on onions and millets or on millets only, respectively. In the current study, we developed a pan-genome using the whole genome sequencing of newly identified/classified Psi strains from both pathovars [pv. cepacicola (n = 4) and pv. setariae (n = 13)]. The full spectrum of the pan-genome contained 7030 genes. Among these, 3546 (present in genomes of all 17 strains) were the core genes that were a subset of 3682 soft-core genes (present in ≥16 strains). The accessory genome included 1308 shell genes and 2040 cloud genes (present in ≤2 strains). The pan-genome showed a clear linear progression with >6000 genes, suggesting that the pan-genome of Psi is open. Comparative phylogenetic analysis showed differences in phylogenetic clustering of Pantoea spp. using PAVs/wgMLST approach in comparison with core genome SNPs-based phylogeny. Further, we conducted a horizontal gene transfer (HGT) study using Psi strains from both pathovars along with strains from other Pantoea species, namely, P. stewartii subsp. stewartii LMG 2715T, P. ananatis LMG 2665T, P. agglomerans LMG L15, and P. allii LMG 24248T. A total of 317 HGT events among four Pantoea species were identified with most gene transfer events occurring between Psi pv. cepacicola and Psi pv. setariae. Pan-GWAS analysis predicted a total of 154 genes, including seven gene-clusters, which were associated with the pathogenicity phenotype (necrosis on seedling) on onions. One of the gene-clusters contained 11 genes with known functions and was found to be chromosomally located.

scholarly journals A genome-wide strategy for the identification of essential genes in Staphylococcus aureus

2002 ◽  
Vol 43 (6) ◽  
pp. 1387-1400 ◽  
Author(s):  
R. Allyn Forsyth ◽  
Robert J. Haselbeck ◽  
Kari L. Ohlsen ◽  
Robert T. Yamamoto ◽  
Howard Xu ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Essential Genes ◽  
Genome Wide ◽  
A Genome

The Early Life and Pilgrimage of Al-Ḥājj Muḥammad Al-Amīn the Soninke (d. 1887)

1970 ◽  
Vol 11 (1) ◽  
pp. 51-69 ◽  
Author(s):  
Humphrey Fisher
Keyword(s):  
Middle East ◽  
West Africa ◽  
Early Life ◽  
Oral Tradition ◽  
African Politics ◽  
Considerable Time ◽  
Careful Handling ◽  
Internal Affairs ◽  
Almost All ◽  
Military Activity

Al-Ḥājj Muḥammad al-Amīn, often known as Momodu Lamine, was a Soninke leader, engaged in political and military activity on the upper Senegal and Gambia rivers in 1885–1887. This activity, culminating in clashes with the French, has sometimes encouraged an interpretation of his career in anti-European-colonialist terms. In fact, religion and local African politics may have been more important. This study examines his life before 1885, particularly his pilgrimage. Almost all the material comes from oral tradition, both that preserved in early French publications and that collected recently in West Africa.Muḥammad al-Amīn was born about 1830 or 1840. He studied in various places in the Senegal region. Later he may have served with al-Ḥājj 'Umar. On his pilgrimage he travelled through Wadai; the report that he became a Sanūsī seems doubtful. He spent some time in the Middle East and renewed there his Tijānīya allegiance. He also apparently prepared for jihād. He may, though this is less clear, have shared in the apocalyptic expectancy of the time, centred on hopes of a Mahdi.On his way home he passed through Timbuktu and Masina and came to Segu, capital of the Tokolor empire, then under Sultan Aḥmadu the son of al-Ḥājj 'Umar. Here Muḥammad al-Amīn stopped for several years, more or less under duress, and escaped several attempts on his life. These attempts are described in miraculous terms, and sometimes parallel other episodes in the legends of Muslim West Africa.This clash between the returning pilgrim and the head of the Segu theocracy, both men devout Muslims, is curious. It resembles al-Ḥājj 'Umar's reception in Bornu on his way back from pilgrimage. The reasons for it, at least at present, can only be surmised. Muḥammad al-Amīn may have been suspected of meddling in the internal affairs of the Segu empire, for he had stopped for a considerable time in Masina, a dependency, before coming to Segu the capital. His activity in spreading the Tijānīya order, or his version of it, was resented. He may have claimed to be the spiritual heir to al-Ḥājj 'Umar; and/or he may have somehow slighted the memory of al-Ḥāajj 'Umar. He may have appeared as a Soninke patriot, championing his people against Tokolor overlordship; but the theme of tribal loyalties, though indubitably important, needs careful handling. About 1885, he returned to Goundiourou, his birthplace, near Kayes.

scholarly journals Comprehensive Analysis Reveals the Evolution and Pathogenicity of Aeromonas, Viewed from Both Single Isolated Species and Microbial Communities

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Chaofang Zhong ◽  
Maozhen Han ◽  
Pengshuo Yang ◽  
Chaoyun Chen ◽  
Hui Yu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microbial Communities ◽  
Virulence Factors ◽  
Evolutionary Dynamics ◽  
Content Type ◽  
Pan Genome ◽  
Gastrointestinal Pathogen ◽  
High Level ◽  
Core Genes ◽  
Isolated Species

ABSTRACT The genus Aeromonas is a common gastrointestinal pathogen associated with human and animal infections. Due to the high level of cross-species similarity, their evolutionary dynamics and genetic diversity are still fragmented. Hereby, we investigated the pan-genomes of 29 Aeromonas species, as well as Aeromonas species in microbial communities, to clarify their evolutionary dynamics and genetic diversity, with special focus on virulence factors and horizontal gene transfer events. Our study revealed an open pan-genome of Aeromonas containing 10,144 gene families. These Aeromonas species exhibited different functional constraints, with the single-copy core genes and most accessory genes experiencing purifying selection. The significant congruence between core genome and pan-genome trees revealed that core genes mainly affected evolutionary divergences of Aeromonas species. Gene gains and losses revealed a high level of genome plasticity, exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. The selective constraints shaped virulence gene pools of these Aeromonas strains, where genes encoding hemolysin were ubiquitous. Of these strains, Aeromonas aquatica MX16A seemed to be more resistant, as it harbored most resistance genes. Finally, the virulence factors of Aeromonas in microbial communities were quite dynamic in response to environment changes. For example, the virulence diversity of Aeromonas in microbial communities could reach levels that match some of the most virulent Aeromonas species (such as A. hydrophila) in penetrated-air and modified-air packaging. Our work shed some light onto genetic diversity, evolutionary history, and functional features of Aeromonas, which could facilitate the detection and prevention of infections. IMPORTANCE Aeromonas has long been known as a gastrointestinal pathogen, yet it has many species whose evolutionary dynamics and genetic diversity had been unclear until now. We have conducted pan-genome analysis for 29 Aeromonas species and revealed a high level of genome plasticity exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. These species also contained many virulence factors both identified from single isolated species and microbial community. This pan-genome study could elevate the level for detection and prevention of Aeromonas infections.

Sign in / Sign up

Export Citation Format

Share Document