Graphical pan-genome analysis with compressed suffix trees and the Burrows–Wheeler transform

2015 ◽  
Vol 32 (4) ◽  
pp. 497-504 ◽  
Author(s):  
Uwe Baier ◽  
Timo Beller ◽  
Enno Ohlebusch
Keyword(s):  
Genome Analysis ◽  
Suffix Trees ◽  
Pan Genome ◽  
Burrows Wheeler Transform

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 Mycobacterial Pan-Genome Analysis Suggests Important Role of Plasmids in the Radiation of Type VII Secretion Systems

2016 ◽  
Vol 8 (2) ◽  
pp. 387-402 ◽  
Author(s):  
Emilie Dumas ◽  
Eva Christina Boritsch ◽  
Mathias Vandenbogaert ◽  
Ricardo C. Rodríguez de la Vega ◽  
Jean-Michel Thiberge ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Secretion Systems ◽  
Pan Genome ◽  
Type Vii Secretion

scholarly journals Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria

GigaScience ◽  
2018 ◽  
Vol 7 (4) ◽  
Author(s):  
Harry A Thorpe ◽  
Sion C Bayliss ◽  
Samuel K Sheppard ◽  
Edward J Feil
Keyword(s):  
Genome Analysis ◽  
Large Scale ◽  
Analysis Tool ◽  
Pan Genome ◽  
Intergenic Regions

scholarly journals Pangloss: A Tool for Pan-Genome Analysis of Microbial Eukaryotes

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 521 ◽  
Author(s):  
McCarthy ◽  
Fitzpatrick
Keyword(s):  
Genome Analysis ◽  
Oleaginous Yeast ◽  
Gene Prediction ◽  
Respiratory Pathogen ◽  
Computational Pipeline ◽  
Pan Genome ◽  
Genome Data ◽  
Microbial Eukaryotes ◽  
Functional Characterisation ◽  
Yeast Yarrowia Lipolytica

Although the pan-genome concept originated in prokaryote genomics, an increasing number of eukaryote species pan-genomes have also been analysed. However, there is a relative lack of software intended for eukaryote pan-genome analysis compared to that available for prokaryotes. In a previous study, we analysed the pan-genomes of four model fungi with a computational pipeline that constructed pan-genomes using the synteny-dependent Pan-genome Ortholog Clustering Tool (PanOCT) approach. Here, we present a modified and improved version of that pipeline which we have called Pangloss. Pangloss can perform gene prediction for a set of genomes from a given species that the user provides, constructs and optionally refines a species pan-genome from that set using PanOCT, and can perform various functional characterisation and visualisation analyses of species pan-genome data. To demonstrate Pangloss’s capabilities, we constructed and analysed a species pan-genome for the oleaginous yeast Yarrowia lipolytica and also reconstructed a previously-published species pan-genome for the opportunistic respiratory pathogen Aspergillus fumigatus. Pangloss is implemented in Python, Perl and R and is freely available under an open source GPLv3 licence via GitHub.

Current status of pan-genome analysis for pathogenic bacteria

2020 ◽  
Vol 63 ◽  
pp. 54-62 ◽  
Author(s):  
Yeji Kim ◽  
Changdai Gu ◽  
Hyun Uk Kim ◽  
Sang Yup Lee
Keyword(s):  
Genome Analysis ◽  
Pathogenic Bacteria ◽  
Current Status ◽  
Pan Genome

Pan‐genome analysis of Exiguobacterium reveals species delineation and genomic similarity with Exiguobacterium profundum  PHM 11

2020 ◽  
Vol 12 (6) ◽  
pp. 639-650
Author(s):  
Alok Kumar Srivastava ◽  
Ruchi Srivastava ◽  
Anjney Sharma ◽  
Akhilendra Pratap Bharati ◽  
Praveen Kumar Tiwari ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Species Delineation ◽  
Pan Genome ◽  
Exiguobacterium Profundum ◽  
Genomic Similarity

Pan-genome analysis of Paenibacillus polymyxa strains reveals the mechanism of plant growth promotion and biocontrol

2020 ◽  
Vol 113 (11) ◽  
pp. 1539-1558
Author(s):  
Liangliang Zhou ◽  
Ting Zhang ◽  
Shan Tang ◽  
Xueqin Fu ◽  
Shuijing Yu
Keyword(s):  
Plant Growth ◽  
Plant Growth Promotion ◽  
Genome Analysis ◽  
Growth Promotion ◽  
Paenibacillus Polymyxa ◽  
Pan Genome

scholarly journals A Novel Approach to Helicobacter pylori Pan-Genome Analysis for Identification of Genomic Islands

PLoS ONE ◽  
2016 ◽  
Vol 11 (8) ◽  
pp. e0159419 ◽  
Author(s):  
Ikuo Uchiyama ◽  
Jacob Albritton ◽  
Masaki Fukuyo ◽  
Kenji K. Kojima ◽  
Koji Yahara ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Genome Analysis ◽  
Genomic Islands ◽  
Pan Genome ◽  
Novel Approach
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