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pangenome

Table of Contents


featuring

https://twitter.com/pangenomepapers

definition

https://en.wikipedia.org/wiki/Pan-genome

https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/pan-genome

http://www.metagenomics.wiki/pdf/definition/pangenome Pangenome - Metagenomics Pangenome tools


updates

2019

https://www.frontiersin.org/articles/10.3389/fmicb.2019.00834/full Frontiers | Large-Scale Genomics Reveals the Genetic Characteristics of Seven Species and Importance of Phylogenetic Distance for Estimating Pan-Genome Size | Microbiology , clustering was conducted with UCLUST

https://www.biostars.org/p/360432/ Is it possible to carry-out pan-genome analysis of interspecies bacterial genome? You could take a look at any of: Roary, OrthoMCL, PanOCT, PanSeq, LS-BSR, FindMyFriends, PopPunk, MicroPan and PGAP.

https://bioinformatics.stackexchange.com/questions/2067/what-tools-can-i-use-for-a-bacterial-core-pan-genome-pipeline 1 year, 4 months ago software recommendation - What tools can I use for a bacterial core/pan genome pipeline? - Bioinformatics Stack Exchange

https://bioinformatics.stackovernet.com/ja/q/2455 genome - 細菌コア/パンゲノムのパイプラインにはどのツールを使用でき ...

https://www.ncbi.nlm.nih.gov/pubmed/30714895 Microb Genom. 2019 Feb 4. doi: 10.1099/mgen.0.000243. [Epub ahead of print] Pan-genome analyses of model fungal species. McCarthy CGP1,2, Fitzpatrick DA1,2. , we have investigated the pan-genomes of four model fungal species: Saccharomyces cerevisiae, Candida albicans, Cryptococcus neoformans var. grubii and Aspergillus fumigatus. https://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000243#tab2 Pan-genome analysis of fungal species Analysis of the pan-genomes of the four fungal species in our study was performed using the Perl software PanOCT [ 38 ].

Bacillus cereus and Staphylococcus aureus https://www.microbe.net/2019/01/08/great-paper-on-space-station-microbes-and-how-they-are-not-all-waiting-to-kill-you/ https://www.ncbi.nlm.nih.gov/pubmed/30637341 mSystems. 2019 Jan 8;4(1). pii: e00281-18. doi: 10.1128/mSystems.00281-18. eCollection 2019 Jan-Feb. Pangenomic Approach To Understanding Microbial Adaptations within a Model Built Environment, the International Space Station, Relative to Human Hosts and Soil. Blaustein RA1, McFarland AG1, Ben Maamar S1, Lopez A2, Castro-Wallace S3, Hartmann EM1.

2018

https://www.ncbi.nlm.nih.gov/pubmed/30165579 Bioinformatics. 2018 Aug 25. doi: 10.1093/bioinformatics/bty744. [Epub ahead of print] Large-Scale Comparative Analysis of Microbial Pan-genomes using PanOCT. Inman JM1, Sutton GG1, Beck E1, Brinkac LM1, Clarke TH1, Fouts DE1. J. Craig Venter Institute, Rockville, MD USA.

https://www.ncbi.nlm.nih.gov/pubmed/29942087 Sci Rep. 2018 Jun 25;8(1):9670. doi: 10.1038/s41598-018-27800-8. Pan4Draft: A Computational Tool to Improve the Accuracy of Pan-Genomic Analysis Using Draft Genomes. Veras A1, Araujo F1, Pinheiro K1, Guimarães L1, Azevedo V2, Soares S3, da Costa da Silva A1, Ramos R4.

https://www.ncbi.nlm.nih.gov/pubmed/29635296 Gigascience. 2018 Apr 1;7(4):1-11. doi: 10.1093/gigascience/giy015. Piggy: a rapid, large-scale pan-genome analysis tool for intergenic regions in bacteria. Thorpe HA1, Bayliss SC1, Sheppard SK1, Feil EJ1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5890482/ The large-scale blast score ratio (LS-BSR) introduced a preclustering step that substantially reduced the number of BLAST comparisons, enabling it to be feasibly run on thousands of samples [10]. More recently, the Roary pipeline has rapidly gained popularity for scalable, user-friendly, pan-genome characterization [4].

https://twitter.com/NatureRevMicro/status/969629255352152064 Nature Rev Microbiol on Twitter: "Systematic discovery of antiphage defense systems in the microbial pangenome @SorekLab @sciencemagazine https://t.co/h2NRQymzzT… https://t.co/jA9uWzYMXe" 12:43 PM - 2 Mar 2018

https://www.ncbi.nlm.nih.gov/pubmed/27769991 Brief Bioinform. 2018 Jan 1;19(1):118-135. doi: 10.1093/bib/bbw089. Computational pan-genomics: status, promises and challenges. Computational Pan-Genomics Consortium.

2017

https://twitter.com/NatureMicrobiol/status/940566982742740992 Nature Microbiology on Twitter: "Current issue: #pangenome correspondences: 1. Michiel Vos & @AdamEyreWalker: are #pangenomes adaptive? https://t.co/m71AxCNO78 2. @bjesseshapiro on applying population genetics: https://t.co/Sbvuo86QEQ 3. @jomcinerney @alanmcn1 & @Evol_Molly reply: https://t.co/5q2UQXukrp… https://t.co/gVZeROsJvg" 8:00 AM - 12 Dec 2017

Current issue: #pangenome correspondences:

  1. Michiel Vos & @AdamEyreWalker: are #pangenomes adaptive? http://bit.ly/2nHM5DU

  2. @bjesseshapiro on applying population genetics: http://bit.ly/2nHM82y

  3. @jomcinerney @alanmcn1 & @Evol_Molly reply: http://bit.ly/2nHMaaG

https://www.ncbi.nlm.nih.gov/pubmed/28321969 Environ Microbiol. 2017 Jul;19(7):2588-2603. The pangenome of the genus Clostridium. Udaondo Z1,2, Duque E1,2, Ramos JL1,2.

https://www.ncbi.nlm.nih.gov/pubmed/28350002 Nat Microbiol. 2017 Mar 28;2:17040. doi: 10.1038/nmicrobiol.2017.40. Why prokaryotes have pangenomes. McInerney JO1, McNally A2, O'Connell MJ3.

https://www.ncbi.nlm.nih.gov/pubmed/29183286 BMC Microbiol. 2017 Nov 28;17(1):222. doi: 10.1186/s12866-017-1132-1. First gene-ontology enrichment analysis based on bacterial coregenome variants: insights into adaptations of Salmonella serovars to mammalian- and avian-hosts. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5706153/ a pangenomic approach,

https://twitter.com/jason_sahl/status/924029119871905793 Jason Sahl on Twitter: "Some recent thoughts on LS-BSR/Roary comparisons. Feedback/thoughts welcome: https://t.co/Q9MbJfnmqY" 5:44 PM - 27 Oct 2017

2016

https://www.ncbi.nlm.nih.gov/pubmed/27855160 PLoS Genet. 2016 Nov 17;12(11):e1006401. doi: 10.1371/journal.pgen.1006401. eCollection 2016 Nov. Transcription Factors Encoded on Core and Accessory Chromosomes of Fusarium oxysporum Induce Expression of Effector Genes.

Several DNA binding sites are enriched on accessory chromosomes, and expression of FTF1, its core homolog FTF2 and SGE1 from a constitutive promoter can induce expression of effector genes. The DNA binding sites of only these three transcription factors are enriched among genes up-regulated during infection.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5039349/ Published online 2016 Sep 28. doi: 10.3389/fmicb.2016.01531 Analysis of the Core Genome and Pan-Genome of Autotrophic Acetogenic Bacteria

To decipher the 474 core genes of the 14 acetogenic bacteria, functionally grouped networks of enriched categories were generated for the biological interpretation of core genes using ClueGo version 2.2.4 (Saito et al., 2012), which is a widely used Cytoscape version 3.3.0 (Shannon et al., 2003) plugin.

As a result, 95 GO terms were significantly enriched and categorized into 10 groups according to their kappa scores (Figure ​Figure3A3A).

Based on enrichment p-values, 27 GO terms and 8 KEGG pathways were enriched (Supplementary Table S3) and functionally categorized into 12 groups (Supplementary Figure S2).

June, 2016 https://bivi.co/visualisation/phandango Phandango | Biological Visualisation Community

https://www.slideshare.net/torstenseemann/bioinformatics-tools-for-the-diagnostic-laboratory-tseemann-antimicrobials-2016-melb-au-sat-27-feb-2016 Bioinformatics tools for the diagnostic laboratory - T.Seemann - Antimicrobials 2016 - Melb, AU - sat 27 feb 2016 43. Example pan genome Roary, LS-BSR, OrthoMCL, Degust Rows are genomes, columns are genes.

2015

https://www.ncbi.nlm.nih.gov/pubmed/26032364 J Microbiol Biotechnol. 2015 Oct;25(10):1599-605. doi: 10.4014/jmb.1504.04008. Comparative Genomics Reveals the Core and Accessory Genomes of Streptomyces Species. Kim JN1, Kim Y2, Jeong Y3, Roe JH2, Kim BG1, Cho BK3.

Functional enrichment analysis showed that genes involved in transcription were most abundant in the Streptomyces pan-genome.

https://www.ncbi.nlm.nih.gov/pubmed/27006628 Curr Genomics. 2015 Aug;16(4):245-52. doi: 10.2174/1389202916666150423002311. Inside the Pan-genome - Methods and Software Overview. Guimarães LC1, Florczak-Wyspianska J2, de Jesus LB3, Viana MV3, Silva A2, Ramos RT2, Soares Sde C4, Soares Sde C4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765519/ Table 1 Pan-genome studies. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765519/table/T1/

https://www.ncbi.nlm.nih.gov/pubmed/26442149 New Microbes New Infect. 2015 Jun 26;7:72-85. doi: 10.1016/j.nmni.2015.06.005. eCollection 2015 Sep. The bacterial pangenome as a new tool for analysing pathogenic bacteria. Rouli L1, Merhej V1, Fournier PE1, Raoult D1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4552756/ Table 3 Ratio core/pangenome of several bacterial species according to their life style https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4552756/table/tbl3/

https://www.ncbi.nlm.nih.gov/pubmed/25721608 Genomics Proteomics Bioinformatics. 2015 Feb;13(1):73-6. doi: 10.1016/j.gpb.2015.01.007. Epub 2015 Feb 23. A brief review of software tools for pangenomics. Xiao J1, Zhang Z2, Wu J2, Yu J2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4411478/table/t0005/?report=objectonly Table 1 Software tools for pangenomic studies

https://www.ncbi.nlm.nih.gov/pubmed/25483351 Curr Opin Microbiol. 2015 Feb;23:148-54. doi: 10.1016/j.mib.2014.11.016. Epub 2014 Dec 5. Ten years of pan-genome analyses. Vernikos G1, Medini D2, Riley DR3, Tettelin H4. https://www.sciencedirect.com/science/article/pii/S1369527414001830?via%3Dihub Table 1. Examples of the application of pan-genome approaches at different levels of phylogenetic resolution

Level	Organism	Approacha	# genomes	Core size (# genes)	Year (reference)
中略
Super kingdom	Eubacteria	Gene freq.	573	250	2009 [4••]

https://www.ncbi.nlm.nih.gov/pubmed/19168257 Trends Genet. 2009 Mar;25(3):107-10. doi: 10.1016/j.tig.2008.12.004. Epub 2009 Jan 23. Estimating the size of the bacterial pan-genome. Lapierre P1, Gogarten JP.

2014

https://www.ncbi.nlm.nih.gov/pubmed/24460813 BMC Genomics. 2014 Jan 24;15:65. doi: 10.1186/1471-2164-15-65. CodaChrome: a tool for the visualization of proteome conservation across all fully sequenced bacterial genomes. Rokicki J, Knox D, Dowell RD1, Copley SD.


organism

archaea

September 6, 2018 https://phys.org/news/2018-09-pan-genome-antarctic-archaea.html Defining a pan-genome for Antarctic archaea

SEPTEMBER 5, 2018 https://jgi.doe.gov/defining-a-pan-genome-for-antarctic-archaea/ Defining a Pan-Genome for Antarctic Archaea - DOE Joint Genome Institute

https://twitter.com/msmjetten/status/884694940055416833 Mike Jetten on Twitter: "#FEMS2017 @eugene_koonin open vs closed #pangenome in #bacteria & #archaea with core, shell, & cloud orfs… " 4:44 AM - 11 Jul 2017

https://www.ncbi.nlm.nih.gov/pubmed/23241446 Biol Direct. 2012 Dec 14;7:46. doi: 10.1186/1745-6150-7-46. Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer. Wolf YI1, Makarova KS, Yutin N, Koonin EV. The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether) into 10,335 arCOGs. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3534625/ Indeed, analysis of the commonality distribution [37,38] for the new arCOG collection gives estimates for the size of the “core” (highly conserved) and the “shell” (moderately conserved) components of the archaeal pangenome that are almost unchanged since 2007 (current estimates of ~220 and ~2,200 vs. ~230 and ~2,200, respectively, for the 2007 arCOG set).

https://www.ncbi.nlm.nih.gov/pubmed/27864514 Proc Natl Acad Sci U S A. 2016 Dec 6;113(49):E7937-E7946. Epub 2016 Nov 18. Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers. Kerou M1, Offre P1, Valledor L1, Abby SS1, Melcher M1, Nagler M1, Weckwerth W2, Schleper C3.

https://twitter.com/bioinfobact/status/440791373537898496 bioinfoproka on Twitter: "Ribosomal proteins : rigorous minimal & universal Core Genome #procaryotes #phylogeny http://t.co/TmgIxGmVoc #archaea http://t.co/LItv4B3pLG" 5:10 AM - 4 Mar 2014

Rhodococcus equi

https://www.ncbi.nlm.nih.gov/pubmed/27638249 Genome Biol Evol. 2016 Oct 23;8(10):3140-3148. Pangenome and Phylogenomic Analysis of the Pathogenic Actinobacterium Rhodococcus equi. Anastasi E1, MacArthur I1, Scortti M1,2, Alvarez S1, Giguère S3, Vázquez-Boland JA4,2,5. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5174736/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5174736/figure/evw222-F2/?report=objectonly

Pseudomonas aeruginosa

https://www.ncbi.nlm.nih.gov/pubmed/25961859 PLoS One. 2015 May 11;10(5):e0126468. doi: 10.1371/journal.pone.0126468. eCollection 2015. What It Takes to Be a Pseudomonas aeruginosa? The Core Genome of the Opportunistic Pathogen Updated. Valot B1, Guyeux C2, Rolland JY3, Mazouzi K4, Bertrand X5, Hocquet D5.

https://www.ncbi.nlm.nih.gov/pubmed/25168460 BMC Genomics. 2014 Aug 29;15:737. doi: 10.1186/1471-2164-15-737. Characterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt. Ozer EA1, Allen JP, Hauser AR.


japanese

http://kazumaxneo.hatenablog.com/archive/category/pan-genome pan-genome カテゴリーの記事一覧 - macでインフォマティクス

http://kazumaxneo.hatenablog.com/entry/2019/02/08/073000 オルソログデータベース OrthoDB - macでインフォマティクス OrthoDB v10は、1271の真核生物、5609のバクテリア、404のアーキア、および6488のウイルスをカバーしている(2018年9月現在)。

http://kazumaxneo.hatenablog.com/entry/2018/09/09/131729 Pan-genome解析をwebで実行できる PanWeb - macでインフォマティクス

http://kazumaxneo.hatenablog.com/entry/2017/12/09/014407 バクテリアのPan genome解析ツール FRIPAN - macでインフォマティクス

http://kazumaxneo.hatenablog.com/entry/2018/09/08/194159 パンゲノム解析ツール PGAP - macでインフォマティクス

http://omics-club.blogspot.jp/2014/07/20140707.html Omics Club(オミックス・クラブ): Quasispeciesとは Quasispeciesの拡張概念:Core GenomeとPan Genome

http://gene-nex.com/service/pan-genome.html パンゲノム - 対象研究分野 - Gene Nex — 次世代シーケンス受託解析サービス「ジーンネックス」


tools

https://omictools.com/pangenomics-category Pan-genome analysis bioinformatics tools - omicX

https://www.researchgate.net/post/Favorite_tools_for_pan-genomic_analysis_of_bacterial_genomes


PGAP

https://www.ncbi.nlm.nih.gov/pubmed/30186253 Front Microbiol. 2018 Aug 21;9:1910. doi: 10.3389/fmicb.2018.01910. eCollection 2018. PGAweb: A Web Server for Bacterial Pan-Genome Analysis. Chen X1, Zhang Y2,3,4, Zhang Z2,3, Zhao Y5, Sun C6, Yang M7, Wang J2,3,4, Liu Q1,8, Zhang B1,8, Chen M2,3, Yu J3,4, Wu J3, Jin Z1,8, Xiao J2,3,4.

19 January 2018 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4326-x Pan-genome tool PGAP-X is a cross-platform software to analyze and visualize genome structure dynamics and and gene content [54].

https://pgapx.zhaopage.com/ PGAP-X: Extension on pan-genome analysis pipeline

https://www.ncbi.nlm.nih.gov/pubmed/29363431 BMC Genomics. 2018 Jan 19;19(Suppl 1):36. doi: 10.1186/s12864-017-4337-7. PGAP-X: extension on pan-genome analysis pipeline. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5780747/

As a web server, panX provides an interactive interface to visualize various data, including pan-genome statistical charts, gene cluster table, alignment, comparative phylogenies, metadata table [28]. However, it does not provide information about genome structure, gene distribution on the genome, and genetic variation.

https://www.ncbi.nlm.nih.gov/pubmed/22130594 https://www.ncbi.nlm.nih.gov/pubmed/22130594 Bioinformatics. 2012 Feb 1;28(3):416-8. doi: 10.1093/bioinformatics/btr655. Epub 2011 Nov 29. PGAP: pan-genomes analysis pipeline. Zhao Y1, Wu J, Yang J, Sun S, Xiao J, Yu J.


panX

http://pangenome.de

https://www.ncbi.nlm.nih.gov/pubmed/29077859 Nucleic Acids Res. 2018 Jan 9;46(1):e5. doi: 10.1093/nar/gkx977. panX: pan-genome analysis and exploration. Ding W1, Baumdicker F2, Neher RA1,3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5758898/ Tree building and ancestral reconstruction PanX extracts all variable positions from the nucleotide alignments of all single copy core genes (those gene clusters in which all strains are represented exactly once) to construct a core-genome SNP matrix.

https://www.biorxiv.org/content/early/2018/08/12/286187 Real-time analysis and visualization of pathogen sequence data | bioRxiv Here, we review recent developments in real-time analysis of pathogen sequence data with a particular focus on visualization and integration of sequence and phenotypic data.

https://www.ncbi.nlm.nih.gov/pubmed/29204317 PeerJ. 2017 Nov 30;5:e3948. doi: 10.7717/peerj.3948. eCollection 2017. BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters. Cheng G1,2, Lu Q3, Ma L4, Zhang G4, Xu L5, Zhou Z1. https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/29204317/ The analytical workflow consisted of three toolkits: Prokka v1.11 (Seemann, 2014), panX (Ding, Baumdicker & Neher, 2017), and antiSMASH3.0 (Weber et al., 2015), for prokaryotic genome annotation, pan-genome analysis and visualization, and analysis of biosynthetic gene clusters, respectively.


BPGA

Bacterial Pan Genome Analysis Pipeline http://www.iicb.res.in/bpga/index.html

http://www.ncbi.nlm.nih.gov/pubmed/27071527 Sci Rep. 2016 Apr 13;6:24373. doi: 10.1038/srep24373. BPGA- an ultra-fast pan-genome analysis pipeline. Chaudhari NM1, Gupta VK1, Dutta C1.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4829868/table/t2/ Table 2. Comparison of 7 pan-genome analysis tools (BPGA, Roary, PanGP, PGAP, PGAT, Panseq, ITEP)


2015

Roary

https://sanger-pathogens.github.io/Roary/ Roary: the pan genome pipeline

https://www.ncbi.nlm.nih.gov/pubmed/26198102 Bioinformatics. 2015 Nov 15;31(22):3691-3. doi: 10.1093/bioinformatics/btv421. Epub 2015 Jul 20. Roary: rapid large-scale prokaryote pan genome analysis. Page AJ1, Cummins CA1, Hunt M1, Wong VK2, Reuter S3, Holden MT4, Fookes M1, Falush D5, Keane JA1, Parkhill J1.


2014

ITEP

https://hood-price.systemsbiology.org/research/itep/ ITEP: Integrated Toolkit for Exploration of Pan-genomes | The Hood-Price Lab for Systems Biomedicine

https://www.ncbi.nlm.nih.gov/pubmed/24387194 BMC Genomics. 2014 Jan 3;15:8. doi: 10.1186/1471-2164-15-8. ITEP: an integrated toolkit for exploration of microbial pan-genomes. Benedict MN, Henriksen JR, Metcalf WW, Whitaker RJ, Price ND1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890548/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890548/figure/F1/


Panseq

https://www.ncbi.nlm.nih.gov/pubmed/20843356 BMC Bioinformatics. 2010 Sep 15;11:461. doi: 10.1186/1471-2105-11-461. Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions. Laing C1, Buchanan C, Taboada EN, Zhang Y, Kropinski A, Villegas A, Thomas JE, Gannon VP.


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