The pan-genome of Mycobacterium avium subsp. paratuberculosis (Map) confirms ancestral lineage and reveals gene rearrangements within Map Type S.
CAZymes
IS elements
Mycobacterium avium subsp. paratuberculosis
Pan-genome
PpanGGolin
Prophages
Secondary metabolites
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
31 Oct 2023
31 Oct 2023
Historique:
received:
04
07
2023
accepted:
18
10
2023
medline:
2
11
2023
pubmed:
1
11
2023
entrez:
1
11
2023
Statut:
epublish
Résumé
To date genomic studies on Map have concentrated on Type C strains with only a few Type S strains included for comparison. In this study the entire pan-genome of 261 Map genomes (205 Type C, 52 Type S and 4 Type B) and 7 Mycobacterium avium complex (Mac) genomes were analysed to identify genomic similarities and differences between the strains and provide more insight into the evolutionary relationship within this Mycobacterial species. Our analysis of the core genome of all the Map isolates identified two distinct lineages, Type S and Type C Map that is consistent with previous phylogenetic studies of Map. Pan-genome analysis revealed that Map has a larger accessory genome than Mycobacterium avium subsp. avium (Maa) and Type C Map has a larger accessory genome than Type S Map. In addition, we found large rearrangements within Type S strains of Map and little to none in Type C and Type B strains. There were 50 core genes identified that were unique to Type S Map and there were no unique core genes identified between Type B and Type C Map strains. In Type C Map we identified an additional CE10 CAZyme class which was identified as an alpha/beta hydrolase and an additional polyketide and non-ribosomal peptide synthetase cluster. Consistent with previous analysis no plasmids and only incomplete prophages were identified in the genomes of Map. There were 45 hypothetical CRISPR elements identified with no associated cas genes. This is the most comprehensive comparison of the genomic content of Map isolates to date and included the closing of eight Map genomes. The analysis revealed that there is greater variation in gene synteny within Type S strains when compared to Type C indicating that the Type C Map strain emerged after Type S. Further analysis of Type C and Type B genomes revealed that they are structurally similar with little to no genetic variation and that Type B Map may be a distinct clade within Type C Map and not a different strain type of Map. The evolutionary lineage of Maa and Map was confirmed as emerging after M. hominissuis.
Sections du résumé
BACKGROUND
BACKGROUND
To date genomic studies on Map have concentrated on Type C strains with only a few Type S strains included for comparison. In this study the entire pan-genome of 261 Map genomes (205 Type C, 52 Type S and 4 Type B) and 7 Mycobacterium avium complex (Mac) genomes were analysed to identify genomic similarities and differences between the strains and provide more insight into the evolutionary relationship within this Mycobacterial species.
RESULTS
RESULTS
Our analysis of the core genome of all the Map isolates identified two distinct lineages, Type S and Type C Map that is consistent with previous phylogenetic studies of Map. Pan-genome analysis revealed that Map has a larger accessory genome than Mycobacterium avium subsp. avium (Maa) and Type C Map has a larger accessory genome than Type S Map. In addition, we found large rearrangements within Type S strains of Map and little to none in Type C and Type B strains. There were 50 core genes identified that were unique to Type S Map and there were no unique core genes identified between Type B and Type C Map strains. In Type C Map we identified an additional CE10 CAZyme class which was identified as an alpha/beta hydrolase and an additional polyketide and non-ribosomal peptide synthetase cluster. Consistent with previous analysis no plasmids and only incomplete prophages were identified in the genomes of Map. There were 45 hypothetical CRISPR elements identified with no associated cas genes.
CONCLUSION
CONCLUSIONS
This is the most comprehensive comparison of the genomic content of Map isolates to date and included the closing of eight Map genomes. The analysis revealed that there is greater variation in gene synteny within Type S strains when compared to Type C indicating that the Type C Map strain emerged after Type S. Further analysis of Type C and Type B genomes revealed that they are structurally similar with little to no genetic variation and that Type B Map may be a distinct clade within Type C Map and not a different strain type of Map. The evolutionary lineage of Maa and Map was confirmed as emerging after M. hominissuis.
Identifiants
pubmed: 37907856
doi: 10.1186/s12864-023-09752-0
pii: 10.1186/s12864-023-09752-0
pmc: PMC10619280
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
656Informations de copyright
© 2023. The Author(s).
Références
Adv Biochem Eng Biotechnol. 2000;69:1-39
pubmed: 11036689
J Clin Microbiol. 1990 Jul;28(7):1591-6
pubmed: 2166089
Vet Immunol Immunopathol. 2010 Jun 15;135(3-4):218-25
pubmed: 20053460
Nat Rev Microbiol. 2020 Feb;18(2):67-83
pubmed: 31857715
Genome Biol. 2019 Jun 24;20(1):129
pubmed: 31234903
Bioinformatics. 2018 Jul 1;34(13):i142-i150
pubmed: 29949969
Bioinformatics. 2015 Oct 15;31(20):3350-2
pubmed: 26099265
BMC Genomics. 2016 Jan 26;17:79
pubmed: 26813574
Bioinformatics. 2016 Nov 15;32(22):3380-3387
pubmed: 27466620
Nat Rev Microbiol. 2007 Nov;5(11):883-91
pubmed: 17922044
J Clin Microbiol. 2003 Nov;41(11):5215-23
pubmed: 14605167
Front Bioeng Biotechnol. 2020 Jul 31;8:871
pubmed: 32850729
Sci Rep. 2018 Apr 25;8(1):6529
pubmed: 29695799
J Clin Microbiol. 2002 Apr;40(4):1303-10
pubmed: 11923349
BMC Microbiol. 2021 Apr 1;21(1):101
pubmed: 33789575
Front Microbiol. 2022 Oct 20;13:994421
pubmed: 36338087
BMC Genomics. 2012 Mar 12;13:89
pubmed: 22409516
J Bacteriol. 2000 Aug;182(15):4348-51
pubmed: 10894747
Mol Cell. 2020 May 21;78(4):683-699.e11
pubmed: 32386575
Nature. 1999 Nov 4;402(6757):79-83
pubmed: 10573420
Genome Biol. 2001;2(10):RESEARCH0044
pubmed: 11597336
PLoS One. 2023 Jan 26;18(1):e0279556
pubmed: 36701403
J Clin Microbiol. 2004 Apr;42(4):1703-12
pubmed: 15071028
Proc Natl Acad Sci U S A. 2005 Aug 30;102(35):12344-9
pubmed: 16116077
PLoS One. 2007 Nov 21;2(11):e1193
pubmed: 18030328
PLoS Comput Biol. 2020 Mar 19;16(3):e1007732
pubmed: 32191703
Bioinformatics. 2015 Nov 15;31(22):3691-3
pubmed: 26198102
Nucleic Acids Res. 2015 Jan;43(Database issue):D222-6
pubmed: 25414356
Front Vet Sci. 2017 Nov 06;4:187
pubmed: 29164142
Mol Biol Evol. 2007 May;24(5):1130-9
pubmed: 17322554
Bioinformatics. 2014 May 1;30(9):1312-3
pubmed: 24451623
J Bacteriol. 2008 Apr;190(7):2479-87
pubmed: 18245284
PLoS One. 2016 Feb 12;11(2):e0149017
pubmed: 26871723
BMC Microbiol. 2012 Nov 19;12:264
pubmed: 23164429
Vet Res. 2015 Jun 19;46:64
pubmed: 26092160
BMC Vet Res. 2012 Jan 27;8:11
pubmed: 22284630
BMC Genomics. 2008 Mar 20;9:135
pubmed: 18366709
Mol Cell Probes. 1999 Apr;13(2):115-26
pubmed: 10208802
Infect Genet Evol. 2014 Jan;21:375-83
pubmed: 24345519
Nucleic Acids Res. 2018 Jul 2;46(W1):W246-W251
pubmed: 29790974
PLoS Comput Biol. 2017 Jun 8;13(6):e1005595
pubmed: 28594827
Science. 2007 Mar 23;315(5819):1709-12
pubmed: 17379808
Nucleic Acids Res. 2016 Jul 8;44(W1):W16-21
pubmed: 27141966
BMC Genomics. 2011 Aug 08;12:402
pubmed: 21824423
Science. 2002 Jun 28;296(5577):2376-9
pubmed: 12089438
Can J Microbiol. 2006 Jun;52(6):560-9
pubmed: 16788724
Front Vet Sci. 2021 Feb 15;8:637637
pubmed: 33659287
Bioinformatics. 2018 Aug 1;34(15):2666-2669
pubmed: 29547981
Curr Protein Pept Sci. 2017;18(3):190-210
pubmed: 27480283
Mol Microbiol. 2006 Jun;60(5):1152-63
pubmed: 16689792
Bioinformatics. 2005 Aug 15;21(16):3422-3
pubmed: 15976072
BMC Bioinformatics. 2010 Aug 18;11:431
pubmed: 20718988
J Bacteriol. 2009 Feb;191(3):1018-25
pubmed: 19028885
Trends Microbiol. 2002 May;10(5):246-9
pubmed: 11973159
Virulence. 2013 Jul 1;4(5):354-65
pubmed: 23611873
Methods Mol Biol. 2009;551:105-16
pubmed: 19521870
Microorganisms. 2020 Dec 29;9(1):
pubmed: 33383865
Mol Cell Probes. 2001 Jun;15(3):139-45
pubmed: 11352594
Genome Res. 2004 Jul;14(7):1394-403
pubmed: 15231754
Microb Pathog. 2010 Dec;49(6):311-4
pubmed: 20638467
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W445-51
pubmed: 22645317
BMC Microbiol. 2012 May 30;12:87
pubmed: 22646160
BMC Genomics. 2019 Aug 20;20(1):662
pubmed: 31429698
Mol Microbiol. 2003 Jul;49(2):277-300
pubmed: 12886937
mBio. 2018 Feb 13;9(1):
pubmed: 29440578
Crit Rev Microbiol. 2016;42(2):262-75
pubmed: 25163812
Infect Immun. 2006 Jun;74(6):3530-7
pubmed: 16714585
Mol Cell Probes. 2005 Dec;19(6):371-84
pubmed: 16226868
Vet Res. 1997 Sep-Oct;28(5):439-47
pubmed: 9342821
Front Cell Infect Microbiol. 2014 Aug 14;4:110
pubmed: 25177550
Infect Immun. 2013 Jun;81(6):2242-57
pubmed: 23569115
Bioinformatics. 2014 Jul 15;30(14):2068-9
pubmed: 24642063
Genome Biol Evol. 2015 Sep 17;7(9):2585-2601
pubmed: 26384038
BMC Microbiol. 2007 Mar 12;7:18
pubmed: 17352818
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
J Cell Biochem. 2012 Jul;113(7):2464-73
pubmed: 22396173
Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314
pubmed: 30418610
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D32-6
pubmed: 16381877
Nucleic Acids Res. 2019 Jul 2;47(W1):W81-W87
pubmed: 31032519
Curr Opin Genet Dev. 2005 Dec;15(6):589-94
pubmed: 16185861
Mol Cell Probes. 1998 Dec;12(6):349-58
pubmed: 9843652