Table 1.
Characteristics of Mycobacterium bovis genomes used in this work.
| M. bovis ID | Clonal complex(a) | Country | Year | Host species | References | Type of sequence |
|---|---|---|---|---|---|---|
| Mb0220 | w/o CC | Portugal | 2003 | Cattle | 40 | Newly sequenced |
| Mb0261 | Eu2 | Portugal | 2006 | Red deer | 40 | Newly sequenced |
| Mb0601 | Eu2 | Portugal | 2007 | Cattle | 40 | Newly sequenced |
| Mb0769 | Eu2 | Portugal | 2008 | Cattle | 40 | Newly sequenced |
| Mb0783 | Eu2 | Portugal | 2008 | Wild boar | 40 | Newly sequenced |
| Mb0865 | Eu2 | Portugal | 2008 | Cattle | 40 | Newly sequenced |
| Mb0891 | Eu2 | Portugal | 2009 | Red deer | 40 | Newly sequenced |
| Mb0893 | Eu2 | Portugal | 2008 | Wild boar | 40 | Newly sequenced |
| Mb1317 | Eu2 | Portugal | 2010 | Cattle | 40 | Newly sequenced |
| Mb1339 | Eu2 | Portugal | 2010 | Cattle | 40 | Newly sequenced |
| Mb1458 | w/o CC | Portugal | 2010 | Wild boar | 40 | Newly sequenced |
| Mb1480 | w/o CC | Portugal | 2010 | Cattle | 40 | Newly sequenced |
| Mb1654 | Eu2 | Portugal | 2011 | Cattle | 40 | Newly sequenced |
| Mb1670 | w/o CC | Portugal | 2011 | Red deer | 40 | Newly sequenced |
| Mb1711 | Eu2 | Portugal | 2011 | Red deer | 40 | Newly sequenced |
| Mb1712 | Eu2 | Portugal | 2011 | Red deer | 40 | Newly sequenced |
| Mb1714 | Eu2 | Portugal | 2011 | Cattle | 40 | Newly sequenced |
| Mb1744 | w/o CC | Portugal | 2012 | Wild boar | 40 | Newly sequenced |
| Mb1746 | Eu2 | Portugal | 2012 | Red deer | 40 | Newly sequenced |
| Mb1758 | Eu2 | Portugal | 2012 | Cattle | 40 | Newly sequenced |
| Mb1769 | Eu2 | Portugal | 2012 | Wild boar | 40 | Newly sequenced |
| Mb1785 | Eu2 | Portugal | 2012 | Red deer | 40 | Newly sequenced |
| Mb1789 | Eu2 | Portugal | 2012 | Cattle | 40 | Newly sequenced |
| Mb1841 | Eu2 | Portugal | 2012 | Cattle | 40 | Newly sequenced |
| Mb1870 | Eu2 | Portugal | 2012 | Wild boar | 40 | Newly sequenced |
| Mb1915 | Eu2 | Portugal | 2013 | Red deer | 40 | Newly sequenced |
| Mb1948 | w/o CC | Portugal | 2013 | Red deer | 40 | Newly sequenced |
| Mb1960 | Eu2 | Portugal | 2013 | Red deer | 40 | Newly sequenced |
| Mb2026 | Eu2 | Portugal | 2013 | Cattle | 40 | Newly sequenced |
| Mb2043 | Eu2 | Portugal | 2013 | Red deer | 40 | Newly sequenced |
| Mb2067 | Eu2 | Portugal | 2013 | Wild boar | 40 | Newly sequenced |
| Mb2206 | Eu2 | Portugal | 2014 | Cattle | 40 | Newly sequenced |
| Mb2235 | w/o CC | Portugal | 2014 | Red deer | 40 | Newly sequenced |
| Mb2277 | w/o CC | Portugal | 2014 | Red deer | 40 | Newly sequenced |
| Mb2300 | Eu2 | Portugal | 2014 | Wild boar | 40 | Newly sequenced |
| Mb2310 | Eu2 | Portugal | 2015 | Red deer | 40 | Newly sequenced |
| Mb2313 | Eu2 | Portugal | 2015 | Wild boar | 40 | Newly sequenced |
| Mb2325 | Eu2 | Portugal | 2015 | Red deer | 40 | Newly sequenced |
| Mb2328 | Eu2 | Portugal | 2015 | Red deer | 40 | Newly sequenced |
| Mb2347 | w/o CC | Portugal | 2015 | Wild boar | 40 | Newly sequenced |
| Mb2395 | Eu2 | Portugal | 2015 | Wild boar | 40 | Newly sequenced |
| Mb2397 | Eu2 | Portugal | 2015 | Wild boar | 40 | Newly sequenced |
| Mb502499 | Af1 | Ghana | NA | Human | 30,41 | SRA deposited |
| Mb502526 | Af1 | Ghana | NA | Human | 30,41 | SRA deposited |
| Mb1203064 | Af1 | Ghana | NA | Human | 30,41 | SRA deposited |
| Mb4117155 | Af2 | France | NA | Wild boar | 30,42 | SRA deposited |
| Mb1791710 | Af2 | Tanzania | NA | Chimpanzee | 30,43 | SRA deposited |
| Mb1791712 | Af2 | Tanzania | NA | Chimpanzee | 30,43 | SRA deposited |
| Mb1792006 | Eu1 | USA | 2006 | Cattle | 43 | SRA deposited |
| Mb1792127 | Eu1 | USA | 2008 | Cattle | 43 | SRA deposited |
| Mb1792361 | Eu1 | USA | 2013 | Cattle | 43 | SRA deposited |
| Mb7240242 | Eu1 | USA | 2016 | Cattle | 43 | SRA deposited |
| Mb7240415 | Eu1 | USA | 2014 | Cattle | 43 | SRA deposited |
| Mb1791984 | Eu1 | USA | 2005 | Cattle | 43 | SRA deposited |
| MBE1 | w/o CC | Egypt | 2014 | Cattle | NA | assemble/draft genomes NCBI |
| MBE3 | w/o CC | Egypt | 2014 | Cattle | NA | assemble/draft genomes NCBI |
| MBE4 | w/o CC | Egypt | 2014 | Cattle | NA | assemble/draft genomes NCBI |
| MBE10 | w/o CC | Egypt | 2015 | Cattle | NA | assemble/draft genomes NCBI |
| Mb0077 | w/o CC | Canada | 2006 | Elk | NA | assemble/draft genomes NCBI |
| Mb0565 | w/o CC | Canada | 2011 | Cattle | NA | assemble/draft genomes NCBI |
| BMR25 | w/o CC | Canada | 1985 | Bison | NA | assemble/draft genomes NCBI |
| Mb3601 | Eu3 | France | 2014 | Cattle | 29 | assemble/draft genomes NCBI |
| Mb0476 | Eu2 | Canada | 2002 | Cattle | NA | assemble/draft genomes NCBI |
| MbSP38 | Eu2 | Brazil | 2010 | Cattle | 44 | assemble/draft genomes NCBI |
| Mb1595 | w/o CC | Korea | 2012 | Cattle | 45 | assemble/draft genomes NCBI |
| Mb0030 | w/o CC | China | NA | NA | 46 | assemble/draft genomes NCBI |
| Mb0001 | Eu2 | Brazil | 2015 | Tapirus terrestris | NA | assemble/draft genomes NCBI |
| Mb0003 | w/o CC | India | 1986 | Cattle | NA | assemble/draft genomes NCBI |
| Mb31150 | Af2 | Uganda | NA | Chimpanzee | 30,47 | assemble/draft genomes NCBI |
Eu1: European 1, Eu2: European 2, Eu3: European 3, Af1: African 1, Af2: African 2, and w/o CC: without clonal complex.
NA: non-available information.