Additional File 2 — Full 6S RNA phylogeny
Sequence- and structure-based reconstruction of 6S RNA phylogeny in LAB. Canonical 6S RNAs were clustered hierarchically usingRNAclustandmlocarna. Family membership is indicated by color. 6S-1 RNA fromB. subtilis is used as outgroup. The full number of represented genomes is indicated in blue boxes in the outer ring. Circles in the outer ring indicate whether and where a potential cre-site were identified at the 6S RNA locus.
cre-site within 6S RNA gene
cre-site at both locations 1
1 66 1 1 2 1 7 1 2 2 2 1 2 1 1 1 1 10 1 1 1 2 1 12 1 9 31 5 1 1 1 1 1 5 2 1 1 1 1 6 1 18
11
1
61
11
1 7 11 1 2 2 1 3 1 12 12 2 11 4 1 1 1 1 4 1 4 1 1 1 3 2 1 16
1 1 41 1
2 3 1 1 3 2 1 2 2 2 2 1 1 4 1
62 1
4 4935 3
1 1
51 1
11 2 79
12127 13 1 1 510
35
2 3
34
4 2 13
2 1 1 1 2 1 1 1 1 1 1 2 1 2 1 7
1 2 13
15
11
1 7 5
3 114
5 6
1 4
2 1
1 1 35
3 1 1 17
Distance: 1
Bacillus subtilis 6S-1 RNA Lactobacillus herbarum Lactobacillus paraplantarum Lactobacillus xiangfangensis Vagococcus fl
uvialis Vagococcus mart Vagococcus penaeiis Trichococcus alkaliph
ilus Jeotgalibaca
dankookensis Carnobacterium
inhibens Carnobacterium
alterfun ditum Carnobacterium
funditu m Carnobacterium
divergens Carnobacterium
gallinarum Abiotrop
hia defectiva Marinilactibacil
lus psychrotole rans Lacticigenium
naphtae Alkalibact
erium olivapovlit
icus Dolosigranulum
pigrum Atopococcu
s tabaci Allofust
is seminis Granulicat
ella adiacens Atopoba
cter phocae Bavariicoccus
seileri Lactobacillus
sakei Lactobacillus
curvatus Lactobacillus
fuchuensis Lactobacillus
rennini Lactobacillus
coryniformis Lactobacillus
biferment
ans Lactobacillus
backii Globicate
lla sanguinis Facklamia so
urekii Facklamia i
gnava Eremococcus co
leocola Dolosicoccus pauci
vorans Tetragenococcus
halophilus Enterococcu
s aquimarinus Enterococcu
s saccharolyticus Enterococcu
s italicus Enterococcu
s rivorum Enterococcu
s faecalis Enterococcu
s phoeniculicola Enterococcu
s casseliflavus Enterococcu
s canis
Enterococcu s canintest
ini
Enterococcu s asini
Enterococcu s durans
Enterococcu s pallens
Enterococcu s hermanniensis Enterococcu
s avium
Enterococcu s columbae
Enterococcu s caccae
Melissococcus plut onius
Lactobacillus wasatchensis
Lactobacillus hokkaidonensis Lactobacillus
suebicus
Lactobacillus vaccinostercus Lactobacillus
ingluviei
Lactobacillus fermentum
Lactobacillus vaginalis
Lactobacillus reuteri
Lactobacillus pontis
Lactobacillus panis
Lactobacillus antri
Lactobacillus frument
i
Lactobacillus secaliphilus Lactobacillus
similis
Lactobacillus odoratit
ofui
Lactobacillus mixtipabuli
Lactobacillus kimchicus
Lactobacillus collinoides Lactobacillus
spicheri
Lactobacillus namurensis Lactobacillus
senmaizukei Lactobacillus
hammesii Lactobacillus
acidifarinae Lactobacillus
paucivorans Lactobacillus
brevis Lactobacillus
koreensis Lactobacillus
saniviri Lactobacillus
brantae Lactobacillus
casei Lactobacillus
perolens Lactobacillus harbinensis Aerococcus uAerococcus christenseniiAerococcus saAerococcus urinaeequiStreptococcus uberisAerococcus urinaerinaehominisnguinicola Streptococcus pseudoporci
nus Streptococcus bovimast
itidis Streptococcus parauberisStreptococcus ictal uri Streptococcus didelphi
s Strept
ococcus iniae Strept
ococcus castore us Strept
ococcus canis Strept
ococcus phocae Strept
ococcus equi Strept
ococcus agalact iae Strept
ococcus suis Strept
ococcus suis Strept
ococcus ovis Strept
ococcus minor Strept
ococcus azizii Strept
ococcus ente ricus Strept
ococcus porci Strept
ococcus plurext
orum Strept
ococcus orisratt
i Strept
ococcus parasangui
nis Strept
ococcus anginosus Strept
ococcus marimammalium Strept
ococcus pluranimal
ium Strept
ococcus hyovaginal
is Strept
ococcus halot
olerans Strept
ococcus mutan
s Strept
ococcus caballi Strept
ococcus devriesei Strept
ococcus pant
holopis Strept
ococcus macacae Strept
ococcus criceti Strept
ococcus gallolyt
icus Strept
ococcus equinus Lactococcus p
lantarum Lactococcus ch
ungangensis Lactococcus l
actis Lactococcus g
arvieae Leuconostoc
pseudomesenteroide
s Leuconostoc
mesenteroides Leuconostoc
garlicum Leuconostoc
citreum Leuconostoc
carnosum
Leuconostoc
kimchii
Leuconostoc gelidum
Lactobacillus vini
Lactobacillus satsumensis
Lactobacillus oeni
Lactobacillus nagelii
Lactobacillus ghanensis
Lactobacillus sucicola
Lactobacillus aquaticus
Lactobacillus capillatus
Lactobacillus mali
Lactobacillus hordei
Lactobacillus salivarius
Lactobacillus hayakitensis
Lactobacillus ceti
Lactobacillus aviarius
Lactobacillus apodemi
Lactobacillus animalis
Lactobacillus saerimneri
Lactobacillus ruminis
Pediococcus stilesii
Pediococcus pentosaceus
Pediococcus acidilactici
Pediococcus claussenii
Lactobacillus kefiranof
aciens
Lactobacillus gallinarum
Lactobacillus amylovorus
Lactobacillus acidophilus
Lactobacillus crispatus
Lactobacillus gigeriorum
Lactobacillus hamsteri
Lactobacillus amylolyticus
Lactobacillus acetotol
erans
Lactobacillus kalixensis Lactobacillus
johnsonii Lactobacillus
gasseri Lactobacillus
hominis Lactobacillus
equicursoris Lactobacillus delbrueckii
1
