Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss

Table 3 Overview of selected genome characteristics of Listeria genomes used for comparative analysis

Strain	No. of strain specific ORFs^a	No. of internalin genes	% ORFs introduced by HGT^b	No. of prophages^c	No. of monocins^d	R-M system^e	CRISPR^fpresence	Plasmid presence	No. of Transposons^g
*L. monocytogenes*
F2365	8	26	3.4	0	1	II	no	no	0
EGD-e	36	25	3.4	1*	1	-	yes	no	1
CLIP81459	9	28	3.2	0	1	I	no	no	0
HCC23	44	18	4.8	3	0	II	yes	no	0
FSL F2-208	101	23	4.6	1*	1	I	yes	no	1
*L. marthii*
FSL S4-120	74	19	6.4	0	1	I	yes	no	0
*L. innocua*
CLIP11262	159	20	4.0	5*	1	I	yes	yes	0
FSL S4-378	108	19	5.9	2	1	I	yes	no	0
FSL J1-023	47	17	4.5	0	1	II (2)	no	no	0
*L. welshimeri*
SLCC5334	113	9	3.6	1	0	I	no	no	1
*L. ivanovii*
FSL F6-596	230	20	2.0	1	2	-	yes	no	0
*L. seeligeri*
FSL S4-171	91	17	3.0	1*	2	I	no	no	0
FSL N1-067	234	15	4.3	2*	1	I & III	yes	yes	0

^a ORFs were designated as 'strain specific' if they were only present in one strain (based on comparisons with the other genomes included in our study here
^b These ORFs were detected as derived from horizontal gene transfer by the SIGI-HMM program [47].
^c An asterisk indicates that one of the prophages is inserted in comK.
^d The number of regions encoding monocins, defective prophage or satellite prophages.
^e I = Type I Restriction-Modification (R-M) system, II = Type II R-M system, III = Type III R-M system, - = no R-M system.
^f CRISPR stands for Clustered, regularly interspaced, short palindromic repeat loci.
^g The integrative and conjugative element found in the genome of L. welshimeri (Genbank accession AM 263198: lwe0767-lwe0796) was not reported in the original publication of this genome.

ISSN: 1471-2164