Also, genome encodes an erm(41) gene which mutations were reported to confer clarithromycin resistance [50]

Also, genome encodes an erm(41) gene which mutations were reported to confer clarithromycin resistance [50]. associated infections [9]. Not only humans but also cats [10, 11] and dolphins [12C14] are infected while fishes are uniquely infected by comprises two subspecies named subsp. and subsp. or and from and forming the complex, has been retained for clarity. The availability of 39?and two genomes in the National Center for BioInformatics (NCBI) genome database provides new opportunities to assess the diversity of this species. Here, we review 14 complete published complex genomes and compare them with the re-annotated H37Rv genome (Table?1) in order to in-depth analyse the diversity of complex pan- and core-genome complex genomes comprise one circular chromosome. In addition, ATCC 19977 contains one 23-kb plasmid identical to the pMM23 plasmid, encoding mer operon and mercury reductase protein, which may confer resistance to organo-mercury compounds [25]. In order to normalize the predicted proteins and to minimize the differences of presence/absence of genes and length, coding sequences were predicted using prodigal software [26]. We identified a total of 70,309 protein-coding sequences which number varies from 4,651 to 5,079 in each genome (Table?2). TPO agonist 1 The core-genome contains 57,172 protein sequences accounting for 64.15% of the pan-genome. This figure ITGAL indicates a non-conservative genome contrary to that of T4954–strain GO 064944–M9347331111M9448411010M1524762– T496233M18466388M1544651– C2B 47?J264766–M115480244M139475444M17250792020 T473399 C3B M2449602323 complex diversity The average percentage of amino-acid sequence identity (AAI) of core proteins was determined as previously described [29]. The AAI values indicate that complex forms three main clusters: cluster TPO agonist 1 1 (C1) includes type strain and strains M93, 94, M152 and Go06; cluster 2 (C2) contains two subclusters: cluster 2A (C2A) includes type strain and strains M154 and M18; cluster 2B (C2B) includes strains 47?J26, M115, M172 and M139; cluster 3 (C3) includes two subclusters: cluster 3A (C3A) includes type strain and cluster 3B (C3B) includes strain M24 (Table?3). Table 3 Average nucleodite identity and characteristics of TTTcomplex proteomes were further aligned using Mauve software [30] to infer phylogeny using the Neighbor-Net algorithm in the package SplitsTree4 [31]. The phylogenomic network confirms the three clusters C1, C2 and C3 (Figure?1A). A phylogenomic tree based on gene content (i.e., the presence or absence of orthologs) (Figure?1B) organizes differently from the whole genome TPO agonist 1 concatenated tree (Figure?1A) or even the phylogenetic tree based on gene repertoires have different evolutionary histories and suggests that differential gene loss and lateral gene acquisition are playing important roles in the evolution of some strains. Notably, the situation of strain Go06 is confusing, as it presents 98.4% AAI with type strain in C1 TPO agonist 1 (Figure?1A) whereas its and and is the only example compatible with a lateral transfer of complex than the one currently suggested by the nomenclature, which recognizes only two subspecies within abscis in fact comprising of three genomospecies, corresponding to previous nomenclature of (C1), (C2) and (C3). Using an AAI 97% threshold would further determine two subspecies in (C2A and C2B) and in (C3A and C3B). Recent whole genome sequencing analyses of clinical isolates in Great Britain also clearly distinguished three clusters in agreement with the three here reported [8]. All these data support revaluating the taxonomy of complex, to recognize three genomospecies (C1), (C2), and (C3); and four unnamed subspecies C2A, C2B; C3A, C3B. prophagome median GC% content is 64.2%, ranging from 62.7% (ATCC 19977) to 64.2% (strain Go 06). The GC% is not characteristic of the clusters as the median GC% content of C1, C2A and C3 is 64.2%, close to the median 64.1% GC% content in C2B. However, there is a TPO agonist 1 significant 14.7% variation in the genome length from 4.8-Mb (M154) to 5.51-Mb (M24) with a median.