Agriculture Victoria, AgriBio, La Trobe University, Bundoora, VIC, Australia.
School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, VIC, Australia.
BMC Genomics. 2023 Oct 31;24(1):656. doi: 10.1186/s12864-023-09752-0.
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.
迄今为止，对 Map 的基因组研究集中在 C 型菌株上，仅纳入了少数 S 型菌株进行比较。在这项研究中，对 261 株 Map 基因组（205 株 C 型、52 株 S 型和 4 株 B 型）和 7 株禽分枝杆菌复合体（Mac）基因组的全基因组进行了分析，以确定菌株之间的基因组相似性和差异性，并更深入地了解该分枝杆菌种内的进化关系。
我们对所有 Map 分离株的核心基因组进行分析，确定了两个不同的谱系，S 型和 C 型 Map，这与之前对 Map 的系统发育研究一致。全基因组分析表明，Map 的辅助基因组比禽分枝杆菌亚种禽分枝杆菌（Maa）大，而 C 型 Map 的辅助基因组比 S 型 Map 大。此外，我们发现 Map 的 S 型菌株中存在大量重排，而 C 型和 B 型菌株中几乎没有。我们确定了 50 个核心基因是 S 型 Map 所特有的，而 B 型和 C 型 Map 菌株之间没有独特的核心基因。在 C 型 Map 中，我们鉴定出了一个额外的 CE10 CAZyme 类，该类被鉴定为 alpha/beta 水解酶和一个额外的聚酮和非核糖体肽合成酶簇。与之前的分析一致，Map 基因组中没有发现质粒，只有不完全的前噬菌体。鉴定出了 45 个假设的 CRISPR 元件，但没有相关的 cas 基因。
这是迄今为止对 Map 分离株基因组内容最全面的比较，包括对 8 个 Map 基因组的封闭。分析表明，S 型菌株的基因同线性内存在更大的变异，表明 C 型 Map 菌株是在 S 型之后出现的。对 C 型和 B 型基因组的进一步分析表明，它们结构相似，遗传变异很小，B 型 Map 可能是 C 型 Map 的一个独特分支，而不是 Map 的另一种菌株类型。Maa 和 Map 的进化谱系被证实是在 M. hominissuis 之后出现的。
