Comparative genomics reveals Lysinibacillus sphaericus group comprises a novel species

BMC Genomics

Research Article

Jenny Dussán¹  Alejandra Hernández-Santana¹  Camilo Gómez-Garzón¹ 

[1] Centro de Investigaciones Microbiológicas (CIMIC), Universidad de los Andes, Cra 1 N. 18 A-12, Bogotá, Colombia;

关键词: Lysinibacillus sphaericus;    Pan-genome;    Core-genome;    Phylogeny;    Larvicidal;   

DOI  :  10.1186/s12864-016-3056-9

 received in 2016-06-11, accepted in 2016-08-27,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundEarly in the 1990s, it was recognized that Lysinibacillus sphaericus, one of the most popular and effective entomopathogenic bacteria, was a highly heterogeneous group. Many authors have even proposed it comprises more than one species, but the lack of phenotypic traits that guarantee an accurate differentiation has not allowed this issue to be clarified. Now that genomic technologies are rapidly advancing, it is possible to address the problem from a whole genome perspective, getting insights into the phylogeny, evolutive history and biology itself.ResultsThe genome of the Colombian strain L. sphaericus OT4b.49 was sequenced, assembled and annotated, obtaining 3 chromosomal contigs and no evidence of plasmids. Using these sequences and the 13 other L. sphaericus genomes available on the NCBI database, we carried out comparative genomic analyses that included whole genome alignments, searching for mobile elements, phylogenomic metrics (TETRA, ANI and in-silico DDH) and pan-genome assessments. The results support the hypothesis about this species as a very heterogeneous group. The entomopathogenic lineage is actually a single and independent species with 3728 core genes and 2153 accessory genes, whereas each non-toxic strain seems to be a separate species, though without a clear circumscription. Toxin-encoding genes, binA, B and mtx1, 2, 3 could be acquired via horizontal gene transfer in a single evolutionary event. The non-toxic strain OT4b.31 is the most related with the type strain KCTC 3346.ConclusionsThe current L. sphaericus is actually a sensu lato due to a sub-estimation of diversity accrued using traditional non-genomics based classification strategies. The toxic lineage is the most studied with regards to its larvicidal activity, which is a greatly conserved trait among these strains and thus, their differentiating feature. Further studies are needed in order to establish a univocal classification of the non-toxic strains that, according to our results, seem to be a paraphyletic group.

【 授权许可】

CC BY   
© The Author(s). 2016