Genome sequencing and pan-genome analysis of 23 Corallococcus spp. strains reveal unexpected diversity, with particular plasticity of predatory gene sets
MetadataDangos cofnod eitem llawn
Corallococcus is an abundant genus of predatory soil myxobacteria, containing two species, C. coralloides (for which a genome sequence is available) and C. exiguus. To investigate the genomic basis of predation, we genome-sequenced 23 Corallococcus strains. Genomic similarity metrics grouped the sequenced strains into at least nine distinct genomospecies, divided between two major sub-divisions of the genus, encompassing previously described diversity. The Corallococcus pan-genome was found to be open, with strains exhibiting highly individual gene sets. On average, only 30.5% of each strain’s gene set belonged to the core pan-genome, while more than 75% of the accessory pan-genome genes were present in less than four of the 24 genomes. The Corallococcus accessory pan-proteome was enriched for the COG functional category “Secondary metabolism,” with each genome containing on average 55 biosynthetic gene clusters (BGCs), of which only 20 belonged to the core pan-genome. Predatory activity was assayed against ten prey microbes and found to be mostly incongruent with phylogeny or BGC complement. Thus, predation seems multifactorial, depending partially on BGC complement, but also on the accessory pan-genome – genes most likely acquired horizontally. These observations encourage further exploration of Corallococcus as a source for novel bioactive secondary metabolites and predatory proteins.
Frontiers in Microbiology;
Livingstone, P.G., Morphew, R. and Whitworth, D.E. (2018) ‘Genome Sequencing and Pan-Genome Analysis of 23 Corallococcus spp. Strains Reveal Unexpected Diversity, With Particular Plasticity of Predatory Gene Sets’, Frontiers in Microbiology, 9, p.3187. DOI: 10.3389/fmicb.2018.03187.
Dynodwr Gwrthrych Digidol (DOI)https://doi.org/10.3389/fmicb.2018.03187
Article published in Frontiers in Microbiology on 19 December 2018 (online), available open access at: https://doi.org/10.3389/fmicb.2018.03187.
Genome sequencing was provided by MicrobesNG (http://www.microbesng.uk) which is supported by th Biotechnology and Biological Sciences Research Council (BBSRC Grant No. BB/L024209/1) and the Centre for Genomic Research, Liverpool (sequencing of AB011P and AB038B was funded by the Natural Environment Research Council – grant NBAF1033). IBERS receives strategic funding from the BBSRC.
Yn dangos eitemau sy’n perthyn drwy deitl, awdur, pwnc a chrynodeb.
Wilkinson, G.W.; Davison, A.J.; Tomasec, P.; Fielding, C.A.; Aicheler, Rebecca; Murrell, I.; Seirafian, S.; Wang, E.C.; Weekes, M.; Lehner, P.J.; Wilkie, G.S.; Stanton, R.J. (Springer, 2015-04-17)In celebrating the 60th anniversary of the first isolation of human cytomegalovirus (HCMV), we reflect on the merits and limitations of the viral strains currently being used to develop urgently needed treatments. HCMV ...
Maddocks, Sarah (ASM Press, 2016)During the golden age of antibiotic discovery, from the 1930s through the 1960s, methods of antibiotic identification relied solely on scientific observation, and while chemical analogues such as amoxicillin, derived from ...
Genome sequencing and comparative transcriptomics provide a holistic view of 4-nitrophenol degradation and concurrent fatty acid catabolism by Rhodococcus sp. strain BUPNP1 Sengupta, Kriti; Swain, Martin; Livingstone, Paul; Whitworth, David; Saha, Pradipta (Frontiers Media, 2019-01-04)Rhodococcus sp.strain BUPNP1 can utilize the priority environmental pollutant 4-nitrophenol (4-NP) as its sole source of carbon and energy. In this study, genome and transcriptome sequencing were used to gain mechanistic ...