A treasure trove of 1,034 actinomycete genomes
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Abstract
Filamentous Actinobacteria, previously Actinomycetia, are the most prolific source of microbial bioactive natural products. Studies on biosynthetic gene clusters benefit from or require chromosome-level assemblies. Here, we provide DNA sequences from more than 1,000 isolates: 881 complete genomes and 153 near-complete genomes, representing 28 genera and 389 species, including 244 likely novel species. All genomes are from filamentous isolates of the class Actinomycetia from the NBC culture collection. The largest genus is Streptomyces with 886 genomes including 742 complete assemblies. We use this data to show that analysis of complete genomes can bring biological understanding not previously derived from more fragmented sequences or less systematic datasets. We document the central and structured location of core genes and distal location of specialized metabolite biosynthetic gene clusters and duplicate core genes on the linear Streptomyces chromosome, and analyze the content and length of the terminal inverted repeats which are characteristic for Streptomyces . We then analyze the diversity of trans-AT polyketide synthase biosynthetic gene clusters, which encodes the machinery of a biotechnologically highly interesting compound class. These insights have both ecological and biotechnological implications in understanding the importance of high quality genomic resources and the complex role synteny plays in Actinomycetia biology.
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We provide analysis of their phylogeny, genomic organization, BGC content and provide an example of how this large dataset can be used to identify novel BGCs
I left some minor suggestions, but I wanted to say that I really enjoyed this paper! Such a cool resource.
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(RiPP),
Could be interesting to also look at these genomes using a RiPP specific prediction tool such as RiPPer https://academic.oup.com/nar/article/47/9/4624/5420534
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29,024 regions encoding BGCs were identified in the genomes.
Could you add here what % of these predictions were related to known metabolites vs unknown?
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sequencing
Could you also include information on which chemistry version/flow cell version was used? Newer nanopore chemistries have a lot of improvements in error rate, so it would be good to know what was used here.
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We isolated almost 2000 strains of filamentous Actinomycetia from soil, and sequenced more than 1,000 of them, with ∼90% of them assembling into complete chromosomes.
This is such an amazing contribution!
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he bar chart on the outer ring denote the number of BGCs.
it might be helpful to label this on the actual figure panel somehow, I wouldnt have expect this number to be related to BGCs from just looking at the figure
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I love that you put this on github! It might be good to add to the readme a brief description of usage instructions
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the sample was excluded from further analysis
how many samples did this happen for?
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The coverage plot inspection revealed large scale assembly artifacts of some of the chromosomes, resulting in 11 genomes which needed to be reassembled after Filtlong removal of half the raw nanopore data. These errors related to the TIRs of Streptomyces genomes.
It is awesome that you made the effort to make sure these genome assemblies were as high quality as possible! I am curious if there is anything specific about the TIRs of these 11 genomes- are they particularly complex ?
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Nanopore MinION platform, with either the SQK-RBK004 or SQK-RBK110-96 kit, both
It would be nice here to include information on the sequencing statistics. I see the kit enables 96 barcodes, but how many samples were actually pooled per flow cell? What were the yields of the sequencing runs and what was the distribution of read sizes?
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ISP4, AIM-Avicel, and AIM-xylose
maybe it would be good to explain here what these media are, or provide a reference, for readers who are not familiar with Actino-specific media? And to help explain why antifungals/gram negative inhibitors aren't needed?
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we picked single colonies
Were colonies just selected based on morphology?
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Soil samples were collected
I see that this information is in the results/discussion, but it might be nice to also include here at least a list of countries that these samples were collected from, or reference where in the paper this information is
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