DOI: 10.5061/dryad.8sf7m0cpp
title: Supplementary information provided with Murray et al.: Discovery of an Antarctic ascidian-associated uncultivated Verrucomicrobia with antimelanoma palmerolide biosynthetic potential

description: The Antarctic marine ecosystem harbors a wealth of biological and chemical
 innovation that has risen in concert over millennia since the isolation of
 the continent and formation of the Antarctic circumpolar current.
 Scientific inquiry into the novelty of marine natural products produced by
 Antarctic benthic invertebrates led to the discovery of a bioactive
 macrolide, palmerolide A, that has specific activity against melanoma and
 holds considerable promise as an anticancer therapeutic. While this
 compound was isolated from the Antarctic ascidian Synoicum adareanum, its
 biosynthesis has since been hypothesized to be microbially mediated, given
 structural similarities to microbially-produced hybrid non-ribosomal
 peptide-polyketide macrolides. Here, we describe a metagenome-enabled
 investigation aimed at identifying the biosynthetic gene cluster (BGC) and
 palmerolide A-producing organism. A 74 Kbp candidate BGC encoding the
 multi-modular enzymatic machinery (hybrid Type I-trans-AT polyketide
 synthase-non-ribosomal peptide synthetase and tailoring functional
 domains) was identified and found to harbor key features predicted as
 necessary for palmerolide A biosynthesis. Surveys of ascidian microbiome
 samples targeting the candidate BGC revealed a high correlation between
 palmerolide-gene targets and a single 16S rRNA gene variant (R=0.83 –
 0.99). Through repeated rounds of metagenome sequencing followed by
 binning contigs into metagenome-assembled genomes, we were able to
 retrieve a near-complete genome (10 contigs) of the BGC-producing
 organism, a novel verrucomicrobium within the Opitutaceae family that we
 propose here as Candidatus Synoicihabitans palmerolidicus. The refined
 genome assembly harbors five highly similar BGC copies, along with
 structural and functional features that shed light on the host-associated
 nature of this unique bacterium.
description: See the publication for details (main text and supplemental
 methods section). Briefly, we used a metagenomic approach to sequence a
 microbial community from an Antarctic ascidian, <em>Synoicum
 adareanum</em>.  From this we assembled a nearly complete metagenome
 assembled genome (MAG) that encodes a candidate palmerolide A biosynthetic
 gene cluster of a verrucomicrobium affiliated new bacterium named in this
 manuscript as <em>Candidatus</em> Synoicihabitans
 palmerolidicus.  The supplemental material provided in
 this data set includes (i) Figure S1 which provides correlation
 coefficients derived between real time PCR data (methods described in the
 manuscript) and amplicon sequence variant (ASV) occurrences across a data
 set of 63 samples.  (ii) Figure S2 displays the taxonomic classification
 of predicted proteins in the assembled MAG derived from an annotation
 pipeline called MetaERG. (iii) The annotation of the Ca. S. palmerolidicus
 genome, as a GFF file formatted file.
description: The GFF File needs to be read in a genome editing program.