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Supplemental Information

Flow charts outlining analyses performed in each part of the methods

The sections covered include profiling taxonomic and functional compositions of selected metagenomes, de novo and reference-guided CRISPR detection, mapping virus-host interactions with CRISPR spacers, comparative analysis of virus and host sequence characteristics, and assembling metagenomes and detecting halobacterial cas genes in metagenomic contigs.

DOI: 10.7287/peerj.preprints.2106v2/supp-1

Percentage of reads mapping to reference library in taxonomic profiling steps (MetaPhyler)

DOI: 10.7287/peerj.preprints.2106v2/supp-2

Percentage of reads mapping to reference library in functional profiling steps (ShotMAP)

DOI: 10.7287/peerj.preprints.2106v2/supp-3

Number of CRISPR spacers detected by de novo and reference guided methods, normalized by millions of reads in each metagenome

Spacers were detected either with the de novo detection method (Crass) or the reference-guided method (MetaCRAST) with corresponding maximum edit distances (from 0 to 3) described in Materials and Methods that used a query of 29 halobacterial CRISPR direct repeat sequences. All spacer counts are reported after clustering initially detected spacers with CD-HIT (with a clustering similarity threshold of 0.9).

DOI: 10.7287/peerj.preprints.2106v2/supp-4

Network of virus-host interactions generated from spacers detected in the genome of Haloquadratum walsbyi strain C23

The library of haloviral genomes screened is listed in Table S1. Nodes represent either viruses or spacers, while edges represent BLAST alignments linking spacers to viruses. Viruses are marked in orange and spacers in blue. Visualization was performed with Cytoscape.

DOI: 10.7287/peerj.preprints.2106v2/supp-5

Measures of the number of contig BLAST hits to cas genes extracted from three different halobacterial orders (Halobacteriales, Haloferacales, and Natrialbales)

DOI: 10.7287/peerj.preprints.2106v2/supp-6

Taxonomic affiliation of all BLAST hits of cas genes against contigs (not only best hits)

Detected contigs assembled with Newbler and Velvet were aligned against a library of cas genes from three halobacterial orders (Halobacteriales, Haloferacales, and Natrialbales). The taxonomic affiliations of all hits for each contig were tabulated into profiles for each order and assembly method.

DOI: 10.7287/peerj.preprints.2106v2/supp-7

The library of haloviral genomes examined

The library included 326 contigs more than 500 bp in length assembled from Chula Vista metaviromes (http://data.imicrobe.us/project/view/58) and the following haloviral genomes obtained from NCBI GenBank.

DOI: 10.7287/peerj.preprints.2106v2/supp-8

Sequence assembly statistics for three different metagenomes and two different assembly algorithms

DOI: 10.7287/peerj.preprints.2106v2/supp-9

Alignments of combined Santa Pola CRISPR direct repeats identified with Crass against a library of taxonomically annotated direct repeat sequences obtained from CRISPRdb

DOI: 10.7287/peerj.preprints.2106v2/supp-10

Query sequences used for reference-guided CRISPR search and associated archaeal hosts

DOI: 10.7287/peerj.preprints.2106v2/supp-11

Summary of CRISPR virus-host pairings in Cahuil (C34) metagenome

CRISPR spacers were detected with the reference-guided method.

DOI: 10.7287/peerj.preprints.2106v2/supp-12

Summary of CRISPR virus-host pairings in SS13 metagenome

CRISPR spacers were detected with the reference-guided method.

DOI: 10.7287/peerj.preprints.2106v2/supp-13

Summary of CRISPR virus-host pairings in SS19 metagenome

CRISPR spacers were detected with the reference-guided method.

DOI: 10.7287/peerj.preprints.2106v2/supp-14

Summary of CRISPR virus-host pairings in IC21 metagenome

CRISPR spacers were detected with the reference-guided method.

DOI: 10.7287/peerj.preprints.2106v2/supp-15

Summary of CRISPR virus-host pairings in SS33 metagenome

CRISPR spacers were detected with the reference-guided method.

DOI: 10.7287/peerj.preprints.2106v2/supp-16

Summary of CRISPR virus-host pairings in SS37 metagenome

CRISPR spacers were detected with the reference-guided method.

DOI: 10.7287/peerj.preprints.2106v2/supp-17

The library of cas genes identified in Halobacteriales genomes that were used in cas operon detection

The library was aligned against Newbler contigs assembled from the Cahuil/C34, combined Chula Vista, and combined Santa Pola/Isla Cristina metagenomes.

DOI: 10.7287/peerj.preprints.2106v2/supp-18

The library of cas genes identified in Haloferacales genomes that were used in cas operon detection

The library was aligned against Newbler contigs assembled from the Cahuil/C34, combined Chula Vista, and combined Santa Pola/Isla Cristina metagenomes.

DOI: 10.7287/peerj.preprints.2106v2/supp-19

The library of cas genes identified in Natrialbales genomes that were used in cas operon detection

The library was aligned against Newbler contigs assembled from the Cahuil/C34, combined Chula Vista, and combined Santa Pola/Isla Cristina metagenomes.

DOI: 10.7287/peerj.preprints.2106v2/supp-20

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Abraham G Moller conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Chun Liang conceived and designed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

Sequence Read Archive

SRX328504

SRX024859

SRX352042

SRX347883

SRX090229

SRX680116

iMicrobe

http://data.imicrobe.us/project/view/58

Data Deposition

The following information was supplied regarding data availability:

GitHub. MetaCRAST (reference-guided CRISPR detection). https://github.com/molleraj/MetaCRAST

Funding

The project was funded partially by the Committee on Faculty Research (CFR) program, the Office for the Advancement of Research & Scholarship (OARS), and by an Academic Challenge grant from the Department of Biology (Miami University). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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