Comparative genomic analysis identifies potential adaptive variation in Mycoplasma ovipneumoniae

Mycoplasma ovipneumoniae is associated with respiratory disease in wild and domestic Caprinae globally, with wide variation in disease outcomes within and between host species. To gain insight into phylogenetic structure and mechanisms of pathogenicity for this bacterial species, we compared M. ovipneumoniae genomes from six countries (Australia, Bosnia and Herzegovina, Brazil, China, France, USA) and four host species (domestic sheep, domestic goats, bighorn sheep, caribou)., Deep nasal swab samples were collected from domestic sheep, domestic goats, bighorn sheep, and caribou. Swab samples were selectively enriched for Mycoplasma ovipneumoniae using a two-step procedure involving incubation in mycoplasma broth, followed by incubation in SP4 broth with glucose. Genomic DNA was extracted using the QIAamp DNA Mini Kit (Qiagen). Whole-genome shotgun libraries were prepared using Illumina Nextera DNA kits and sequenced on an Illumina MiSeq using the v3 600 cycle sequencing kit. Oxford Nanopore Technologies (ONT) shotgun sequencing was also performed for samples with sufficient genomic DNA remaining after Illumina sequencing. Barcoded ONT libraries were created using the SQK-LSK109 library prep kit, and sequencing was performed for 48 hours on FLO-MIN106D flowcells. 
Raw Illumina sequence reads were cleaned using HTStream to filter PhiX reads, PCR duplicates, adapter sequences, and low-quality reads. Raw ONT sequence reads were demultiplexed by barcode and base-c..., , # Comparative genomic analysis identifies potential adaptive variation in *Mycoplasma ovipneumoniae*

[https://doi.org/10.5061/dryad.ffbg79d2h](https://doi.org/10.5061/dryad.ffbg79d2h)

## Description of the data and file structure

This dataset includes all *Mycoplasma ovipneumoniae* genome assemblies that were used in this study, including 74 assemblies that were generated for the study, and an additional 25 assemblies from prior studies that were publicly available on NCBI at the time of the study. Metadata for each assembly is provided in Table S1. The assemblies that were generated for this study are indicated by the presence of \"Y\" in the \"New_assemblies\" column of Table S1. Assemblies are provided in fasta format, with filenames corresponding to the \"Sample\" column in Table S1. The NCBI accessions that correspond to each sample can be found in Table S1.

The content for each column in Table S1 is described below:

Sample: Sample name used in this study.

LabID: Identifier used du...