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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #391264

Research Project: Developing a Systems Biology Approach to Enhance Efficiency and Sustainability of Beef and Lamb Production

Location: Genetics and Animal Breeding

Title: Discrete distributions of simple sequence repeat lengths in DNA template vary at individual loci in Mannheimia haemolytica isolates

item Harhay, Gregory
item Harhay, Dayna
item Smith, Timothy - Tim

Submitted to: American Society for Microbiology
Publication Type: Proceedings
Publication Acceptance Date: 3/23/2022
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: In both gram-negative and gram-positive bacteria, some simple sequence repeats (SSR) have been shown to exhibit hypermutable overall length variation by changing the number of repeat units through slipped strand mispairing during DNA replication. SSR length variation provides potential molecular switches (e.g., frameshifts) and has been associated with phase variation. We assessed the distribution of SSR length variants at individual loci from cultures of three M. haemolytica isolates inoculated from single colonies by direct, amplification-free single molecule sequencing of genomic DNA template. A minimum 1000-fold coverage of high-fidelity reads was generated for each isolate and aligned to the cognate finished genome sequence to identify reads spanning the SSR, defined as the region of interest (ROI), and immediate flanking sequence to ensure that the ROI completely represents the SSR from the template. The ROI were filtered for quality (average phred quality score (Q) > 30 and every base having Q = 20) and fraction base composition to identify and remove reads with sequencing error as described previously (1). All ROI in the genomes with SSR = 30 bp with repeat units = 2 and = 20 bp were examined, revealing that the read frequency x ROI length distributions are discrete, while the observed ROI lengths differed by an integer number of repeat units. SSR lengths in the assembled genomes correspond to modes of the observed distributions; other characteristics of the distribution such as skewness, kurtosis, and standard deviation will be presented. The impact of these observations on the stochastic structural potential of the bacterial chromosome harboring SSR will be discussed, as well as how the genome contexts of discrete SSR length distributions at different loci provide new insights into environmental adaptability, virulence and pathogenicity.