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A computational approach to identify CRISPR-Cas loci in the complete genomes of the lichen-associated Burkholderia sp. PAMC28687 and PAMC26561
- Authors
- Shrestha, P.; Han, S.-R.; Lee, J.H.; Park, H.; Oh, T.-J.
- Issue Date
- May-2021
- Publisher
- Academic Press Inc.
- Keywords
- Burkholderia PAMC26561; Burkholderia PAMC28687; CRISPR-Cas classification; Lichen
- Citation
- Genomics, v.113, no.3, pp.881 - 888
- Indexed
- SCIE
SCOPUS
- Journal Title
- Genomics
- Volume
- 113
- Number
- 3
- Start Page
- 881
- End Page
- 888
- ISSN
- 0888-7543
- Abstract
- The genus Burkholderia and its strains PAMC28687 and PAMC26561 are lichen-associated bacteria isolated from the Antarctic region. Our study is the first to provide the genome sequence of the Burkholderia sp. PAMC26561 strain. The genus Burkholderia includes bacteria that are pathogenic to plants, animals, and humans. Computational analysis of complete genomes of strains from the uncategorized Burkholderia group was performed using the NCBI databank and PATRIC (for genome sequence information) and CRISPRCasFinder (online and offline versions) software in order to predict the CRISPR loci and Cas genes. The RNAfold Webserver online software was used to predict RNA secondary structures. Our study showed that strain MSMB0852 (plasmid) possesses CRISPR-Cas system Class 2, and two lichen-associated strains, PAMC28687 (chromosome I) and PAMC26561 (chromosome I), possess CRISPR-Cas system Class 1. Additionally, only the two lichen-associated strains possess a variety of Cas genes. © 2021 Elsevier Inc.
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