Re-sequencing and optical mapping reveals misassemblies and real inversions on Corynebacterium pseudotuberculosis genomes.
Sci Rep, 2019/11/08;9(1):16387.
Sousa TJ[1], Parise D[1], Profeta R[1], Parise MTD[1], Gomide ACP[1], Kato RB[1], Pereira FL[2], Figueiredo HCP[2], Ramos R[3], Brenig B[4], Costa da Silva ALD[3], Ghosh P[5], Barh D[6], Góes-Neto A[1], Azevedo V[7]
Affiliations
PMID: 31705053DOI: 10.1038/s41598-019-52695-4
Impact factor: 4.996
Abstract
The number of draft genomes deposited in Genbank from the National Center for Biotechnology Information (NCBI) is higher than the complete ones. Draft genomes are assemblies that contain fragments of misassembled regions (gaps). Such draft genomes present a hindrance to the complete understanding of the biology and evolution of the organism since they lack genomic information. To overcome this problem, strategies to improve the assembly process are developed continuously. Also, the greatest challenge to the assembly progress is the presence of repetitive DNA regions. This article highlights the use of optical mapping, to detect and correct assembly errors in Corynebacterium pseudotuberculosis. We also demonstrate that choosing a reference genome should be done with caution to avoid assembly errors and loss of genetic information.
MeSH terms
Chromosome Inversion; Chromosome Mapping; Corynebacterium pseudotuberculosis; Databases, Nucleic Acid; Genome, Bacterial; High-Throughput Nucleotide Sequencing; Sequence Alignment; Sequence Analysis, DNA; Whole Genome Sequencing
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