Comparison of short and long reads in structural and functional annotation of non-model bacteria.

Comparison of short and long reads in structural and functional annotation of non-model bacteria.

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. DNA sequencing is a unique way to gain insight into the structure of the genome and the functions of an organism. In this study, we compared the widely used Illumina short reads and Oxford Nanopore long reads sequencing technologies in structural and functional annotation of non-model bacteria. We examined Schlegelella thermodepolymerans subspecies DSM 15264, LMG 21645, and CCUG 50061, non-model Gramnegative industrially utilizable representatives. Although these bacteria have a significant potential for the production of polyhydroxyalkanoates - degradable bioplastics by utilizing waste from the agro-food industry, assemblies of their genomes are not available. The results revealed the Nanopore as the more efficient approach for initial genome characterization. Compared to Illumina, Nanopore revealed more structural genomic features and assigned more genes to the Clusters of Orthologous Groups (COGs). Moreover, Nanopore resulted in the largest contig and N50 many times higher and the number of contigs many times lower than Illumina assemblies. On the other hand, Nanopore sequencing has been shown to be error-prone. Consequently, assemblies of Nanopore's individual genomic features are less accurate, resulting in incomplete structural annotation and incorrect functional annotation in several cases. Illumina sequencing is, therefore, more applicable for detailed studies of specific genomic regions.

. DNA sequencing is a unique way to gain insight into the structure of the genome and the functions of an organism. In this study, we compared the widely used Illumina short reads and Oxford Nanopore long reads sequencing technologies in structural and functional annotation of non-model bacteria. We examined Schlegelella thermodepolymerans subspecies DSM 15264, LMG 21645, and CCUG 50061, non-model Gramnegative industrially utilizable representatives. Although these bacteria have a significant potential for the production of polyhydroxyalkanoates - degradable bioplastics by utilizing waste from the agro-food industry, assemblies of their genomes are not available. The results revealed the Nanopore as the more efficient approach for initial genome characterization. Compared to Illumina, Nanopore revealed more structural genomic features and assigned more genes to the Clusters of Orthologous Groups (COGs). Moreover, Nanopore resulted in the largest contig and N50 many times higher and the number of contigs many times lower than Illumina assemblies. On the other hand, Nanopore sequencing has been shown to be error-prone. Consequently, assemblies of Nanopore's individual genomic features are less accurate, resulting in incomplete structural annotation and incorrect functional annotation in several cases. Illumina sequencing is, therefore, more applicable for detailed studies of specific genomic regions.