First Complete Genome of the Thermophilic Polyhydroxyalkanoates-Producing Bacterium Schlegelella thermodepolymerans DSM 15344

Abstract

Schlegelella thermodepolymerans is a moderately thermophilic bacterium capable of producing polyhydroxyalkanoates—biodegradable polymers representing an alternative to conventional plastics. Here, we present the first complete genome of the type strain S. thermodepolymerans DSM 15344 that was assembled by hybrid approach using both long (Oxford Nanopore) and short (Illumina) reads. The genome consists of a single 3,858,501-bp-long circular chromosome with GC content of 70.3%. Genome annotation identified 3,650 genes in total, whereas 3,598 open reading frames belonged to protein-coding genes. Functional annotation of the genome and division of genes into clusters of orthologous groups revealed a relatively high number of 1,013 genes with unknown function or unknown clusters of orthologous groups, which reflects the fact that only a little is known about thermophilic polyhydroxyalkanoates-producing bacteria on a genome level. On the other hand, 270 genes involved in energy conversion and production were detected. This group covers genes involved in catabolic processes, which suggests capability of S. thermodepolymerans DSM 15344 to utilize and biotechnologically convert various substrates such as lignocellulose-based saccharides, glycerol, or lipids. Based on the knowledge of its genome, it can be stated that S. thermodepolymerans DSM 15344 is a very interesting, metabolically versatile bacterium with great biotechnological potential.

Genomic and phenotypic comparison of polyhydroxyalkanoates producing strains of genus Caldimonas/Schlegelella

“…The majority of all ORFs consist of protein-coding sequences (CDSs), but several pseudogenes were also identified. Table 1 summarizes the main features of the newly assembled genomes along with the genome of the type strain C. thermodepolymerans DSM 15344 T [37] , available in the GenBank NCBI database under the accession CP064338.…”

“…Moreover, an extraordinary ability of the type strain S. thermodepolymerans DSM 15344 T to utilize xylose and synthesize 3-hydroxybutyrate and 3-hydroxyvalerate copolymers was recently reported by our group [26] and the bacterium was identified as a promising candidate for industrial production of PHAs from various xylose rich lignocellulose-based resources [25] . Subsequently, we provided the first complete genome assembly and the functional annotation of S. thermodepolymerans DSM 15344 T [37] . With the availability of complete genome sequences, Schlegelella thermodepolymerans was found to be a homotypic synonym of Caldimonas thermodepolymerans [31] .…”

Genomic and Phenotypic Comparison of Polyhydroxyalkanoates Producing Strains of genusCaldimonas/Schlegelella

“…The majority of all ORFs consist of protein-coding sequences (CDSs), but several pseudogenes were also identified. Table 1 summarizes the main features of the newly assembled genomes along with the genome of the type strain C. thermodepolymerans DSM 15344 T (Musilova et al 2021), available in the GenBank NCBI database under the accession CP064338. 1.…”

“…Moreover, an extraordinary ability of the type strain S. thermodepolymerans DSM 15344 T to utilize xylose and synthesize 3-hydroxybuytrate and 3-hydroxyvalerate copolymers was recently reported by our group (Kourilova et al 2020) and the bacterium was identified as a promising candidate for industrial production of PHAs from various xylose rich lignocellulose-based resources (Kourilova et al 2021). Subsequently, we provided the first complete genome assembly and the functional annotation (Musilova et al 2021). With the availability of complete genome sequences, Schlegelella thermodepolymerans was found to be a homotypic synonym of Caldimonas thermodepolymerans (Liu et al 2022).…”