Draft Genome Sequence of Anaerolineae Strain TC1, a Novel Isolate from a Methanogenic Wastewater Treatment System.

We report the draft genome sequence of Anaerolineae bacterium strain TC1, newly isolated from a methanogenic wastewater treatment system. The assembly contains 16 contigs in 3 scaffolds representing 3,510,630 bp in total with a G+C content of 41.35%. The genome is predicted to contain 2,793 protein-coding genes and 56 RNAs.

GENOME ANNOUNCEMENT

Cultivation-independent surveys have demonstrated that members of the class Anaerolineae are frequent inhabitants of a wide range of ecosystems (1). However, the taxon is currently represented by only a few cultured isolates, limiting our understanding of the phenotypic traits harbored within the class Anaerolineae. To further explore the genomic and physiological diversity of this class, a novel Anaerolineae strain (designated strain TC1) was isolated from a methanogenic wastewater treatment system operated in Hungary. The 16S rRNA gene sequence of strain TC1 (DDBJ/EMBL/GenBank accession number LC049585) shared less than 90% similarity to those of other characterized Anaerolineae species, with Ornatilinea apprima strain P3M-1 (accession number JQ292916) showing the highest 16S rRNA gene sequence identity (88.3%) to strain TC1. This suggests that strain TC1 may represent a novel genus within the class of the Anaerolineae. We determined the genome sequence of strain TC1, to complement its ongoing physiological characterization.

The draft genome of Anaerolineae bacterium strain TC1 was produced by constructing indexed Nextera XT sequencing libraries with 300- to 700-bp insert sizes and Nextera mate-pair (2 to 10 kb) sequencing libraries for the genomic DNA extracted from the strain. Pooled paired-end and mate-pair libraries were used for sequencing using an Illumina MiSeq instrument to generate 2 × 250-bp paired-end reads with average coverage of 50×. Mate-pair libraries were also sequenced on the MiSeq with 2 × 250-bp paired-end reads to obtain 10× coverage of the genome. Illumina sequence raw reads were merged with SeqPrep (https://github.com/jstjohn/SeqPrep) using default settings, and Illumina sequencing adapters were removed. Unmerged reads were quality trimmed and filtered using Nesoni v0.112 (https://github.com/Victorian-Bioinformatics-Consortium/nesoni). The merged and trimmed reads were assembled using SPAdes v2.5.0 (2). Further scaffolding and manual refinement of the assembly using the mate-pair data were performed as described previously (3). Annotation of the genome was performed within the Integrated Microbial Genomes (IMG) platform (4).

The final high-quality draft assembly of Anaerolineae strain TC1 genome contains 16 contigs in 3 scaffolds; average genome coverage was 60×. The genome size (3,510,630) is comparable to that of other Anaerolineae species (3.69 to 4.44 Mbp) while the G+C content (41.35%) is lower (46.82% to 57.36% for other Anaerolineae species) (5). Annotation indicated the presence of 2,793 protein-coding and 56 RNA genes; two sets of rRNA genes were identified. The vast majority of Chloroflexi-specific phylogenetic marker genes (179 out of 198 genes, 90.4%) were identified using Phyla-AMPHORA (6), indicating that the draft genome is nearly complete. We expect that the availability of a draft genome of strain TC1, together with other Anaerolineae genomes (5), will shed light on the metabolic potential and possible ecological role of members of the class Anaerolineae in different ecosystems.

Nucleotide sequence accession numbers.

The whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number BBYH00000000 for Anaerolineae bacterium strain TC1. The version described in this paper is version BBYH01000000.