Complete Genome Sequence of the Halophilic Methylotrophic Methanogen Archaeon Methanohalophilus portucalensis Strain FDF-1^T

ABSTRACT

We report here the complete genome sequence (2.08 Mb) of Methanohalophilus portucalensis strain FDF-1^T, a halophilic methylotrophic methanogen isolated from the sediment of a saltern in Figeria da Foz, Portugal. The average nucleotide identity and DNA-DNA hybridization analyses show that Methanohalophilus mahii, M. halophilus, and M. portucalensis are three different species within the Methanosarcinaceae family.

GENOME ANNOUNCEMENT

Methanohalophilus portucalensis strain FDF-1^T (DSM 7471^T, OCM 59) was described as a new species by Boone et al. (1). The strictly anaerobic species is able to produce methane by reducing methyl compounds and grows optimally at 40°C within a pH range of 6.5 to 7.5 and a salinity range of 0.5 to 2 M NaCl.

The complete genome of M. portucalensis was sequenced using a combination of the following three sequencing approaches: a 300-bp paired-end library sequenced on an Illumina MiSeq platform (Bioscience Core Lab, KAUST, Thuwal, Saudi Arabia), a 100-bp paired-end library sequenced on an Illumina HiSeq platform (Beckman Coulter Genomics, Inc., Danvers, MA, USA), and a PacBio RS library (Genotoul, Toulouse, France). The 13,835,892 paired reads of 300 bp were quality trimmed (Q30) and de novo assembled into contigs using SPAdes version 3.6.1 (2). The 17 resulting contigs were then scaffolded with SSPACE version 3.0 (3) using the 60,686,211 paired-end reads of 100 bp, leading to an intermediate version of the assemblage containing 9 scaffolds. A final scaffolding step was performed with SSPACE LongRead version 1.1 (4) using the 317,258 PacBio RS-filtered subreads. We finally obtained 3 scaffolds with a total size of 2,084,275 bp (without an unspecified base) and an average coverage of approximately 5,300×. Finally, a fully circularized version of the genome with expected gaps between oriented scaffolds was produced after comparison with the M. mahii genome using CONTIGuator (5).

The M. portucalensis genome consists of a circular chromosome of 2,084,875 bp with a GC content of 41.95%. A total of 2,198 coding DNA sequences were identified with the MaGe platform (6, 7), as well as 2 6S-23S operons, 3 5S rRNAs, 46 tRNAs, and 4 miscellaneous RNAs.

The M. portucalensis genome size is close to that of M. mahii strain SLP^T (2,012,424 bp) (8) and M. halophilus strain Z-7982 (2,022,959 bp) (9). M. mahii, M. halophilus, and M. portucalensis are physiologically very similar, and their separation into three different species was previously based on DNA reassociation and electrophoretic analysis of whole-cell proteins and on the need to maintain the genus Methanohalophilus for taxonomic stability (1). The average nucleotide identity (ANI) scores are 92.59% (SD, 2.91) between M. halophilus and M. portucalensis, 92.59% (SD, 2.91) between M. halophilus and M. mahii, and 92.59% (SD, 2.91) between M. mahii and M. portucalensis. An ANI score below 95% has been defined for the delineation of a new species (10). Thus, the ANI score comparisons indicate that the three strains are on the boundary of the species delineation. Afterward, we calculated the in silico DNA-DNA hybridization (DDH) values using the genome-to-genome distance calculator GGDC2.1 (11), which indicated values of 44.8% between M. halophilus and M. mahii, 44.4% between M. portucalensis and M. mahii, and 50.50% between M. halophilus and M. mahii. The ANI and DDH values confirm that M. mahii, M. halophilus, and M. portucalensis represent three phylogenetically closely related species.

Accession number(s).

This whole-genome sequence has been deposited at GenBank under the accession number CP017881.