Comparative Analysis of <i>Lacinutrix</i> Genomes and Their Association with Bacterial Habitat

<div><p>The genus <i>Lacinutrix</i>, which belongs to the family <i>Flavobacteriaceae</i>, consists of seven bacterial species that were mainly isolated from marine life and sediments. As most bacteria in the family <i>Flavobacteriaceae</i> favor aerobic conditions, the seven bacterial species in the genus <i>Lacinutrix</i> also showed aerobic growth. We selected four monophyletic bacterial species living in a polar environment. Two of these species were isolated from sediment and two types were isolated from algae. In a comparative analysis, we investigated how these different environments were related to genomic features of these four species in the genus <i>Lacinutrix</i>. We found that the gene sets for glycolysis, the Krebs cycle, and oxidative phosphorylation were conserved in these four type strains. However, the presence of nitrous oxide reductase for denitrification and the absence of essential components related to thiamin biosynthesis for aerobic respiration were only found in isolates from sediment. Elevated bacterial metabolism on the surface of marine sediments might limit the oxygen penetration into sediment, and such an environment might affect the genomes of bacteria isolated from these habitats.</p></div

Draft genome annotation statistics.

<p>Draft genome annotation statistics.</p

Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences showing the relationships of <i>Lacinutrix</i> species and other closely related members of the family <i>Flavobacteriaceae</i>.

<p>Bootstrap values (>60%) based on 1,000 resamplings are shown above the nodes. Bar, 0.01 substitution per nucleotide position. <i>Flavobacterium fluvii</i> H7 was used as the outgroup.</p

An overview of the predicted central metabolism and respiration pathways of the four type strains.

<p>Red arrows and text show genes absent in bacteria isolated from sediments. White arrows indicate the genes gained by bacteria isolated from sediment. Green arrows denote genes lost from PAMC 27137^T. Amino acids are shown in violet</p

General genomic features of the four <i>Lacinutrix</i> species.

<p>(A) The number of coding DNA sequences (CDS) in each bacterial subsystem and the number of roles they perform, (B) the number of genes by bacterial subsystem (shown in red text) are the bacterial subsystems that have a relatively small number of genes in PAMC 27137^T compared to that in other <i>Lacinutrix</i>. (C) The similarity of CDS among the four type strains was calculated using BLASTp</p

<i>Lacinutrix</i> genome assembly statistics.

<p><i>Lacinutrix</i> genome assembly statistics.</p

Venn diagram showing the overlap in the gene families of the four type strains.

<p>In strains from sediment and algae, 5 and 12 GO terms were significantly enriched, respectively</p

Advantages of Single-Molecule Real-Time Sequencing in High-GC Content Genomes

<div><p>Next-generation sequencing has become the most widely used sequencing technology in genomics research, but it has inherent drawbacks when dealing with high-GC content genomes. Recently, single-molecule real-time sequencing technology (SMRT) was introduced as a third-generation sequencing strategy to compensate for this drawback. Here, we report that the unbiased and longer read length of SMRT sequencing markedly improved genome assembly with high GC content via gap filling and repeat resolution.</p></div

AMP activity against <i>Psychrobacter</i> sp. <i>PAMC 25501</i>, <i>Flavobacteria</i> sp. PAMC 22217, and <i>Lacinutrix algicola</i> AKS293^T.

<p>AMP activity against <i>Psychrobacter</i> sp. <i>PAMC 25501</i>, <i>Flavobacteria</i> sp. PAMC 22217, and <i>Lacinutrix algicola</i> AKS293^T.</p

Microbial strains and culture conditions.

<p>Microbial strains and culture conditions.</p