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July 7, 2019  |  

MethSMRT: an integrative database for DNA N6-methyladenine and N4-methylcytosine generated by single-molecular real-time sequencing

DNA methylation is an important type of epigenetic modifications, where 5- methylcytosine (5mC), 6-methyadenine (6mA) and 4-methylcytosine (4mC) are the most common types. Previous efforts have been largely focused on 5mC, providing invaluable insights into epigenetic regulation through DNA methylation. Recently developed single-molecule real-time (SMRT) sequencing technology provides a unique opportunity to detect the less studied DNA 6mA and 4mC modifications at single-nucleotide resolution. With a rapidly increased amount of SMRT sequencing data generated, there is an emerging demand to systematically explore DNA 6mA and 4mC modifications from these data sets. MethSMRT is the first resource hosting DNA 6mA and 4mC methylomes. All the data sets were processed using the same analysis pipeline with the same quality control. The current version of the database provides a platform to store, browse, search and download epigenome-wide methylation profiles of 156 species, including seven eukaryotes such as Arabidopsis, C. elegans, Drosophila, mouse and yeast, as well as 149 prokaryotes. It also offers a genome browser to visualize the methylation sites and related information such as single nucleotide polymorphisms (SNP) and genomic annotation. Furthermore, the database provides a quick summary of statistics of methylome of 6mA and 4mC and predicted methylation motifs for each species. MethSMRT is publicly available at http://sysbio.sysu.edu.cn/methsmrt/ without use restriction.

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July 7, 2019  |  

Complete genome sequence of a bacterium representing a deep uncultivated lineage within the Gammaproteobacteria associated with the degradation of polycyclic aromatic hydrocarbons.

The bacterial strain TR3.2, representing a novel deeply branching lineage within the Gammaproteobacteria, was isolated and its genome sequenced. This isolate is the first cultivated representative of the previously described “Pyrene Group 2” (PG2) and represents a variety of environmental sequences primarily associated with petrochemical contamination and aromatic hydrocarbon degradation. Copyright © 2016 Singleton et al.

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July 7, 2019  |  

Comparative genomics of biotechnologically important yeasts.

Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.

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July 7, 2019  |  

An improved high-quality draft genome sequence of Carnobacterium inhibens subsp. inhibens strain K1(T).

Despite their ubiquity and their involvement in food spoilage, the genus Carnobacterium remains rather sparsely characterized at the genome level. Carnobacterium inhibens K1(T) is a member of the Carnobacteriaceae family within the class Bacilli. This strain is a Gram-positive, rod-shaped bacterium isolated from the intestine of an Atlantic salmon. The present study determined the genome sequence and annotation of Carnobacterium inhibens K1(T). The genome comprised 2,748,608 bp with a G?+?C content of 34.85 %, which included 2621 protein-coding genes and 116 RNA genes. The strain contained five contigs corresponding to presumptive plasmids of sizes: 19,036; 24,250; 26,581; 65,272; and 65,904 bp.

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July 7, 2019  |  

Near-complete genome sequence of Thalassospira sp. strain KO164 isolated from a lignin-enriched marine sediment microcosm.

Thalassospira sp. strain KO164 was isolated from eastern Mediterranean seawater and sediment laboratory microcosms enriched on insoluble organosolv lignin under oxic conditions. The near-complete genome sequence presented here will facilitate analyses into this deep-ocean bacterium’s ability to degrade recalcitrant organics such as lignin. Copyright © 2016 Woo et al.

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July 7, 2019  |  

Serinibacter

The genus Serinibacter belongs, based on the phylogenetic analysis of the nearly full-length 16S rRNA gene, to the Beutenbergiaceae together with the genera Beutenbergia, Salana, and Miniimonas. The two species of the genus Serinibacter shared 99.6% 16S rRNA gene sequence similarity but low DNA DNA relatedness. Cells are irregular rods, Gram-stain positive, not acid-fast. Endospores are not formed. Nonmotile. Aerobic to anaerobic. Oxidase-negative, catalase-positive. The peptidoglycan type is A4a with an l-Ser residue at position 1 of the peptide subunit. The acyl type is acetyl. The major cell-wall sugar is galactose. The predominant menaquinone is MK-8(H4). The major polar lipids consist of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, and unidentified phospholipids. Phosphatidylethanolamine is absent. The cellular fatty acid profile is dominated by the occurrence of iso- and anteiso-branched-chain acids. Mycolic acids are absent. The genomic G+C content is 70.7 to 72.8 mol%.

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July 7, 2019  |  

Genome sequencing to develop Paenibacillus donghaensis strain JH8T (KCTC 13049T=LMG 23780T) as a microbial fertilizer and correlation to its plant growth-promoting phenotype

Paenibacillus donghaensis JH8T (KCTC 13049T=LMG 23780T) is a Gram-positive, mesophilic, endospore-forming bacterium isolated from East Sea sediment at depth of 500m in Korea. The strain exhibited plant cell wall hydrolytic and plant growth promoting abilities. The complete genome of P. donghaensis strain JH8T contains 7602 protein-coding sequences and an average GC content of 49.7% in its chromosome (8.54Mbp). Genes encoding proteins related to the degradation of plant cell wall, nitrogen-fixation, phosphate solubilization, and synthesis of siderophore were existed in the P. donghaensis strain JH8T genome, indicating that this strain can be used as an eco-friendly microbial agent for increasing agricultural productivity.

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July 7, 2019  |  

Strategies for high-altitude adaptation revealed from high-quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01.

A light pink coloured bacterial strain ERGS5:01 isolated from glacial stream water of Sikkim Himalaya was affiliated to Janthinobacterium lividum based on 16S rRNA gene sequence identity and phylogenetic clustering. Whole genome sequencing was performed for the strain to confirm its taxonomy as it lacked the typical violet pigmentation of the genus and also to decipher its survival strategy at the aquatic ecosystem of high elevation. The PacBio RSII sequencing generated genome of 5,168,928 bp with 4575 protein-coding genes and 118 RNA genes. Whole genome-based multilocus sequence analysis clustering, in silico DDH similarity value of 95.1% and, the ANI value of 99.25% established the identity of the strain ERGS5:01 (MCC 2953) as a non-violacein producing J. lividum. The genome comparisons across genus Janthinobacterium revealed an open pan-genome with the scope of the addition of new orthologous cluster to complete the genomic inventory. The genomic insight provided the genetic basis of freezing and frequent freeze-thaw cycle tolerance and, for industrially important enzymes. Extended insight into the genome provided clues of crucial genes associated with adaptation in the harsh aquatic ecosystem of high altitude.

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July 7, 2019  |  

Complete genome sequence of Celeribacter baekdonensis strain LH4, a thiosulfate-oxidizing alphaproteobacterial isolate from Gulf of Mexico continental slope sediments.

We report here the closed genome sequences of Celeribacter baekdonensis strain LH4 and five unnamed plasmids obtained through PacBio sequencing with 99.99% consensus concordance. The genomes contained several distinctive features not found in other published Celeribacter genomes, including the potential to aerobically degrade styrene and other phenolic compounds. Copyright © 2018 Flood et al.

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July 7, 2019  |  

New reference genome sequences for 17 bacterial strains of the honey bee gut microbiota.

We sequenced the genomes of 17 strains isolated from the gut of honey bees, including strains representing the genera Lactobacillus, Bifidobacterium, Gilliamella, Snodgrassella, Frischella, and Commensalibacter. These genome sequences represent an important step forward in the development of a comprehensive reference database to aid future analysis of this emerging gut microbiota model.

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