The complete genome sequence of Desulfovibrio indicus J2T, a member of the family Desulfovibrionaceae, consists of 3,966,573-bp in one contig and encodes 3,461 predicted genes, 5 noncoding RNAs, 3 rRNAs operons, and 52 tRNA-encoding genes. The genome is consistent with a heterotrophic, anaerobic lifestyle including the sulfate reduction pathway.
A Gram-negative, rod-shaped, red-pink in color, and UV radiation-resistant bacterium Hymenobacter sp. strain PAMC26554 was isolated from Usnea sp., an Antarctic lichen, and belongs to the class of Cytophagia and the phylum of Bacteroidetes. The complete genome of Hymenobacter sp. PAMC26554 consists of one chromosome (5,244,843bp) with two plasmids (199,990bp and 6421bp). The genomic sequence indicates that Hymenobacter sp. strain PAMC26554 possesses several genes involved in the nucleotide excision repair pathway that protects damaged DNA. This complete genome information will help us to understand its adaptation and novel survival strategy in the Antarctic extreme cold environment. Copyright © 2016 Elsevier B.V. All rights reserved.
Mucilaginibacter sp. PAMC26640 is a xylan-degrading bacterium isolated from the Arctic lichen Stereocaulon sp. Here, we present the first complete genome sequence of Mucilaginibacter sp. strain PAMC26640, which contains several genes involved in xylan utilization. This genome information provides new insights into the genetic basis of its physiology and further analysis of key metabolic genes related to the xylan degradation pathway. Copyright © 2016. Published by Elsevier B.V.
Like many other Bacteroides species, Bacteroides vulgatus strain mpk, a mouse fecal isolate which was shown to promote intestinal homeostasis, utilizes a variety of mobile elements for genome evolution. Based on sequences collected by Pacific Biosciences SMRT sequencing technology, we discuss the challenges of assembling and studying a bacterial genome of high plasticity. Additionally, we conducted comparative genomics comparing this commensal strain with the B. vulgatus type strain ATCC 8482 as well as multiple other Bacteroides and Parabacteroides strains to reveal the most important differences and identify the unique features of B. vulgatus mpk. The genome of B. vulgatus mpk harbors a large and diverse set of mobile element proteins compared with other sequenced Bacteroides strains. We found evidence of a number of different horizontal gene transfer events and a genome landscape that has been extensively altered by different mobilization events. A CRISPR/Cas system could be identified that provides a possible mechanism for preventing the integration of invading external DNA. We propose that the high genome plasticity and the introduced genome instabilities of B. vulgatus mpk arising from the various mobilization events might play an important role not only in its adaptation to the challenging intestinal environment in general, but also in its ability to interact with the gut microbiota.
Sphingorhabdus sp. M41, capable of degrading aliphatic and aromatic hydrocarbons, was isolated from crude oil-contaminated costal sediment by an enrichment culture and its complete genome was sequenced. The genome of strain M41 has a chromosome with a size of 3,324,420bp, including 44 tRNAs, 6 rRNAs, and 3118 protein-coding genes. In addition, many potential genes responsible for the biodegradation of aliphatic and aromatic hydrocarbons were identified from the genome. This is the first complete genome of the genus Sphingorhabdus, which will provide insights into the bioremediation of crude oil-contaminated costal sediment by strain M41. Copyright © 2016. Published by Elsevier B.V.
Here, we report the first complete genome sequence of Frondihabitans sp. strain PAMC28766, which was found to consist of three plasmids, one chromosome (4,345,897bp), and a series of genes involved in carotenoid biosynthesis and nucleotide excision repair. An analysis of the Frondihabitans sp. PAMC28766 genome will improve our understanding of the carotenoid biosynthesis pathway. Furthermore, the sequence data will provide novel insight into UV radiation-resistance in extremely cold environments. Copyright © 2016 Elsevier B.V. All rights reserved.
Environmentally sensitive plant gene families like NBS-LRRs, receptor kinases, defensins and others, are known to be highly variable. However, most existing strategies for discovering and describing structural variation in complex gene families provide incomplete and imperfect results. The move to de novo genome assemblies for multiple accessions or individuals within a species is enabling more comprehensive and accurate insights about gene family variation. Earlier array-based genome hybridization and sequence-based read mapping methods were limited by their reliance on a reference genome and by misplacement of paralogous sequences. Variant discovery based on de novo genome assemblies overcome the problems arising from a reference genome and reduce sequence misplacement. As de novo genome sequencing moves to the use of longer reads, artifacts will be minimized, intact tandem gene clusters will be constructed accurately, and insights into rapid evolution will become feasible. Copyright © 2016 Elsevier Ltd. All rights reserved.
Ionizing radiation-resistant Hymenobacter sp. strain PAMC26628 was isolated from Stereocaulon sp., an Arctic lichen. Complete genome sequencing of Hymenobacter sp. PAMC26628 revealed one chromosome (5,277,381bp), one plasmid (89,596bp), and several genes involved in nucleotide excision repair, a DNA damage removal pathway. An analysis of the Hymenobacter sp. PAMC26628 genome will help us understand its evolution and provide novel insight into the adaptations that allow this organism to survive in the extreme cold of the Arctic. Copyright © 2016 Elsevier B.V. All rights reserved.
We report the complete genome sequence of Burkholderia sp. PAMC28687, which was isolated from the Antarctica lichen Useea sp., for better understanding of its catabolic traits in utilizing octopine as a source of carbon/nitrogen between Burkholderia and lichen. The genome consists of three circular chromosomes with five circular plasmids for the total 6,881,273bp sized genome with a G+C content of 58.14%. Copyright © 2016 Elsevier B.V. All rights reserved.
Thiosulfate-oxidizing Bosea sp. strain PAMC26642 was isolated from the Arctic lichen Stereocaulon sp. Complete genome sequencing of Bosea sp. PAMC26642 revealed several genes involved in thiosulfate oxidation. An analysis of the Bosea sp. PAMC26642 genome will provide novel insight into the genetic basis of its physiology and enable further analysis of key genes in the thiosulfate oxidation pathway. Copyright © 2016 Elsevier B.V. All rights reserved.
We report the complete genome sequence of Variovorax sp. strain PAMC28711 isolated from the Antarctic lichen Himantormia sp. Whole genome sequencing revealed opine oxidase- and octopine dehydrogenase-related gene clusters that are involved in octopine utilization. These data will lead to future genetic and biochemical studies on the unusual catabolic traits of opine and octopine utilization in extremely cold environments. Copyright © 2016 Elsevier B.V. All rights reserved.
Microbacterium sp. strain PAMC28756, of the family Microbacteriaceae, was isolated from Stereocaulon sp., an Antarctic lichen. Complete genome sequencing of Microbacterium sp. PAMC28756 revealed, for the first time in the genus Microbacterium, a series of key genes involved in C50 carotenoid biosynthesis. An analysis of the Microbacterium sp. PAMC28756 genome will lead to a better understanding of the carotenoid biosynthesis pathway. Furthermore, the sequence data will provide novel insight into UV radiation resistance in extremely cold environments. Copyright © 2016 Elsevier B.V. All rights reserved.
The complete genome of Salmonella entericaserovar Typhimurium strain SO3 (sequence type 302), isolated from a fatal meningitis infection in Mexico, was determined using PacBio technology. The chromosome hosts six complete prophages and is predicted to harbor 51 genomic islands, including 13 pathogenicity islands (SPIs). It carries the Salmonella virulence plasmid (pSTV). Copyright © 2016 Vinuesa et al.
A genome of 5.88Mb with 46.83% G+C content is reported for an endoglucanase-producing bacterium Paenibacillus sp. strain IHB B 3084 isolated from the cold environments of the Indian Trans-Himalayas. The psychrotrophic bacterium produces low-temperature active and alkaline-stable endoglucanases of industrial importance. The genomic data has provided insight into genomic basis of cellulase production and survival of the bacterium in the cold environments. Copyright © 2016. Published by Elsevier B.V.
Here, we report the complete genome sequence of Streptomyces venezuelae ATCC 15439, a producer of the methymycin/pikromycin family of macrolide antibiotics and a model host for natural product studies, obtained exclusively using PacBio sequencing technology. The 9.03-Mbp genome harbors 8,775 genes and 11 polyketide and nonribosomal peptide natural product gene clusters. Copyright © 2016 He et al.
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