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Asset Tag: Pacific Biosciences

July 7, 2019

Complete genome sequence of deoxynivalenol-degrading bacterium Devosia sp. strain A16.

The strain A16, capable of degrading deoxynivalenol was isolated from a wheat field and identified preliminarily as Devosia sp. Here, we present the genome sequence of the Devosia sp. A16, which has a size of 5,032,994bp, with 4913 coding sequences (CDSs). The annotated full genome sequence of the Devosia sp. A16 strain might shed light on the function of its degradation. Copyright © 2015 Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome sequence of Hymenobacter sp. DG25B, a novel bacterium with gamma-radiation resistance isolated from soil in South Korea.

A Gram-negative, rod-shaped, non-motile, gamma and UV radiation resistant bacterium Hymenobacter radioresistens DG25B was isolated from a soil sample collected in South Korea. The complete genome sequence of H. radioresistens DG25B consists of one circular chromosome (3,874,646bp). The bacterium was isolated from gamma ray irradiated soil and contains the genomic features of enzymes involved in the nucleotide excision repair (NER) pathway that protect the damaged DNA. The genome also contains other genes involved in the efficient removal of double-strand breaks (DSB) caused by the ionizing radiations. Copyright © 2015 Elsevier B.V. All rights reserved.

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July 7, 2019

Novel FANCI mutations in Fanconi anemia with VACTERL association.

Fanconi anemia (FA) is an inherited bone marrow failure syndrome caused by mutations in DNA repair genes; some of these patients may have features of the VACTERL association. Autosomal recessive mutations in FANCI are a rare cause of FA. We identified FANCI mutations by next generation sequencing in three patients in our FA cohort among several whose mutated gene was unknown. Four of the six mutations are novel and all mutations are likely deleterious to protein function. There are now 16 reported cases of FA due to FANCI of whom 7 have at least 3 features of the VACTERL association (44%). This suggests that the VACTERL association in patients with FA may be seen in patients with FANCI mutations more often than previously recognized. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

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July 7, 2019

Complete genome sequence of the Variibacter gotjawalensis GJW-30(T) from soil of lava forest, Gotjawal.

Variibacter gotjawalensis GJW-30(T) is a gram-negative, strictly aerobic bacterium to form pleomorphic. Here we present the 4.5-Mb genome sequence of the type strain of V. gotjawalensis GJW-30(T), which consists a chromosome for the total 4,586,237bp with a G+C content of 62.2mol%. This is the first report of the full genome sequence of a species of the novel genus Variibacter isolated from Gotjawal, a unique area in Jeju, Republic of Korea. Copyright © 2015 Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome of Pseudoalteromonas phenolica KCTC 12086(T) (= O-BC30(T)), a marine bacterium producing polybrominated aromatic compounds.

Pseudoalteromonas phenolica is a Gram-negative, rod-shaped, flagellated, aerobic, antibiotic-producing bacterium that was isolated from seawater off Ogasawara Island, Japan. Here, we report the complete genome of P. phenolica KCTC 12086(T) (= O-BC30(T)), which consists of 4,868,993 bp (G+C content of 40.6%) with two chromosomes, 4168 protein-coding genes, 113 tRNAs and 9 rRNA operons. In addition, several genes related to phenolic anti-methicillin-resistant Staphylococcus aureus substances were detected in the genome suggesting that biosynthesis of industrially important polybrominated aromatic compounds could be better understood with the availability of genome data of P. phenolica. Copyright © 2015 Elsevier B.V. All rights reserved.

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July 7, 2019

hybridSPAdes: an algorithm for hybrid assembly of short and long reads.

Recent advances in single molecule real-time (SMRT) and nanopore sequencing technologies have enabled high-quality assemblies from long and inaccurate reads. However, these approaches require high coverage by long reads and remain expensive. On the other hand, the inexpensive short reads technologies produce accurate but fragmented assemblies. Thus, a hybrid approach that assembles long reads (with low coverage) and short reads has a potential to generate high-quality assemblies at reduced cost.We describe hybridSPAdes algorithm for assembling short and long reads and benchmark it on a variety of bacterial assembly projects. Our results demonstrate that hybridSPAdes generates accurate assemblies (even in projects with relatively low coverage by long reads) thus reducing the overall cost of genome sequencing. We further present the first complete assembly of a genome from single cells using SMRT reads.hybridSPAdes is implemented in C++?as a part of SPAdes genome assembler and is publicly available at http://bioinf.spbau.ru/en/spades CONTACT: d.antipov@spbu.ruSupplementary information: supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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July 7, 2019

Complete genome sequence of Massilia sp. WG5, an efficient phenanthrene-degrading bacterium from soil.

Massilia sp. strain WG5 is a phenanthrene-degrading bacterium isolated from polycyclic aromatic hydrocarbons contaminated soil in Jiangsu, China. Here we present the features of the strain WG5 and its complete genome sequenced by two SMRTs-cell of PacBio RS II and corrected by Miseq. The genome contains one circular chromosome and two plasmids, which is including 6,049,576 nucleotides with 65.51% G+C content, 5,140 protein-coding genes, 111 RNA genes. Copyright © 2015 Elsevier B.V. All rights reserved.

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July 7, 2019

Timing, rates and spectra of human germline mutation.

Germline mutations are a driving force behind genome evolution and genetic disease. We investigated genome-wide mutation rates and spectra in multi-sibling families. The mutation rate increased with paternal age in all families, but the number of additional mutations per year differed by more than twofold between families. Meta-analysis of 6,570 mutations showed that germline methylation influences mutation rates. In contrast to somatic mutations, we found remarkable consistency in germline mutation spectra between the sexes and at different paternal ages. In parental germ line, 3.8% of mutations were mosaic, resulting in 1.3% of mutations being shared by siblings. The number of these shared mutations varied significantly between families. Our data suggest that the mutation rate per cell division is higher during both early embryogenesis and differentiation of primordial germ cells but is reduced substantially during post-pubertal spermatogenesis. These findings have important consequences for the recurrence risks of disorders caused by de novo mutations.

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July 7, 2019

The complete chloroplast genome of Gentiana straminea (Gentianaceae), an endemic species to the Sino-Himalayan subregion.

Endemic to the Sino-Himalayan subregion, the medicinal alpine plant Gentiana straminea is a threatened species. The genetic and molecular data about it is deficient. Here we report the complete chloroplast (cp) genome sequence of G. straminea, as the first sequenced member of the family Gentianaceae. The cp genome is 148,991bp in length, including a large single copy (LSC) region of 81,240bp, a small single copy (SSC) region of 17,085bp and a pair of inverted repeats (IRs) of 25,333bp. It contains 112 unique genes, including 78 protein-coding genes, 30 tRNAs and 4 rRNAs. The rps16 gene lacks exon2 between trnK-UUU and trnQ-UUG, which is the first rps16 pseudogene found in the nonparasitic plants of Asterids clade. Sequence analysis revealed the presence of 13 forward repeats, 13 palindrome repeats and 39 simple sequence repeats (SSRs). An entire cp genome comparison study of G. straminea and four other species in Gentianales was carried out. Phylogenetic analyses using maximum likelihood (ML) and maximum parsimony (MP) were performed based on 69 protein-coding genes from 36 species of Asterids. The results strongly supported the position of Gentianaceae as one member of the order Gentianales. The complete chloroplast genome sequence will provide intragenic information for its conservation and contribute to research on the genetic and phylogenetic analyses of Gentianales and Asterids. Copyright © 2015 Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome sequence of an aromatic compound degrader Arthrobacter sp. YC-RL1.

Arthrobacter sp. YC-RL1, isolated from a petroleum-contaminated soil, is capable of degrading and utilizing a wide range of aromatic compounds for growth. Here we report the complete genome sequence of strain YC-RL1, which may facilitate the investigation of environmental bioremediation and provide new gene resources for biotechnology and gene engineering. Copyright © 2015 Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome sequence of Celeribacter marinus IMCC12053(T), the host strain of marine bacteriophage P12053L.

Isolated from coastal seawater from Yellow Sea of Korea, Celeribacter marinus IMCC12053 was used as the host bacterium for bacteriophage P12053L. Here we report the complete genome sequence of strain IMCC12053 for further study of the marine bacteriophage P12053L functional genes. Single molecule real-time technology (PacBio RSII) was used for the single circular chromosome that is 3,096,705 base pairs in length and the GC content is 56.24%. It contains 3155 ORFs with 45 tRNAs and 6 rRNAs genes. N(6)-methyladenosine patterns were also investigated for 32 unmethylated genes and intergenic regions that covered many regulators and phage genes as well as ribosomal RNA genes and tRNA genes. Cryptic N(4)-methylcytosine pattern was investigated to speculate GpC methylase activity throughout the genome. Comparative genomics with other Celeribacter genomes were carried out for polyaromatic hydrocarbon degradation, but there were no aromatic ring oxygenases in IMCC12053 when compared to Celeribacter indicus P73. Copyright © 2015 Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome sequence of Agarivorans gilvus WH0801(T), an agarase-producing bacterium isolated from seaweed.

Agarivorans gilvus WH0801(T), an agarase-producing bacterium, was isolated from the surface of seaweed. Here, we present the complete genome sequence, which consists of one circular chromosome of 4,416,600bp with a GC content of 45.9%. This genetic information will provide insight into biotechnological applications of producing agar for food and industry. Copyright © 2015 Elsevier B.V. All rights reserved.

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July 7, 2019

CauloBrowser: A systems biology resource for Caulobacter crescentus.

Caulobacter crescentus is a premier model organism for studying the molecular basis of cellular asymmetry. The Caulobacter community has generated a wealth of high-throughput spatiotemporal databases including data from gene expression profiling experiments (microarrays, RNA-seq, ChIP-seq, ribosome profiling, LC-ms proteomics), gene essentiality studies (Tn-seq), genome wide protein localization studies, and global chromosome methylation analyses (SMRT sequencing). A major challenge involves the integration of these diverse data sets into one comprehensive community resource. To address this need, we have generated CauloBrowser (www.caulobrowser.org), an online resource for Caulobacter studies. This site provides a user-friendly interface for quickly searching genes of interest and downloading genome-wide results. Search results about individual genes are displayed as tables, graphs of time resolved expression profiles, and schematics of protein localization throughout the cell cycle. In addition, the site provides a genome viewer that enables customizable visualization of all published high-throughput genomic data. The depth and diversity of data sets collected by the Caulobacter community makes CauloBrowser a unique and valuable systems biology resource.© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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July 7, 2019

OxyR-dependent formation of DNA methylation patterns in OpvABOFF and OpvABON cell lineages of Salmonella enterica.

Phase variation of the Salmonella enterica opvAB operon generates a bacterial lineage with standard lipopolysaccharide structure (OpvAB(OFF)) and a lineage with shorter O-antigen chains (OpvAB(ON)). Regulation of OpvAB lineage formation is transcriptional, and is controlled by the LysR-type factor OxyR and by DNA adenine methylation. The opvAB regulatory region contains four sites for OxyR binding (OBSA-D), and four methylatable GATC motifs (GATC1-4). OpvAB(OFF) and OpvAB(ON) cell lineages display opposite DNA methylation patterns in the opvAB regulatory region: (i) in the OpvAB(OFF) state, GATC1 and GATC3 are non-methylated, whereas GATC2 and GATC4 are methylated; (ii) in the OpvAB(ON) state, GATC2 and GATC4 are non-methylated, whereas GATC1 and GATC3 are methylated. We provide evidence that such DNA methylation patterns are generated by OxyR binding. The higher stability of the OpvAB(OFF) lineage may be caused by binding of OxyR to sites that are identical to the consensus (OBSA and OBSc), while the sites bound by OxyR in OpvAB(ON) cells (OBSB and OBSD) are not. In support of this view, amelioration of either OBSB or OBSD locks the system in the ON state. We also show that the GATC-binding protein SeqA and the nucleoid protein HU are ancillary factors in opvAB control.© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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