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Asset Tag: Complete genome

July 7, 2019

Genome mining of astaxanthin biosynthetic genes from Sphingomonas sp. ATCC 55669 for heterologous overproduction in Escherichia coli.

As a highly valued keto-carotenoid, astaxanthin is widely used in nutritional supplements and pharmaceuticals. Therefore, the demand for biosynthetic astaxanthin and improved efficiency of astaxanthin biosynthesis has driven the investigation of metabolic engineering of native astaxanthin producers and heterologous hosts. However, microbial resources for astaxanthin are limited. In this study, we found that the a-Proteobacterium Sphingomonas sp. ATCC 55669 could produce astaxanthin naturally. We used whole-genome sequencing to identify the astaxanthin biosynthetic pathway using a combined PacBio-Illumina approach. The putative astaxanthin biosynthetic pathway in Sphingomonas sp. ATCC 55669 was predicted. For further confirmation, a high-efficiency targeted engineering carotenoid synthesis platform was constructed in E. coli for identifying the functional roles of candidate genes. All genes involved in astaxanthin biosynthesis showed discrete distributions on the chromosome. Moreover, the overexpression of exogenous E. coli idi in Sphingomonas sp. ATCC 55669 increased astaxanthin production by 5.4-fold. This study described a new astaxanthin producer and provided more biosynthesis components for bioengineering of astaxanthin in the future. © 2015 The Authors. Biotechnology Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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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

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

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

Complete genome sequence of Acinetobacter baumannii XH386 (ST208), a multi-drug resistant bacteria isolated from pediatric hospital in China.

Acinetobacter baumannii is an important bacterium that emerged as a significant nosocomial pathogen worldwide. The rise of A. baumannii was due to its multi-drug resistance (MDR), while it was difficult to treat multi-drug resistant A. baumannii with antibiotics, especially in pediatric patients for the therapeutic options with antibiotics were quite limited in pediatric patients. A. baumannii ST208 was identified as predominant sequence type of carbapenem resistant A. baumannii in the United States and China. As we knew, there was no complete genome sequence reproted for A. baumannii ST208, although several whole genome shotgun sequences had been reported. Here, we sequenced the 4087-kilobase (kb) chromosome and 112-kb plasmid of A. baumannii XH386 (ST208), which was isolated from a pediatric hospital in China. The genome of A. baumannii XH386 contained 3968 protein-coding genes and 94 RNA-only encoding genes. Genomic analysis and Minimum inhibitory concentration assay showed that A. baumannii XH386 was multi-drug resistant strain, which showed resistance to most of antibiotics, except for tigecycline. The data may be accessed via the GenBank accession number CP010779 and CP010780.

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July 7, 2019

Long read and single molecule DNA sequencing simplifies genome assembly and TAL effector gene analysis of Xanthomonas translucens.

The species Xanthomonas translucens encompasses a complex of bacterial strains that cause diseases and yield loss on grass species including important cereal crops. Three pathovars, X. translucens pv. undulosa, X. translucens pv. translucens and X. translucens pv.cerealis, have been described as pathogens of wheat, barley, and oats. However, no complete genome sequence for a strain of this complex is currently available.A complete genome sequence of X. translucens pv. undulosa strain XT4699 was obtained by using PacBio long read, single molecule, real time (SMRT) DNA sequences and Illumina sequences. Draft genome sequences of nineteen additional X. translucens strains, which were collected from wheat or barley in different regions and at different times, were generated by Illumina sequencing. Phylogenetic relationships among different Xanthomonas strains indicates that X. translucens are members of a distinct clade from so-called group 2 xanthomonads and three pathovars of this species, undulosa, translucens and cerealis, represent distinct subclades in the group 1 clade. Knockout mutation of type III secretion system of XT4699 eliminated the ability to cause water-soaking symptoms on wheat and barley and resulted in a reduction in populations on wheat in comparison to the wild type strain. Sequence comparison of X. translucens strains revealed the genetic variation on type III effector repertories among different pathovars or within one pathovar. The full genome sequence of XT4699 reveals the presence of eight members of the Transcription-Activator Like (TAL) effector genes, which are phylogenetically distant from previous known TAL effector genes of group 2 xanthomonads. Microarray and qRT-PCR analyses revealed TAL effector-specific wheat gene expression modulation.PacBio long read sequencing facilitates the assembly of Xanthomonas genomes and the multiple TAL effector genes, which are difficult to assemble from short read platforms. The complete genome sequence of X. translucens pv. undulosa strain XT4699 and draft genome sequences of nineteen additional X. translucens strains provides a resource for further genetic analyses of pathogenic diversity and host range of the X. translucens species complex. TAL effectors of XT4699 strain play roles in modulating wheat host gene expressions.

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July 7, 2019

Complete genome of brown algal polysaccharides-degrading Pseudoalteromonas issachenkonii KCTC 12958(T) (=KMM 3549(T)).

Pseudoalteromonas issachenkonii is a Gram-negative, rod-shaped, flagellated, aerobic, chemoorganotrophic marine bacterium that was isolated from the thallus of Fucus evanescens (marine brown macroalgae) sampled from the Kraternaya Bight of the Kurile Islands in the Pacific Ocean. Here, we report the complete genome of P. issachenkonii KCTC 12958(T) (=KMM 3549(T)=LMG 19697(T)=CIP 106858(T)), which consists of 4,131,541bp (G+C content of 40.3%) with two chromosomes, 3538 protein-coding genes, 102 tRNAs and 8 rRNA operons. Several genes related to glycoside hydrolases, proteases, and bacteriolytic- and hemolytic activities were detected in the genome that help explain how the strain mediates degradation of algal cell wall and decomposes algal polysaccharides into industrially applicable products. Copyright © 2015 Elsevier B.V. All rights reserved.

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