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Asset Tag: Industrial biotechnology

July 7, 2019

Whole genome de novo sequencing and genome annotation of the world popular cultivated edible mushroom, Lentinula edodes.

Lentinula edodes, the popular shiitake mushroom, is one of the most important cultivated edible mushrooms. It is used as a food and for medicinal purposes. Here, we present the 46.1Mb draft genome of L. edodes, comprising 13,028 predicted gene models. The genome assembly consists of 31 scaffolds. Gene annotation provides key information about various signaling pathways and secondary metabolites. This genomic information should help establish the molecular genetic markers for MAS/MAB and increase our understanding of the genome structure and function. Copyright © 2016 Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome sequence of opine-utilizing Variovorax sp. strain PAMC28711 isolated from an Antarctic lichen.

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.

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July 7, 2019

Complete genome sequence of carotenoid-producing Microbacterium sp. strain PAMC28756 isolated from an Antarctic lichen.

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.

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July 7, 2019

Complete genome sequence of Pedobacter cryoconitis PAMC 27485, a CRISPR-Cas system-containing psychrophile isolated from Antarctica.

Pedobacter cryoconitis PAMC 27485, an aerobic, Gram-negative, facultatively psychrophilic bacterium, was isolated from Antarctic soil. Here we report the complete genome of P. cryoconitis PAMC 27485, which contains a type II CRISPR-Cas system and genes encoding useful enzymes (e.g. proteases). The genome sequence of P. cryoconitis PAMC 27485 could provide insights into its adaptive immune system against foreign genetic elements and biotechnological potential. Copyright © 2016 Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome sequence of Deinococcus actinosclerus BM2(T), a bacterium with Gamma-radiation resistance isolated from soil in South Korea.

A Gram-positive, short-rod shaped and non-motile bacterium Deinococcus actinosclerus BM2(T), resistant to gamma and UV radiation, was isolated from a soil sample collected in South Korea. Strain BM2(T) showed high resistance to gamma radiation with D10 value of 9 kGy. The complete genome of D. actinosclerus BM2(T) consists of a single chromosome (3,264,334bp). The genome features showed the presence of intracellular proteases that help to eliminate radiation-induced ROS during recovery from ionizing radiation damage. Copyright © 2016 Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome sequence of a psychotrophic Arthrobacter strain A3 (CGMCC 1.8987), a novel long-chain hydrocarbons producer.

Arthrobacter strain A3, a psychotrophic bacterium isolated from the Tian Shan Mountain of China, can degrade the cellulose and synthesis the long-chain hydrocarbons efficiently in low temperature. Here we report the complete genome sequence of this bacterium. The complete genome sequence of Arthrobacter strain A3, consisting of a cycle chromosome with a size of 4.26 Mbp and a cycle plasmid with a size of 194kbp. In this genome, a hydrocarbon biosynthesis gene cluster (oleA, oleB/oleC and oleD) was identified. To resistant the extreme environment, this strain contains a unique mycothiol-biosynthetic pathway (mshA-D), which has not been found in other Arthrobacter species before. The availability of this genome sequence allows us to investigate the genetic basis of adaptation to growth in a nutrient-poor permafrost environment and to evaluate of the biofuel-synthetic potential of this species. Copyright © 2016. Published by Elsevier B.V.

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July 7, 2019

Cloning of the ?-secalin gene family in a wheat 1BL/1RS translocation line using BAC clone sequencing

Wheat 1BL/1RS translocation lines are planted around the world for their disease resistance and high yield. Most of them are poor in bread making, which is partially caused by ?-secalins that are encoded by the ?-secalin gene family, which is located on the short arm of rye chromosome 1R (1RS). However, information on the structure and evolution of the ?-secalin gene family is still limited.

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July 7, 2019

Genome sequence of the nicotine-degrading Agrobacterium tumefaciens S33.

Agrobacterium tumefaciens S33 is capable of growing with nicotine as the sole source of carbon and nitrogen, and has the potential to dispose of tobacco wastes and transform nicotine into functionalized pyridines intermediates, which are important precursors for some valuable drugs and insecticides. Here we report the complete genome sequence of strain S33 and predict the gene cluster involved in nicotine catabolism according to the annotation. Copyright © 2016 Elsevier B.V. All rights reserved.

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July 7, 2019

Genome sequence of Aeromicrobium erythreum NRRL B-3381, an erythromycin-producing bacterium of the Nocardioidaceae.

Aeromicrobium erythreumNRRL B-3381 has a 3,629,239-bp circular genome that has 72% G+C content. There are at least 3,121 coding sequences (CDSs), two rRNA gene operons, and 47 tRNAs. The genome and erythromycin (ery) biosynthetic gene sequences provide resources for metabolic and combinatorial engineering of polyketides. Copyright © 2016 Harrell and Miller.

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July 7, 2019

Complete genome sequence of a low-temperature active and alkaline-stable endoglucanase-producing Paenibacillus sp. strain IHB B 3084 from the Indian Trans-Himalayas.

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.

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July 7, 2019

De novo assembly of complete genome sequence of Planococcus kocurii ATCC 43650(T), a potential plant growth promoting bacterium.

Planococcus kocurii ATCC 43650(T) is a halotolerant and psychrotolerant bacterium isolated from the skin of a North sea cod. Here, we present the first complete genome and annotation of P. kocurii ATCC 43650(T), identifying its potential as a plant growth promoting bacterium and its capability in the biosynthesis of butanol. Copyright © 2016 Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome sequence of Lactobacillus plantarum ZJ95, a potential probiotic strain producing bacteriocins and B-group vitamin riboflavin.

Lactobacillus plantarum ZJ95 is a potential probiotic isolated from newborn infant fecal and it is identified to produce riboflavin with great antimicrobial activity. The complete genome sequence of this strain was reported in the present study. The genome contains a 3,261,418-bp chromosome and two plasmids. Genes, related to the biosynthesis of bacteriocins and riboflavin, were identified. This work will facilitate to reveal the biosynthetic mechanism of bacteriocins and B-group vitamins in lactic acid bacteria and provide evidence for its potential application in food industry. Copyright © 2016. Published by Elsevier B.V.

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July 7, 2019

Complete genome sequence of probiotic Lactobacillus reuteri ZLR003 isolated from healthy weaned pig.

Lactobacillus reuteri ZLR003 was isolated from the caecum mucosa of healthy weaned pigs with displaying probiotic properties in our laboratory. Here, we present the complete genome sequence of L. reuteri ZLR003, which consists of a circular 2, 234, 097bp chromosome (G+C content of 38.66%). Such information will provide insights into the molecular mechanism of its probiotic activity and facilitate its application in animal production. Copyright © 2016. Published by Elsevier B.V.

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