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Sunday, October 25, 2020

PAG Conference: Phylogenetic insights into the endophyte symbiosis using PacBio ribosomal DNA sequencing

Jana U’Ren of the University of Arizona discusses the fungi that live inside of plants at a PacBio workshop at the PAG 2020 conference. U’Ren studies the biology and evolution of mycorrhizal fungi found in the photosynthetic tissue of plant leaves, which are grouped together functionally as endophytes. In this video, she shares some of her preliminary findings collecting and analyzing samples from Boreal forests around the world.

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Sunday, July 7, 2019

Complete genome sequence of endophytic nitrogen-fixing Klebsiella variicola strain DX120E.

Klebsiella variicola strain DX120E (=CGMCC 1.14935) is an endophytic nitrogen-fixing bacterium isolated from sugarcane crops grown in Guangxi, China and promotes sugarcane growth. Here we summarize the features of the strain DX120E and describe its complete genome sequence. The genome contains one circular chromosome and two plasmids, and contains 5,718,434 nucleotides with 57.1% GC content, 5,172 protein-coding genes, 25 rRNA genes, 87 tRNA genes, 7 ncRNA genes, 25 pseudo genes, and 2 CRISPR repeats.

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Sunday, July 7, 2019

Draft genome sequence of Raoultella terrigena R1Gly, a diazotrophic endophyte.

Raoultella terrigena R1Gly is a diazotrophic endophyte isolated from surface-sterilized roots of Nicotiana tabacum. The whole-genome sequence was obtained to investigate the endophytic characteristics of this organism at the genetic level, as well as to compare this strain with its close relatives. To our knowledge, this is the first genome obtained from the Raoultella terrigena species and only the third genome from the Raoultella genus, after Raoultella ornitholytic and Raoultella planticola. This genome will provide a foundation for further comparative genomic, metagenomic, and functional studies of this genus. Copyright © 2015 Schicklberger et al.

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Sunday, July 7, 2019

Draft genome sequence of Paenibacillus polymyxa strain Mc5Re-14, an antagonistic root endophyte of Matricaria chamomilla.

Paenibacillus polymyxa strain Mc5Re-14 was isolated from the inner root tissue of Matricaria chamomilla (German chamomile). Mc5Re-14 revealed promising in vitro antagonistic activity against plant and opportunistic human pathogens. The 6.0-Mb draft genome reveals genes putatively involved in pathogen suppression and direct and indirect plant growth promotion. Copyright © 2015 Köberl et al.

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Sunday, July 7, 2019

Complete genome sequence of Kosakonia sacchari type strain SP1(T.).

Kosakonia sacchari sp. nov. is a new species within the new genus Kosakonia, which was included in the genus Enterobacter. K sacchari is a nitrogen-fixing bacterium named for its association with sugarcane (Saccharum officinarum L.). K sacchari bacteria are Gram-negative, aerobic, non-spore-forming, motile rods. Strain SP1(T) (=CGMCC1.12102(T)=LMG 26783(T)) is the type strain of the K sacchari sp. nov and is able to colonize and fix N2 in association with sugarcane plants, thus promoting plant growth. Here we summarize the features of strain SP1(T) and describe its complete genome sequence. The genome contains a single chromosome and no plasmids, 4,902,024 nucleotides…

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Sunday, July 7, 2019

Plant growth-promoting effect and genomic analysis of the beneficial endophyte Streptomyces sp. KLBMP 5084 isolated from halophyte Limonium sinense

Background and aims: Soil salinity is a worldwide environmental problem that can hinder plant development and therefore negatively impact crop production. Inoculation of halophytic plants with plant growth-promoting (PGP) actinobacteria has been suggested as one strategy to improve salt tolerance. Here we performed a glasshouse experiment to test the effect of a PGP halotolerant endophytic actinomycete strain, KLBMP 5084 on the performance of the halophyte Limonium sinense under conditions of salt stress. Methods: Strain KLBMP 5084 was identified and screened for multiple PGP traits. The complete genome of strain KLBMP 5084 was sequenced and analyzed. L. sinense control seedlings (no…

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Sunday, July 7, 2019

Complete genome sequence of Kosakonia oryzae type strain Ola 51(T).

Strain Ola 51(T) (=LMG 24251(T)?=?CGMCC 1.7012(T)) is the type strain of the species Kosakonia oryzae and was isolated from surface-sterilized roots of the wild rice species Oryza latifolia grown in Guangdong, China. Here we summarize the features of the strain Ola 51(T) and describe its complete genome sequence. The genome contains one circular chromosome of 5,303,342 nucleotides with 54.01% GC content, 4773 protein-coding genes, 16 rRNA genes, 76 tRNA genes, 13 ncRNA genes, 48 pseudo genes, and 1 CRISPR array.

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Sunday, July 7, 2019

Whole-genome sequence of endophytic plant growth-promoting Escherichia coli USML2.

Escherichia coli strain USML2 was originally isolated from the inner leaf tissues of surface-sterilized phytopathogenic-free oil palm (Elaeis guineensis Jacq.). We present here the whole-genome sequence of this plant-endophytic strain. The genome consists of a single circular chromosome of 4,502,758 bp, 4,315 predicted coding sequences, and a G+C content of 50.8%. Copyright © 2017 Tharek et al.

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Sunday, July 7, 2019

Characterization of four endophytic fungi as potential consolidated bioprocessing hosts for conversion of lignocellulose into advanced biofuels.

Recently, several endophytic fungi have been demonstrated to produce volatile organic compounds (VOCs) with properties similar to fossil fuels, called “mycodiesel,” while growing on lignocellulosic plant and agricultural residues. The fact that endophytes are plant symbionts suggests that some may be able to produce lignocellulolytic enzymes, making them capable of both deconstructing lignocellulose and converting it into mycodiesel, two properties that indicate that these strains may be useful consolidated bioprocessing (CBP) hosts for the biofuel production. In this study, four endophytes Hypoxylon sp. CI4A, Hypoxylon sp. EC38, Hypoxylon sp. CO27, and Daldinia eschscholzii EC12 were selected and evaluated for their…

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Sunday, July 7, 2019

Draft genome sequence of Streptomyces scabrisporus NF3, an endophyte isolated from Amphipterygium adstringens.

We report the draft genome sequence of Streptomyces scabrisporus NF3, an endophyte isolated from Amphipterygium adstringens in Chiapas, Mexico. This strain produces a new modified linaridin peptide. The genome harbors at least 50 gene clusters for synthases of polyketide and nonribosomal peptides, suggesting a prospective production of various secondary metabolites. Copyright © 2017 Vazquez-Hernandez et al.

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Sunday, July 7, 2019

Complete genome sequence of the drought resistance-promoting endophyte Klebsiella sp. LTGPAF-6F.

Bacterial endophytes with capacity to promote plant growth and improve plant tolerance against biotic and abiotic stresses have importance in agricultural practice and phytoremediation. A plant growth-promoting endophyte named Klebsiella sp. LTGPAF-6F, which was isolated from the roots of the desert plant Alhagi sparsifolia in north-west China, exhibits the ability to enhance the growth of wheat under drought stress. The complete genome sequence of this strain consists of one circular chromosome and two circular plasmids. From the genome, we identified genes related to the plant growth promotion and stress tolerance, such as nitrogen fixation, production of indole-3-acetic acid, acetoin, 2,3-butanediol,…

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Sunday, July 7, 2019

Draft genome sequence of Grammothele lineata SDL-CO-2015-1, a jute endophyte with a potential for paclitaxel biosynthesis.

Grammothele lineata strain SDL-CO-2015-1, a basidiomycete fungus, was identified as an endophyte from a jute species, Corchorus olitorius var. 2015, and found to produce paclitaxel, a diterpenic polyoxygenated pseudoalkaloid with antitumor activity. Here, we report the draft genome sequence (42.8 Mb with 9,395 genes) of this strain. Copyright © 2017 Das et al.

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Sunday, July 7, 2019

Complete genome sequence of endophyte Bacillus flexus KLBMP 4941 reveals its plant growth promotion mechanism and genetic basis for salt tolerance.

Bacillus flexus KLBMP 4941 is a halotolerant endophyte isolated from the halophyte Limonium sinense. This strain can improve host seedling growth under salt stress conditions. We here report the complete genome information of endophyte KLBMP 4941. It has a circular chromosome and two plasmids for a total genome 4,104,242 bp in size with a G+C content of 38.09%. Genes related to plant growth promotion (PGP), such as those associated with nitrogen fixation, siderophore, spermidine, and acetoin synthesis were found in the KLBMP 4941 genome. Some genes responsible for high salinity tolerance, like genes associated with the Na(+)/H(+) antiporter, glycine betaine…

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Sunday, July 7, 2019

Complete genome sequence analysis of Enterobacter sp. SA187, a plant multi-stress tolerance promoting endophytic bacterium

Enterobacter sp. SA187 is an endophytic bacterium that has been isolated from root nodules of the indigenous desert plant Indigofera argentea. SA187 could survive in the rhizosphere as well as in association with different plant species, and was able to provide abiotic stress tolerance to Arabidopsis thaliana. The genome sequence of SA187 was obtained by using Pacific BioScience (PacBio) single-molecule sequencing technology, with average coverage of 275X. The genome of SA187 consists of one single 4,429,597 bp chromosome, with an average 56% GC content and 4,347 predicted protein coding DNA sequences (CDS), 153 ncRNA, 7 rRNA, and 84 tRNA. Functional…

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