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July 7, 2019

Identification of repetitive DNA sequences in the Chrysanthemum boreale genome

We previously revealed that the Chrysanthemum boreale genome is highly repetitive; however, the types and nucleotide sequences of repetitive DNA in this diploid wild chrysanthemum are not known. Here, we characterized repetitive DNA sequences in the C. boreale genome by analysing genomic sequences obtained by Illumina sequencing and confirmed their repetitive nature by conducting fluorescence in situ hybridization (FISH) analyses. Annotation of the obtained DNA sequences revealed that microsatellite-containing genomic sequences exhibited similarity with genomic sequences in Chrysanthemum morifolium, indicating sequence conservation of repetitive DNA sequences between the two Chrysanthemum species. Two superfamilies of repetitive DNA, Copia and Gypsy, belonging to the long-terminal repeat (LTR) class of retrotransposons, are abundant in the C. boreale genome. We propose that Copia and Gypsy retroelements contribute to the current genome architecture of C. boreale. Whole genome sequencing, which is currently in progress, will reveal the extent to which these repetitive DNA sequences contribute.

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July 7, 2019

Identification of Pseudomonas mosselii BS011 gene clusters required for suppression of Rice Blast Fungus Magnaporthe oryzae.

Pseudomonas is a Gram-negative, rod-shaped bacteria. Many members of this genus displayed remarkable physiological and metabolic activity against different plant pathogens. However, Pseudomonas mosselii has not yet been characterized in biocontrol against plant disease. Here we isolated a strain of P. mosselii BS011 from the rhizosphere soil of rice plants, and the isolate showed strong inhibitory activity against the rice blast fungus Magnaporthe oryzae. Further we sequenced the complete genome of BS011, which consist of 5.75?Mb with a circular chromosome, 5,170 protein-coding genes, 23 rRNA and 78 tRNA operons. Bioinformatic analysis revealed that seven gene clusters may be involved in the biosynthesis of metabolites. Gene deletion experiments demonstrated that the gene cluster c-xtl is required for inhibitory activity against M. oryzae. Bioassay showed that the crude extract from BS011 fermentation sample significantly inhibited the development of M. oryzae at a concentration of 10?µg/ml. Besides, we illustrated that the crude extract of BS011 impaired the appressorial formation in a dose dependent manner. Collectively our results revealed that P. mosselii BS011 is a promising biocontrol agent and the gene cluster c-xtl is essential for inhibiting the development of M. oryzae. Copyright © 2018. Published by Elsevier B.V.

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July 7, 2019

Phylogeny of dermatophytes with genomic character evaluation of clinically distinct Trichophyton rubrum and T. áviolaceum

Trichophyton rubrum and T. violaceum are prevalent agents of human dermatophyte infections, the former being found on glabrous skin and nail, while the latter is confined to the scalp. The two species are phenotypically different but are highly similar phylogenetically. The taxonomy of dermatophytes is currently being reconsidered on the basis of molecular phylogeny. Molecular species definitions do not always coincide with existing concepts which are guided by ecological and clinical principles. In this article, we aim to bring phylogenetic and ecological data together in an attempt to develop new species concepts for anthropophilic dermatophytes. Focus is on the T. rubrum complex with analysis of rDNA ITS supplemented with LSU, TUB2, TEF3 and ribosomal protein L10 gene sequences. In order to explore genomic differences between T. rubrum and T. violaceum, one representative for both species was whole genome sequenced. Draft sequences were compared with currently available dermatophyte genomes. Potential virulence factors of adhesins and secreted proteases were predicted and compared phylogenetically. General phylogeny showed clear gaps between geophilic species of Arthroderma, but multilocus distances between species were often very small in the derived anthropophilic and zoophilic genus Trichophyton. Significant genome conservation between T. rubrum and T. violaceum was observed, with a high similarity at the nucleic acid level of 99.38 % identity. Trichophyton violaceum contains more paralogs than T. rubrum. About 30 adhesion genes were predicted among dermatophytes. Seventeen adhesins were common between T. rubrum and T. violaceum, while four were specific for the former and eight for the latter. Phylogenetic analysis of secreted proteases reveals considerable expansion and conservation among the analyzed species. Multilocus phylogeny and genome comparison of T. rubrum and T. violaceum underlined their close affinity. The possibility that they represent a single species exhibiting different phenotypes due to different localizations on the human body is discussed.

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July 7, 2019

The case for not masking away repetitive DNA

In the course of analyzing whole-genome data, it is common practice to mask or filter out repetitive regions of a genome, such as transposable elements and endogenous retroviruses, in order to focus only on genes and thus simplify the results. This Commentary is a plea from one member of the Mobile DNA community to all gene-centric researchers: please do not ignore the repetitive fraction of the genome. Please stop narrowing your findings by only analyzing a minority of the genome, and instead broaden your analyses to include the rich biology of repetitive and mobile DNA. In this article, I present four arguments supporting a case for retaining repetitive DNA in your genome-wide analysis.

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July 7, 2019

The complete mitochondrial genome of Sanghuangporus sanghuang (Hymenochaetaceae, Basidiomycota)

Sanghuang is a polypore mushroom, which has been widely used in oriental medicine. Since recent molecular phylogenetic studies elucidated its species delimitation, Sanghaungporus sanghuang became the official name of this fungus. In this study, the complete sequence of the mitochondrial DNA of S. sanghuang was determined. The whole genome was 112,060?bp containing 14 proteins, 2 ribosomal RNA subunits, and 45 transfer RNAs. The overall GC content of the genome was 23.21%. A neighbour-joining tree based on atp6 sequence data showed its close relationship with the species of Ganoderma and Trametes.

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July 7, 2019

Draft genome sequence of a bacterial plant pathogen Erwinia pyrifoliae strain EpK1/15 isolated from an apple twig showing black shoot blight

Erwinia pyrifoliae is a Gram-negative bacterium causing black shoot blight in apple and Asian pear trees. E. pyrifoliae strain EpK1/15 was isolated in 2014 from an apple twig from the Pocheon, Gyeonggi-do, South Korea. In this study, we report the draft genome sequence of E. pyrifoliae EpK1/15 using PacBio RS II platform. The draft genome is comprised of a circular chromosome with 4,027,225 bp and 53.4% G + C content and a plasmid with 48,456 bp and 50.3% G + C content. The draft genome includes 3,798 protein-coding genes, 22 rRNA genes, 77 tRNA genes, 13 non-coding RNA genes, and 231 pseudo genes.

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July 7, 2019

Complete genome of Pseudoalteromonas marina ECSMB14103, a mussel settlement-inducing bacterium isolated from the East China Sea

Pseudoalteromonas marina ECSMB14103, a strain isolated from natural multiple-species biofilms formed in the East China Sea, induces the settlement of larvae and plantigrades in Mytilus coruscus. Here, we report the complete genome of this strain; the genome is 3,441,076?bp in size, has a GC content of 39.90% and contains a total of 3200 predicted genes. These genomic data will provide significant datasets to help improve understanding of the physiological potential and molecular mechanisms of settlement induction by P. marina ECSMB14103.

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July 7, 2019

Genome sequence resources for the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) and the barley stripe rust pathogen (Puccinia striiformis f. sp. hordei)

Puccinia striiformis f. sp. tritici causes devastating stripe (yellow) rust on wheat and P. striiformis f. sp. hordei causes stripe rust on barley. Several P. striiformis f. sp. tritici genomes are available, but no P. striiformis f. sp. hordei genome is available. More genomes of P. striiformis f. sp. tritici and P. striiformis f. sp. hordei are needed to understand the genome evolution and molecular mechanisms of their pathogenicity. We sequenced P. striiformis f. sp. tritici isolate 93-210 and P. striiformis f. sp. hordei isolate 93TX-2, using PacBio and Illumina technologies and RNA sequencing. Their genomic sequences were assembled to contigs with high continuity and showed significant structural differences. The circular mitochondria genomes of both were complete. These genomes provide high-quality resources for deciphering the genomic basis of rapid evolution and host adaptation, identifying genes for avirulence and other important traits, and studying host-pathogen interactions.

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July 7, 2019

Optimise wheat A-genome.

The wild einkorn wheat Triticum urartu (Tu) is the A-genome progenitor of tetraploid (AABB) and hexaploid (AABBDD) wheat. A draft genome of Tu was published in 2013, but a better reference sequence is urgently needed by scientists and breeders. Hong-Qing Ling, from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and colleagues have now completed a high-quality Tu genome using multiple methods.

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July 7, 2019

The draft genome of the lichen-forming fungus Lasallia hispanica (Frey) Sancho & A. Crespo

Lasallia hispanica (Frey) Sancho & A. Crespo is one of three Lasallia species occurring in central-western Europe. It is an orophytic, photophilous Mediterranean endemic which is sympatric with the closely related, widely distributed, highly clonal sister taxon L. pustulata in the supra- and oro-Mediterranean belts. We sequenced the genome of L. hispanica from a multispore isolate. The total genome length is 41·2 Mb, including 8488 gene models. We present the annotation of a variety of genes that are involved in protein secretion, mating processes and secondary metabolism, and we report transposable elements. Additionally, we compared the genome of L. hispanica to the closely related, yet ecologically distant, L. pustulata and found high synteny in gene content and order. The newly assembled and annotated L. hispanica genome represents a useful resource for future investigations into niche differentiation, speciation and microevolution in L. hispanica and other members of the genus.

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July 7, 2019

Complete genome sequence of a novel mutant strain of Vibrio parahaemolyticus from Pacific White Shrimp (Penaeus vannamei).

The acute hepatopancreatic necrosis disease (AHPND) of Penaeus vannamei shrimp is caused by Vibrio parahaemolyticus carrying toxin genes, pirA and pirB We report the complete genome sequence of the novel V. parahaemolyticus strain R14, which did not display AHPND symptoms in P. vannamei despite containing the binary toxin genes. Copyright © 2018 Kanrar and Dhar.

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July 7, 2019

Complete genome sequences of three Bacillus amyloliquefaciens strains that inhibit the growth of Listeria monocytogenes in vitro.

Here, we report the complete genome sequences of three Bacillus amyloliquefaciens strains isolated from alfalfa, almond drupes, and grapes that inhibited the growth of Listeria monocytogenes strain 2011L-2857 in vitro We also report multiple gene clusters encoding secondary metabolites that may be responsible for the growth inhibition of L. monocytogenes. Copyright © 2018 Tran et al.

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