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July 7, 2019  |  

Genome sequences of two cyanobacterial strains, toxic green Microcystis aeruginosa KW (KCTC 18162P) and nontoxic brown Microcystis sp. strain MC19, under xenic culture conditions.

Bloom-forming cyanobacteria pose concerns for the environment and the health of humans and animals by producing toxins and thus lowering water quality. Here, we report near-complete genome sequences of two Microcystis strains under xenic culture conditions, which were originally isolated from two separate freshwater reservoirs from the Republic of Korea. Copyright © 2018 Jeong et al.


July 7, 2019  |  

Complete genome sequence of Colwellia hornerae PAMC 20917, a cold-active enzyme-producing bacterium isolated from the Arctic Ocean sediment

Psychrophilic bacteria are considered a source of cold-active enzymes that can be used in industrial applications. The Arctic bacterium Colwellia hornerae PAMC 20917 strain has been isolated from the offshore sediment near Ny-Ålesund, Svalbard. The optimal growth temperature of the strain was 10?°C on marine agar. The cell lysate showed alkaline phosphatase activities. Analysis of the enzymatic properties showed that the alkaline phosphatase was cold-active and thermolabile. To explore useful cold-active industrial enzymes further, the entire genome of the PAMC 20917 strain was sequenced. The genome of the strain contained 4,684,314 nucleotides, with 37.87% G+C content. Genome mining analysis revealed that, in the complete genome sequence, three proteins were annotated as alkaline phosphatases. The genome of PAMC 20917 encodes cold shock proteins and an ice-binding protein that inhibits the growth of ice, allowing the bacterium to adapt to cold environments. This genome information may be useful for understanding mechanisms of adaptation to cold stress.


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.


July 7, 2019  |  

Darwin: A genomics co-processor provides up to 15,000 X acceleration on long read assembly

of life in fundamental ways. Genomics data, however, is far outpacing Moore’s Law. Third-generation sequencing tech- nologies produce 100× longer reads than second generation technologies and reveal a much broader mutation spectrum of disease and evolution. However, these technologies incur prohibitively high computational costs. Over 1,300 CPU hours are required for reference-guided assembly of the human genome (using [47]), and over 15,600 CPU hours are required for de novo assembly [57]. This paper describes “Darwin” — a co-processor for genomic sequence alignment that, without sacrificing sensitivity, provides up to 15,000× speedup over the state-of-the-art software for reference-guided assembly of third-generation reads. Darwin achieves this speedup through hardware/algorithm co-design, trading more easily accelerated alignment for less memory-intensive filtering, and by optimizing the memory system for filtering. Darwin combines a hardware-accelerated version of D-SOFT, a novel filtering algorithm, with a hardware-accelerated version of GACT, a novel alignment algorithm. GACT generates near-optimal alignments of arbitrarily long genomic sequences using constant memory for the compute-intensive step. Dar- win is adaptable, with tunable speed and sensitivity to match emerging sequencing technologies and to meet the requirements of genomic applications beyond read assembly.


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.


July 7, 2019  |  

ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.

The long-range sequencing information captured by linked reads, such as those available from 10× Genomics (10xG), helps resolve genome sequence repeats, and yields accurate and contiguous draft genome assemblies. We introduce ARKS, an alignment-free linked read genome scaffolding methodology that uses linked reads to organize genome assemblies further into contiguous drafts. Our approach departs from other read alignment-dependent linked read scaffolders, including our own (ARCS), and uses a kmer-based mapping approach. The kmer mapping strategy has several advantages over read alignment methods, including better usability and faster processing, as it precludes the need for input sequence formatting and draft sequence assembly indexing. The reliance on kmers instead of read alignments for pairing sequences relaxes the workflow requirements, and drastically reduces the run time.Here, we show how linked reads, when used in conjunction with Hi-C data for scaffolding, improve a draft human genome assembly of PacBio long-read data five-fold (baseline vs. ARKS NG50?=?4.6 vs. 23.1 Mbp, respectively). We also demonstrate how the method provides further improvements of a megabase-scale Supernova human genome assembly (NG50?=?14.74 Mbp vs. 25.94 Mbp before and after ARKS), which itself exclusively uses linked read data for assembly, with an execution speed six to nine times faster than competitive linked read scaffolders (~?10.5 h compared to 75.7 h, on average). Following ARKS scaffolding of a human genome 10xG Supernova assembly (of cell line NA12878), fewer than 9 scaffolds cover each chromosome, except the largest (chromosome 1, n?=?13).ARKS uses a kmer mapping strategy instead of linked read alignments to record and associate the barcode information needed to order and orient draft assembly sequences. The simplified workflow, when compared to that of our initial implementation, ARCS, markedly improves run time performances on experimental human genome datasets. Furthermore, the novel distance estimator in ARKS utilizes barcoding information from linked reads to estimate gap sizes. It accomplishes this by modeling the relationship between known distances of a region within contigs and calculating associated Jaccard indices. ARKS has the potential to provide correct, chromosome-scale genome assemblies, promptly. We expect ARKS to have broad utility in helping refine draft genomes.


July 7, 2019  |  

The challenge of analyzing the sugarcane genome.

Reference genome sequences have become key platforms for genetics and breeding of the major crop species. Sugarcane is probably the largest crop produced in the world (in weight of crop harvested) but lacks a reference genome sequence. Sugarcane has one of the most complex genomes in crop plants due to the extreme level of polyploidy. The genome of modern sugarcane hybrids includes sub-genomes from two progenitors Saccharum officinarum and S. spontaneum with some chromosomes resulting from recombination between these sub-genomes. Advancing DNA sequencing technologies and strategies for genome assembly are making the sugarcane genome more tractable. Advances in long read sequencing have allowed the generation of a more complete set of sugarcane gene transcripts. This is supporting transcript profiling in genetic research. The progenitor genomes are being sequenced. A monoploid coverage of the hybrid genome has been obtained by sequencing BAC clones that cover the gene space of the closely related sorghum genome. The complete polyploid genome is now being sequenced and assembled. The emerging genome will allow comparison of related genomes and increase understanding of the functioning of this polyploidy system. Sugarcane breeding for traditional sugar and new energy and biomaterial uses will be enhanced by the availability of these genomic resources.


July 7, 2019  |  

Complete genome sequence of oyster isolate Vibrio vulnificus env1.

Vibrio vulnificus, a ubiquitous inhabitant of coastal marine environments, has been isolated from a variety of sources. It is an opportunistic pathogen of both marine animals and humans. Here, the genome sequence of V. vulnificus Env1, an environmental isolate resistant to predation by the ciliate Tetrahymena pyriformis, is reported. Copyright © 2018 Noorian et al.


July 7, 2019  |  

Identification of different putative outer membrane electron conduits necessary for Fe(III) citrate, Fe(III) oxide, Mn(IV) oxide, or electrode reduction by Geobacter sulfurreducens.

At least five gene clusters in the Geobacter sulfurreducens genome encode putative “electron conduits” implicated in electron transfer across the outer membrane, each containing a periplasmic multiheme c-type cytochrome, integral outer membrane anchor, and outer membrane redox lipoprotein(s). Markerless single-gene-cluster deletions and all possible multiple-deletion combinations were constructed and grown with soluble Fe(III) citrate, Fe(III) and Mn(IV) oxides, and graphite electrodes poised at +0.24 V and -0.1 V versus the standard hydrogen electrode (SHE). Different gene clusters were necessary for reduction of each electron acceptor. During metal oxide reduction, deletion of the previously described omcBC cluster caused defects, but deletion of additional components in an ?omcBC background, such as extEFG, were needed to produce defects greater than 50% compared to findings with the wild type. Deletion of all five gene clusters abolished all metal reduction. During electrode reduction, only the ?extABCD mutant had a severe growth defect at both redox potentials, while this mutation did not affect Fe(III) oxide, Mn(IV) oxide, or Fe(III) citrate reduction. Some mutants containing only one cluster were able to reduce particular terminal electron acceptors better than the wild type, suggesting routes for improvement by targeting specific electron transfer pathways. Transcriptomic comparisons between fumarate and electrode-based growth conditions showed all of these ext clusters to be constitutive, and transcriptional analysis of the triple-deletion strain containing only extABCD detected no significant changes in expression of genes encoding known redox proteins or pilus components. These genetic experiments reveal new outer membrane conduit complexes necessary for growth of G. sulfurreducens, depending on the available extracellular electron acceptor.IMPORTANCE Gram-negative metal-reducing bacteria utilize electron conduits, chains of redox proteins spanning the outer membrane, to transfer electrons to the extracellular surface. Only one pathway for electron transfer across the outer membrane of Geobacter sulfurreducens has been linked to Fe(III) reduction. However, G. sulfurreducens is able to respire a wide array of extracellular substrates. Here we present the first combinatorial genetic analysis of five different electron conduits via creation of new markerless deletion strains and complementation vectors. Multiple conduit gene clusters appear to have overlapping roles, including two that have never been linked to metal reduction. Another recently described cluster (ExtABCD) was the only electron conduit essential during electrode reduction, a substrate of special importance to biotechnological applications of this organism. Copyright © 2018 Jiménez Otero et al.


July 7, 2019  |  

An improved approach for reconstructing consensus repeats from short sequence reads

Repeat elements are important components of most eukaryotic genomes. Most existing tools for repeat analysis rely either on high quality reference genomes or existing repeat libraries. Thus, it is still challenging to do repeat analysis for species with highly repetitive or complex genomes which often do not have good reference genomes or annotated repeat libraries. Recently we developed a computational method called REPdenovo that constructs consensus repeat sequences directly from short sequence reads, which outperforms an existing tool called RepARK. One major issue with REPdenovo is that it doesn’t perform well for repeats with relatively high divergence rates or low copy numbers. In this paper, we present an improved approach for constructing consensus repeats directly from short reads. Comparing with the original REPdenovo, the improved approach uses more repeat-related k-mers and improves repeat assembly quality using a consensus-based k-mer processing method.


July 7, 2019  |  

Clustering of circular consensus sequences: accurate error correction and assembly of single molecule real-time reads from multiplexed amplicon libraries.

Targeted resequencing with high-throughput sequencing (HTS) platforms can be used to efficiently interrogate the genomes of large numbers of individuals. A critical issue for research and applications using HTS data, especially from long-read platforms, is error in base calling arising from technological limits and bioinformatic algorithms. We found that the community standard long amplicon analysis (LAA) module from Pacific Biosciences is prone to substantial bioinformatic errors that raise concerns about findings based on this pipeline, prompting the need for a new method.A single molecule real-time (SMRT) sequencing-error correction and assembly pipeline, C3S-LAA, was developed for libraries of pooled amplicons. By uniquely leveraging the structure of SMRT sequence data (comprised of multiple low quality subreads from which higher quality circular consensus sequences are formed) to cluster raw reads, C3S-LAA produced accurate consensus sequences and assemblies of overlapping amplicons from single sample and multiplexed libraries. In contrast, despite read depths in excess of 100X per amplicon, the standard long amplicon analysis module from Pacific Biosciences generated unexpected numbers of amplicon sequences with substantial inaccuracies in the consensus sequences. A bootstrap analysis showed that the C3S-LAA pipeline per se was effective at removing bioinformatic sources of error, but in rare cases a read depth of nearly 400X was not sufficient to overcome minor but systematic errors inherent to amplification or sequencing.C3S-LAA uses a divide and conquer processing algorithm for SMRT amplicon-sequence data that generates accurate consensus sequences and local sequence assemblies. Solving the confounding bioinformatic source of error in LAA allowed for the identification of limited instances of errors due to DNA amplification or sequencing of homopolymeric nucleotide tracts. For research and development in genomics, C3S-LAA allows meaningful conclusions and biological inferences to be made from accurately polished sequence output.


July 7, 2019  |  

Draft genome sequence of Tuber borchii Vittad., a whitish edible truffle.

The ascomycete Tuber borchii (Pezizomycetes) is a whitish edible truffle that establishes ectomycorrhizal symbiosis with trees and shrubs. This fungus is ubiquitous in Europe and is also cultivated outside Europe. Here, we present the draft genome sequence of T. borchii strain Tbo3840 (97.18 Mb in 969 scaffolds, with 12,346 predicted protein-coding genes).


July 7, 2019  |  

Genomic insights into date palm origins.

With the development of next-generation sequencing technology, the amount of date palm (Phoenix dactylifera L.) genomic data has grown rapidly and yielded new insights into this species and its origins. Here, we review advances in understanding of the evolutionary history of the date palm, with a particular emphasis on what has been learned from the analysis of genomic data. We first record current genomic resources available for date palm including genome assemblies and resequencing data. We discuss new insights into its domestication and diversification history based on these improved genomic resources. We further report recent discoveries such as the existence of wild ancestral populations in remote locations of Oman and high differentiation between African and Middle Eastern populations. While genomic data are consistent with the view that domestication took place in the Gulf region, they suggest that the process was more complex involving multiple gene pools and possibly a secondary domestication. Many questions remain unanswered, especially regarding the genetic architecture of domestication and diversification. We provide a road map to future studies that will further clarify the domestication history of this iconic crop.


July 7, 2019  |  

Draft genome sequence of the xanthocidin-producing strain Streptomyces sp. AcE210, isolated from a root nodule of Alnus glutinosa (L.).

Streptomyces sp. strain AcE210 exhibited antibacterial activity toward Gram-positive microorganisms and turned out to be a rare producer of the special- ized metabolite xanthocidin. The 10.6-Mb draft genome sequence gives insight into the complete specialized metabolite production capacity and builds the basis to find and locate the biosynthetic gene cluster of xanthocidin.


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