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July 7, 2019

Genome scaffolding and annotation for the pathogen vector Ixodes ricinus by ultra-long single molecule sequencing.

Global warming and other ecological changes have facilitated the expansion of Ixodes ricinus tick populations. Ixodes ricinus is the most important carrier of vector-borne pathogens in Europe, transmitting viruses, protozoa and bacteria, in particular Borrelia burgdorferi (sensu lato), the causative agent of Lyme borreliosis, the most prevalent vector-borne disease in humans in the Northern hemisphere. To faster control this disease vector, a better understanding of the I. ricinus tick is necessary. To facilitate such studies, we recently published the first reference genome of this highly prevalent pathogen vector. Here, we further extend these studies by scaffolding and annotating the first reference genome by using ultra-long sequencing reads from third generation single molecule sequencing. In addition, we present the first genome size estimation for I. ricinus ticks and the embryo-derived cell line IRE/CTVM19.235,953 contigs were integrated into 204,904 scaffolds, extending the currently known genome lengths by more than 30% from 393 to 516 Mb and the N50 contig value by 87% from 1643 bp to a N50 scaffold value of 3067 bp. In addition, 25,263 sequences were annotated by comparison to the tick’s North American relative Ixodes scapularis. After (conserved) hypothetical proteins, zinc finger proteins, secreted proteins and P450 coding proteins were the most prevalent protein categories annotated. Interestingly, more than 50% of the amino acid sequences matching the homology threshold had 95-100% identity to the corresponding I. scapularis gene models. The sequence information was complemented by the first genome size estimation for this species. Flow cytometry-based genome size analysis revealed a haploid genome size of 2.65Gb for I. ricinus ticks and 3.80 Gb for the cell line.We present a first draft sequence map of the I. ricinus genome based on a PacBio-Illumina assembly. The I. ricinus genome was shown to be 26% (500 Mb) larger than the genome of its American relative I. scapularis. Based on the genome size of 2.65 Gb we estimated that we covered about 67% of the non-repetitive sequences. Genome annotation will facilitate screening for specific molecular pathways in I. ricinus cells and provides an overview of characteristics and functions.

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July 7, 2019

Draft genome sequence of Halolamina pelagica CDK2 isolated from natural salterns from Rann of Kutch, Gujarat, India.

Halolamina pelagica strain CDK2, a halophilic archaeon (growth range 1.36 to 5.12 M NaCl), was isolated from rhizosphere of wild grasses of hypersaline soil of the Rann of Kutch, Gujarat, India. Its draft genome contains 2,972,542 bp and 3,485 coding sequences, depicting genes for halophilic serine proteases and trehalose synthesis. Copyright © 2017 Gaba et al.

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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 inoculation) and seedlings inoculated with KLBMP 5084 were given different NaCl (0, 100 and 250 mM) salt-stress treatments. Growth parameters and physiological responses of L. sinense were determined after harvest. Results: Compared with the control, plants inoculated with strain KLBMP 5084 had greater in fresh weight, root length, leaf length and total chlorophyll and proline contents under both normal and high salinity conditions. Compared with control, inoculated plants had significantly lower leaf malondialdehyde (MDA) content and significantly more antioxidant enzymes. Moreover, inoculated plants had significantly lower accumulation of Na+ in both leaves and roots under high salt-stress conditions. Genomic analysis of strain KLBMP 5084 revealed many PGP related genes, including some genes putatively involved in salt tolerance and harsh environment adaptation. Conclusion: Strain KLBMP 5084 seems to confer salt tolerance to host plant L. sinense through more than one mechanism, suggesting KLBMP 5084 could be a strong PGP agent to improve plant yields and tolerance to salinity stress.

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July 7, 2019

Complete genome sequence of Bradyrhizobium japonicum J5, isolated from a soybean nodule in Hokkaido, Japan.

Soybean bradyrhizobia form root nodules on soybean plants and symbiotically fix N2 Strain J5 is phylogenetically far from well-known representatives within the Bradyrhizobium japonicum linage. The complete genome showed the largest single chromosomal (10.1 Mb) and symbiosis island (998 kb) among complete genomes of soybean bradyrhizobia. Copyright © 2017 Kanehara and Minamisawa.

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July 7, 2019

Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts

In 2010, when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortium began, little was known about the molecular basis of algal biomass or oil production. Very few algal genome sequences were available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy’s Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played by metabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oil yields were in their infancy. Genome sequencing and transcriptional profiling were becoming less expensive, however; and the tools to annotate gene expression profiles under various growth and engineered conditions were just starting to be developed for algae. It was in this context that an integrated algal biology program was introduced in the NAABB to address the greatest constraints limiting algal biomass yield. This review describes the NAABB algal biology program, including hypotheses, research objectives, and strategies to move algal biology research into the twenty-first century and to realize the greatest potential of algae biomass systems to produce biofuels.

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July 7, 2019

Complete genome sequences of six copper-resistant Xanthomonas strains causing bacterial spot of solaneous plants, belonging to X. gardneri, X. euvesicatoria, and X. vesicatoria, using long-read technology.

Xanthomonas vesicatoria, Xanthomonas euvesicatoria, and Xanthomonas gardneri cause bacterial spot disease. Copper has been applied since the 1920s as part of integrated management programs. The first copper-resistant strains were reported some decades later. Here, we fully sequenced six Xanthomonas strains pathogenic to tomato and/or pepper and having a copper-resistant phenotype. Copyright © 2017 Richard et al.

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July 7, 2019

Complete genome sequence of Edwardsiella hoshinae ATCC 35051.

Edwardsiella hoshinae is a Gram-negative facultative anaerobe that has primarily been isolated from avians and reptiles. We report here the complete and annotated genome sequence of an isolate from a monitor lizard (Varanus sp.), which contains a chromosome of 3,811,650 bp and no plasmids. Copyright © 2017 Reichley et al.

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July 7, 2019

Draft genome sequence of Karnal bunt pathogen (Tilletia indica) of wheat provides insights into the pathogenic mechanisms of quarantined fungus.

Karnal bunt disease in wheat is caused by hemibiotrophic fungus, Tilletia indica that has been placed as quarantine pest in more than 70 countries. Despite its economic importance, little knowledge about the molecular components of fungal pathogenesis is known. In this study, first time the genome sequence of T. indica has been deciphered for unraveling the effectors’ functions of molecular pathogenesis of Karnal bunt disease. The T. indica genome was sequenced employing hybrid approach of PacBio Single Molecule Real Time (SMRT) and Illumina HiSEQ 2000 sequencing platforms. The genome was assembled into 10,957 contigs (N50 contig length 3 kb) with total size of 26.7 Mb and GC content of 53.99%. The number of predicted putative genes were 11,535, which were annotated with Gene Ontology databases. Functional annotation of Karnal bunt pathogen genome and classification of identified effectors into protein families revealed interesting functions related to pathogenesis. Search for effectors’ genes using pathogen host interaction database identified 135 genes. The T. indica genome sequence and putative genes involved in molecular pathogenesis would further help in devising novel and effective disease management strategies including development of resistant wheat genotypes, novel biomarkers for pathogen detection and new targets for fungicide development.

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July 7, 2019

The unique genomic landscape surrounding the EPSPS gene in glyphosate resistant Amaranthus palmeri: a repetitive path to resistance.

The expanding number and global distributions of herbicide resistant weedy species threaten food, fuel, fiber and bioproduct sustainability and agroecosystem longevity. Amongst the most competitive weeds, Amaranthus palmeri S. Wats has rapidly evolved resistance to glyphosate primarily through massive amplification and insertion of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene across the genome. Increased EPSPS gene copy numbers results in higher titers of the EPSPS enzyme, the target of glyphosate, and confers resistance to glyphosate treatment. To understand the genomic unit and mechanism of EPSPS gene copy number proliferation, we developed and used a bacterial artificial chromosome (BAC) library from a highly resistant biotype to sequence the local genomic landscape flanking the EPSPS gene.By sequencing overlapping BACs, a 297 kb sequence was generated, hereafter referred to as the “EPSPS cassette.” This region included several putative genes, dense clusters of tandem and inverted repeats, putative helitron and autonomous replication sequences, and regulatory elements. Whole genome shotgun sequencing (WGS) of two biotypes exhibiting high and no resistance to glyphosate was performed to compare genomic representation across the EPSPS cassette. Mapping of sequences for both biotypes to the reference EPSPS cassette revealed significant differences in upstream and downstream sequences relative to EPSPS with regard to both repetitive units and coding content between these biotypes. The differences in sequence may have resulted from a compounded-building mechanism such as repetitive transpositional events. The association of putative helitron sequences with the cassette suggests a possible amplification and distribution mechanism. Flow cytometry revealed that the EPSPS cassette added measurable genomic content.The adoption of glyphosate resistant cropping systems in major crops such as corn, soybean, cotton and canola coupled with excessive use of glyphosate herbicide has led to evolved glyphosate resistance in several important weeds. In Amaranthus palmeri, the amplification of the EPSPS cassette, characterized by a complex array of repetitive elements and putative helitron sequences, suggests an adaptive structural genomic mechanism that drives amplification and distribution around the genome. The added genomic content not found in glyphosate sensitive plants may be driving evolution through genome expansion.

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July 7, 2019

The complete genome sequence of the yogurt isolate Streptococcus thermophilus ACA-DC 2.

Streptococcus thermophilus ACA-DC 2 is a newly sequenced strain isolated from traditional Greek yogurt. Among the 14 fully sequenced strains of S. thermophilus currently deposited in the NCBI database, the ACA-DC 2 strain has the smallest chromosome, containing 1,731,838 bp. The annotation of its genome revealed the presence of 1,850 genes, including 1,556 protein-coding genes, 70 RNA genes and 224 potential pseudogenes. A large number of pseudogenes were identified. This was also accompanied by the absence of pathogenic features suggesting evolution of strain ACA-DC 2 through genome decay processes, most probably due to adaptation to the milk ecosystem. Analysis revealed the existence of one complete lactose-galactose operon, several proteolytic enzymes, one exopolysaccharide cluster, stress response genes and four putative antimicrobial peptides. Interestingly, one CRISPR-cas system and one orphan CRISPR, both carrying only one spacer, were predicted indicating low activity or inactivation of the cas proteins. Nevertheless, four putative restriction-modification systems were determined that may compensate any deficiencies of the CRISPR-cas system. Furthermore, whole genome phylogeny indicated three distinct clades within S. thermophilus. Comparative analysis among selected strains representative for each clade, including strain ACA-DC 2, revealed a high degree of conservation at the genomic scale, but also strain specific regions. Unique genes and genomic islands of strain ACA-DC 2 contained a number of genes potentially acquired through horizontal gene transfer events, that could be related to important technological properties for dairy starters. Our study suggests genomic traits in strain ACA-DC 2 compatible to the production of dairy fermented foods.

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