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  • 1
    Online Resource
    Online Resource
    The transcriptome of Euglena gracilis reveals unexpected metabolic capabilities for carbohydrate and natural product biochemistry
    Royal Society of Chemistry (RSC) ; 2015
    In:  Molecular BioSystems Vol. 11, No. 10 ( 2015), p. 2808-2820
    Details
    In: Molecular BioSystems, Royal Society of Chemistry (RSC), Vol. 11, No. 10 ( 2015), p. 2808-2820
    Type of Medium: Online Resource
    ISSN: 1742-206X , 1742-2051
    URL: Article
    DOI: 10.1039/C5MB00319A
    Language: English
    Publisher: Royal Society of Chemistry (RSC)
    Publication Date: 2015
    detail.hit.zdb_id: 2188635-0
    SSG: 12
    SSG: 15,3
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  • 2
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    RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics
    Springer Science and Business Media LLC ; 2019
    In:  BMC Genomics Vol. 20, No. 1 ( 2019-12)
    Details
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 20, No. 1 ( 2019-12)
    Abstract: Flavonoids are produced in all flowering plants in a wide range of tissues including in berry fruits. These compounds are of considerable interest for their biological activities, health benefits and potential pharmacological applications. However, transcriptomic and genomic resources for wild and cultivated berry fruit species are often limited, despite their value in underpinning the in-depth study of metabolic pathways, fruit ripening as well as in the identification of genotypes rich in bioactive compounds. Results To access the genetic diversity of wild and cultivated berry fruit species that accumulate high levels of phenolic compounds in their fleshy berry(-like) fruits, we selected 13 species from Europe, South America and Asia representing eight genera, seven families and seven orders within three clades of the kingdom Plantae . RNA from either ripe fruits (ten species) or three ripening stages (two species) as well as leaf RNA (one species) were used to construct, assemble and analyse de novo transcriptomes. The transcriptome sequences are deposited in the BacHBerryGEN database ( http://jicbio.nbi.ac.uk/berries ) and were used, as a proof of concept, via its BLAST portal ( http://jicbio.nbi.ac.uk/berries/blast.html ) to identify candidate genes involved in the biosynthesis of phenylpropanoid compounds. Genes encoding regulatory proteins of the anthocyanin biosynthetic pathway (MYB and basic helix-loop-helix (bHLH) transcription factors and WD40 repeat proteins) were isolated using the transcriptomic resources of wild blackberry ( Rubus genevieri ) and cultivated red raspberry ( Rubus idaeus cv. Prestige) and were shown to activate anthocyanin synthesis in Nicotiana benthamiana . Expression patterns of candidate flavonoid gene transcripts were also studied across three fruit developmental stages via the BacHBerryEXP gene expression browser ( http://www.bachberryexp.com ) in R. genevieri and R. idaeus cv. Prestige. Conclusions We report a transcriptome resource that includes data for a wide range of berry(-like) fruit species that has been developed for gene identification and functional analysis to assist in berry fruit improvement. These resources will enable investigations of metabolic processes in berries beyond the phenylpropanoid biosynthetic pathway analysed in this study. The RNA-seq data will be useful for studies of berry fruit development and to select wild plant species useful for plant breeding purposes.
    Type of Medium: Online Resource
    ISSN: 1471-2164
    URL: Article
    DOI: 10.1186/s12864-019-6183-2
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2019
    detail.hit.zdb_id: 2041499-7
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  • 3
    Online Resource
    Online Resource
    BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits
    Springer Science and Business Media LLC ; 2018
    In:  Phytochemistry Reviews Vol. 17, No. 2 ( 2018-4), p. 291-326
    Details
    In: Phytochemistry Reviews, Springer Science and Business Media LLC, Vol. 17, No. 2 ( 2018-4), p. 291-326
    Type of Medium: Online Resource
    ISSN: 1568-7767 , 1572-980X
    URL: Article
    DOI: 10.1007/s11101-017-9532-2
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2018
    detail.hit.zdb_id: 2065661-0
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  • 4
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    Spatio‐temporal expression dynamics differ between homologues of flowering time genes in the allopolyploid Brassica napus
    Wiley ; 2018
    In:  The Plant Journal Vol. 96, No. 1 ( 2018-10), p. 103-118
    Details
    In: The Plant Journal, Wiley, Vol. 96, No. 1 ( 2018-10), p. 103-118
    Abstract: Many economically important crops exhibit extensive gene duplication due to recent or ancestral polyploidisation. This study demonstrates that flowering time genes have been preferentially retained in Brassica napus and that significant differences in the spatio‐temporal expression dynamics occur between gene homologues.
    Type of Medium: Online Resource
    ISSN: 0960-7412 , 1365-313X
    URL: Issue
    URL: Article
    DOI: 10.1111/tpj.2018.96.issue-1
    DOI: 10.1111/tpj.14020
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 2020961-7
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  • 5
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    A Novel and Fast Approach for Population Structure Inference Using Kernel-PCA and Optimization
    Oxford University Press (OUP) ; 2014
    In:  Genetics Vol. 198, No. 4 ( 2014-12-01), p. 1421-1431
    Details
    In: Genetics, Oxford University Press (OUP), Vol. 198, No. 4 ( 2014-12-01), p. 1421-1431
    Abstract: Population structure is a confounding factor in genome-wide association studies, increasing the rate of false positive associations. To correct for it, several model-based algorithms such as ADMIXTURE and STRUCTURE have been proposed. These tend to suffer from the fact that they have a considerable computational burden, limiting their applicability when used with large datasets, such as those produced by next generation sequencing techniques. To address this, nonmodel based approaches such as sparse nonnegative matrix factorization (sNMF) and EIGENSTRAT have been proposed, which scale better with larger data. Here we present a novel nonmodel-based approach, population structure inference using kernel-PCA and optimization (PSIKO), which is based on a unique combination of linear kernel-PCA and least-squares optimization and allows for the inference of admixture coefficients, principal components, and number of founder populations of a dataset. PSIKO has been compared against existing leading methods on a variety of simulation scenarios, as well as on real biological data. We found that in addition to producing results of the same quality as other tested methods, PSIKO scales extremely well with dataset size, being considerably (up to 30 times) faster for longer sequences than even state-of-the-art methods such as sNMF. PSIKO and accompanying manual are freely available at https://www.uea.ac.uk/computing/psiko.
    Type of Medium: Online Resource
    ISSN: 1943-2631
    URL: Article
    DOI: 10.1534/genetics.114.171314
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2014
    detail.hit.zdb_id: 1477228-0
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  • 6
    Online Resource
    Online Resource
    Segmental Structure of the Brassica napus Genome Based on Comparative Analysis With Arabidopsis thaliana
    Oxford University Press (OUP) ; 2005
    In:  Genetics Vol. 171, No. 2 ( 2005-10-01), p. 765-781
    Details
    In: Genetics, Oxford University Press (OUP), Vol. 171, No. 2 ( 2005-10-01), p. 765-781
    Abstract: Over 1000 genetically linked RFLP loci in Brassica napus were mapped to homologous positions in the Arabidopsis genome on the basis of sequence similarity. Blocks of genetically linked loci in B. napus frequently corresponded to physically linked markers in Arabidopsis. This comparative analysis allowed the identification of a minimum of 21 conserved genomic units within the Arabidopsis genome, which can be duplicated and rearranged to generate the present-day B. napus genome. The conserved regions extended over lengths as great as 50 cM in the B. napus genetic map, equivalent to ∼9 Mb of contiguous sequence in the Arabidopsis genome. There was also evidence for conservation of chromosome landmarks, particularly centromeric regions, between the two species. The observed segmental structure of the Brassica genome strongly suggests that the extant Brassica diploid species evolved from a hexaploid ancestor. The comparative map assists in exploiting the Arabidopsis genomic sequence for marker and candidate gene identification within the larger, intractable genomes of the Brassica polyploids.
    Type of Medium: Online Resource
    ISSN: 1943-2631
    URL: Article
    DOI: 10.1534/genetics.105.042093
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2005
    detail.hit.zdb_id: 1477228-0
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  • 7
    Online Resource
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    Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing
    Wiley ; 2009
    In:  Plant Biotechnology Journal Vol. 7, No. 4 ( 2009-05), p. 334-346
    Details
    In: Plant Biotechnology Journal, Wiley, Vol. 7, No. 4 ( 2009-05), p. 334-346
    Abstract: Oilseed rape ( Brassica napus ) was selected as an example of a polyploid crop, and the Solexa sequencing system was used to generate approximately 20 million expressed sequence tags (ESTs) from each of two cultivars: Tapidor and Ningyou 7. A methodology and computational tools were developed to exploit, as a reference sequence, a publicly available set of approximately 94 000 Brassica species unigenes. Sequences transcribed in the leaves of juvenile plants were aligned to approximately 26 Mb of the reference sequences. The aligned sequences enabled the detection of 23 330–41 593 putative single nucleotide polymorphisms (SNPs) between the cultivars, depending on the read depth stringency applied. The majority of the detected polymorphisms (87.5–91.2%) were of a type indicative of transcription from homoeologous genes from the two parental genomes within oilseed rape, and are termed here ‘hemi‐SNPs’. The overall estimated polymorphism rate (~0.047%–0.084%) is consistent with that previously observed between the cultivars analysed. To demonstrate the heritability of SNPs and to assess their suitability for applications such as linkage map construction and association genetics, approximately nine million ESTs were generated, using the Solexa system, from each of four lines of a doubled haploid mapping population derived from a cross between Tapidor and Ningyou 7. Computational tools were developed to score the alleles present in these lines for each of the potential SNPs identified between their parents. For a specimen region of the genome analysed in detail, segregation of alleles largely, although not entirely, followed the pattern expected for genomic markers.
    Type of Medium: Online Resource
    ISSN: 1467-7644 , 1467-7652
    URL: Issue
    URL: Article
    DOI: 10.1111/pbi.2009.7.issue-4
    DOI: 10.1111/j.1467-7652.2008.00396.x
    Language: English
    Publisher: Wiley
    Publication Date: 2009
    detail.hit.zdb_id: 2136367-5
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  • 8
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    Genome distribution of differential homoeologue contributions to leaf gene expression in bread wheat
    Wiley ; 2016
    In:  Plant Biotechnology Journal Vol. 14, No. 5 ( 2016-05), p. 1207-1214
    Details
    In: Plant Biotechnology Journal, Wiley, Vol. 14, No. 5 ( 2016-05), p. 1207-1214
    Abstract: Using a combination of de novo transcriptome assembly, a newly developed 9495‐marker transcriptome SNP genetic linkage map and comparative genomics approaches, we developed an ordered set of nonredundant transcripts for each of the subgenomes of hexaploid wheat: A (47 160 unigenes), B (59 663 unigenes) and D (40 588 unigenes). We used these as reference sequences against which to map Illumina mRNA ‐Seq reads derived from young leaf tissue. Transcript abundance was quantified for each unigene. Using a three‐way reciprocal BLAST approach, 15 527 triplet sets of homoeologues (one from each genome) were identified. Differential expression ( P   〈  0.05) was identified for 5248 unigenes, with 2906 represented at greater abundance than their two homoeologues and 2342 represented at lower abundance than their two homoeologues. Analysis of gene ontology terms revealed no biases between homoeologues. There was no evidence of genomewide dominance effects, rather the more highly transcribed individual genes were distributed throughout all three genomes. Transcriptome display tile plot, a visualization approach based on CMYK colour space, was developed and used to assess the genome for regions of skewed homoeologue transcript abundance. Extensive striation was revealed, indicative of many small regions of genome dominance (transcripts of homoeologues from one genome more abundant than the others) and many larger regions of genome repression (transcripts of homoeologues from one genome less abundant than the others).
    Type of Medium: Online Resource
    ISSN: 1467-7644 , 1467-7652
    URL: Issue
    URL: Article
    DOI: 10.1111/pbi.2016.14.issue-5
    DOI: 10.1111/pbi.12486
    Language: English
    Publisher: Wiley
    Publication Date: 2016
    detail.hit.zdb_id: 2136367-5
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  • 9
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    Online Resource
    Discovery and Biosynthesis of the Antibiotic Bicyclomycin in Distantly Related Bacterial Classes
    American Society for Microbiology ; 2018
    In:  Applied and Environmental Microbiology Vol. 84, No. 9 ( 2018-05)
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 84, No. 9 ( 2018-05)
    Abstract: Bicyclomycin (BCM) is a clinically promising antibiotic that is biosynthesized by Streptomyces cinnamoneus DSM 41675. BCM is structurally characterized by a core cyclo( l -Ile- l -Leu) 2,5-diketopiperazine (DKP) that is extensively oxidized. Here, we identify the BCM biosynthetic gene cluster, which shows that the core of BCM is biosynthesized by a cyclodipeptide synthase, and the oxidative modifications are introduced by five 2-oxoglutarate-dependent dioxygenases and one cytochrome P450 monooxygenase. The discovery of the gene cluster enabled the identification of BCM pathways encoded by the genomes of hundreds of Pseudomonas aeruginosa isolates distributed globally, and heterologous expression of the pathway from P. aeruginosa SCV20265 demonstrated that the product is chemically identical to BCM produced by S. cinnamoneus . Overall, putative BCM gene clusters have been found in at least seven genera spanning Actinobacteria and Proteobacteria ( Alphaproteobacteria , Betaproteobacteria , and Gammaproteobacteria ). This represents a rare example of horizontal gene transfer of an intact biosynthetic gene cluster across such distantly related bacteria, and we show that these gene clusters are almost always associated with mobile genetic elements. IMPORTANCE Bicyclomycin is the only natural product antibiotic that selectively inhibits the transcription termination factor Rho. This mechanism of action, combined with its proven biological safety and its activity against clinically relevant Gram-negative bacterial pathogens, makes it a very promising antibiotic candidate. Here, we report the identification of the bicyclomycin biosynthetic gene cluster in the known bicyclomycin-producing organism Streptomyces cinnamoneus , which will enable the engineered production of new bicyclomycin derivatives. The identification of this gene cluster also led to the discovery of hundreds of bicyclomycin pathways encoded in highly diverse bacteria, including in the opportunistic pathogen Pseudomonas aeruginosa . This wide distribution of a complex biosynthetic pathway is very unusual and provides an insight into how a pathway for an antibiotic can be transferred between diverse bacteria.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.02828-17
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2018
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
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  • 10
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    Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition
    eLife Sciences Publications, Ltd ; 2021
    In:  eLife Vol. 10 ( 2021-11-18)
    Details
    In: eLife, eLife Sciences Publications, Ltd, Vol. 10 ( 2021-11-18)
    Abstract: Potato scab and blight are two major diseases which can cause heavy crop losses. They are caused, respectively, by the bacterium Streptomyces scabies and an oomycete (a fungus-like organism) known as Phytophthora infestans . Fighting these disease-causing microorganisms can involve crop management techniques – for example, ensuring that a field is well irrigated helps to keep S. scabies at bay. Harnessing biological control agents can also offer ways to control disease while respecting the environment. Biocontrol bacteria, such as Pseudomonas , can produce compounds that keep S. scabies and P. infestans in check. However, the identity of these molecules and how irrigation can influence Pseudomonas population remains unknown. To examine these questions, Pacheco-Moreno et al. sampled and isolated hundreds of Pseudomonas strains from a commercial potato field, closely examining the genomes of 69 of these. Comparing the genetic information of strains based on whether they could control the growth of S. scabies revealed that compounds known as cyclic lipopeptides are key to controlling the growth of S. scabies and P. infestans . Whether the field was irrigated also had a large impact on the strains forming the Pseudomonas population. Working out how Pseudomonas bacteria block disease could speed up the search for biological control agents. The approach developed by Pacheco-Moreno et al. could help to predict which strains might be most effective based on their genetic features. Similar experiments could also work for other combinations of plants and diseases.
    Type of Medium: Online Resource
    ISSN: 2050-084X
    URL: Article
    DOI: 10.7554/eLife.71900
    Language: English
    Publisher: eLife Sciences Publications, Ltd
    Publication Date: 2021
    detail.hit.zdb_id: 2687154-3
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