Publications by authors named "David Swarbreck"

49 Publications

Degradome Assisted Plant MicroRNA Prediction under Alternative Annotation Criteria.

IEEE/ACM Trans Comput Biol Bioinform 2021 Sep 24;PP. Epub 2021 Sep 24.

Current microRNA (miRNA) prediction methods are generally based on annotation criteria that tend to miss potential functional miRNAs. Recently, new miRNA annotation criteria have been proposed that could lead to improvements in miRNA prediction methods in plants. Here, we investigate the effect of the new criteria on miRNA prediction in Arabidopsis thaliana and present a new degradome assisted functional miRNA prediction approach. We investigated the effect by applying the new criteria, and a more permissive criteria on miRNA prediction using existing miRNA prediction tools. We also developed an approach to miRNA prediction that is assisted by the functional information extracted from the analysis of degradome sequencing. We demonstrate the improved performance of degradome assisted miRNA prediction compared to unassisted prediction and evaluate the approach using miRNA differential expression analysis. We observe how the miRNA predictions fit under the different criteria and show a potential novel miRNA that has been missed within Arabidopsis thaliana. Additionally, we introduce a freely available software PAREfirst that employs the degradome assisted approach. The study shows that some miRNAs could be missed due to the stringency of the former annotation criteria, and combining a degradome assisted approach with more permissive miRNA criteria can expand confident miRNA predictions.
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http://dx.doi.org/10.1109/TCBB.2021.3115023DOI Listing
September 2021

Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches.

Microbiome 2021 06 21;9(1):143. Epub 2021 Jun 21.

Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3FG, UK.

Background: Gut microbiomes, such as the rumen, greatly influence host nutrition due to their feed energy-harvesting capacity. We investigated temporal ecological interactions facilitating energy harvesting at the fresh perennial ryegrass (PRG)-biofilm interface in the rumen using an in sacco approach and prokaryotic metatranscriptomic profiling.

Results: Network analysis identified two distinct sub-microbiomes primarily representing primary (≤ 4 h) and secondary (≥ 4 h) colonisation phases and the most transcriptionally active bacterial families (i.e Fibrobacteriaceae, Selemondaceae and Methanobacteriaceae) did not interact with either sub-microbiome, indicating non-cooperative behaviour. Conversely, Prevotellaceae had most transcriptional activity within the primary sub-microbiome (focussed on protein metabolism) and Lachnospiraceae within the secondary sub-microbiome (focussed on carbohydrate degradation). Putative keystone taxa, with low transcriptional activity, were identified within both sub-microbiomes, highlighting the important synergistic role of minor bacterial families; however, we hypothesise that they may be 'cheating' in order to capitalise on the energy-harvesting capacity of other microbes. In terms of chemical cues underlying transition from primary to secondary colonisation phases, we suggest that AI-2-based quorum sensing plays a role, based on LuxS gene expression data, coupled with changes in PRG chemistry.

Conclusions: In summary, we show that fresh PRG-attached prokaryotes are resilient and adapt quickly to changing niches. This study provides the first major insight into the complex temporal ecological interactions occurring at the plant-biofilm interface within the rumen. The study also provides valuable insights into potential plant breeding strategies for development of the utopian plant, allowing optimal sustainable production of ruminants. Video Abstract.
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http://dx.doi.org/10.1186/s40168-021-01087-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8215763PMC
June 2021

Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential.

Nat Genet 2021 04 18;53(4):564-573. Epub 2021 Mar 18.

Aquatic and Crop Resource Development, National Research Council, Saskatoon, Saskatchewan, Canada.

Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye's incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye-wheat introgressions.
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http://dx.doi.org/10.1038/s41588-021-00807-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8035072PMC
April 2021

Multiple wheat genomes reveal global variation in modern breeding.

Nature 2020 12 25;588(7837):277-283. Epub 2020 Nov 25.

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome, and the lack of genome-assembly data for multiple wheat lines. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm1, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.
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http://dx.doi.org/10.1038/s41586-020-2961-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7759465PMC
December 2020

Chromosome-Scale Genome Assemblies of Aphids Reveal Extensively Rearranged Autosomes and Long-Term Conservation of the X Chromosome.

Mol Biol Evol 2021 03;38(3):856-875

Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom.

Chromosome rearrangements are arguably the most dramatic type of mutations, often leading to rapid evolution and speciation. However, chromosome dynamics have only been studied at the sequence level in a small number of model systems. In insects, Diptera and Lepidoptera have conserved genome structure at the scale of whole chromosomes or chromosome arms. Whether this reflects the diversity of insect genome evolution is questionable given that many species exhibit rapid karyotype evolution. Here, we investigate chromosome evolution in aphids-an important group of hemipteran plant pests-using newly generated chromosome-scale genome assemblies of the green peach aphid (Myzus persicae) and the pea aphid (Acyrthosiphon pisum), and a previously published assembly of the corn-leaf aphid (Rhopalosiphum maidis). We find that aphid autosomes have undergone dramatic reorganization over the last 30 My, to the extent that chromosome homology cannot be determined between aphids from the tribes Macrosiphini (Myzus persicae and Acyrthosiphon pisum) and Aphidini (Rhopalosiphum maidis). In contrast, gene content of the aphid sex (X) chromosome remained unchanged despite rapid sequence evolution, low gene expression, and high transposable element load. To test whether rapid evolution of genome structure is a hallmark of Hemiptera, we compared our aphid assemblies with chromosome-scale assemblies of two blood-feeding Hemiptera (Rhodnius prolixus and Triatoma rubrofasciata). Despite being more diverged, the blood-feeding hemipterans have conserved synteny. The exceptional rate of structural evolution of aphid autosomes renders them an important emerging model system for studying the role of large-scale genome rearrangements in evolution.
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http://dx.doi.org/10.1093/molbev/msaa246DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7947777PMC
March 2021

An aphid RNA transcript migrates systemically within plants and is a virulence factor.

Proc Natl Acad Sci U S A 2020 06 27;117(23):12763-12771. Epub 2020 May 27.

Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom;

Aphids are sap-feeding insects that colonize a broad range of plant species and often cause feeding damage and transmit plant pathogens, including bacteria, viruses, and viroids. These insects feed from the plant vascular tissue, predominantly the phloem. However, it remains largely unknown how aphids, and other sap-feeding insects, establish intimate long-term interactions with plants. To identify aphid virulence factors, we took advantage of the ability of the green peach aphid to colonize divergent plant species. We found that a clone of near-identical females established stable colonies on nine plant species of five representative plant eudicot and monocot families that span the angiosperm phylogeny. Members of the novel aphid gene family are differentially expressed in aphids on the nine plant species and are coregulated and organized as tandem repeats in aphid genomes. Aphids translocate transcripts into plants, and some transcripts migrate to distal leaves within several plant species. RNAi-mediated knockdown of genes reduces fecundity, and produces more progeny on transgenic plants that heterologously produce one of the systemically migrating transcripts as a long noncoding (lnc) RNA. Taken together, our findings show that beyond a range of pathogens, aphids translocate their own transcripts into plants, including a lncRNA that migrates to distal locations within plants, promotes aphid fecundity, and is a member of a previously undescribed host-responsive aphid gene family that operate as virulence factors.
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http://dx.doi.org/10.1073/pnas.1918410117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293609PMC
June 2020

Sex-specific changes in the aphid DNA methylation landscape.

Mol Ecol 2019 09 22;28(18):4228-4241. Epub 2019 Sep 22.

School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.

Aphids present an ideal system to study epigenetics as they can produce diverse, but genetically identical, morphs in response to environmental stimuli. Here, using whole genome bisulphite sequencing and transcriptome sequencing of the green peach aphid (Myzus persicae), we present the first detailed analysis of cytosine methylation in an aphid and investigate differences in the methylation and transcriptional landscapes of male and asexual female morphs. We found that methylation primarily occurs in a CG dinucleotide (CpG) context and that exons are highly enriched for methylated CpGs, particularly at the 3' end of genes. Methylation is positively associated with gene expression, and methylated genes are more stably expressed than unmethylated genes. Male and asexual female morphs have distinct methylation profiles. Strikingly, these profiles are divergent between the sex chromosome and the autosomes; autosomal genes are hypomethylated in males compared to asexual females, whereas genes belonging to the sex chromosome, which is haploid in males, are hypermethylated. Overall, we found correlated changes in methylation and gene expression between males and asexual females, and this correlation was particularly strong for genes located on the sex chromosome. Our results suggest that differential methylation of sex-biased genes plays a role in aphid sexual differentiation.
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http://dx.doi.org/10.1111/mec.15216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6857007PMC
September 2019

Genome-Wide Transcription During Early Wheat Meiosis Is Independent of Synapsis, Ploidy Level, and the Locus.

Front Plant Sci 2018 4;9:1791. Epub 2018 Dec 4.

John Innes Centre, Norwich, United Kingdom.

Polyploidization is a fundamental process in plant evolution. One of the biggest challenges faced by a new polyploid is meiosis, particularly discriminating between multiple related chromosomes so that only homologous chromosomes synapse and recombine to ensure regular chromosome segregation and balanced gametes. Despite its large genome size, high DNA repetitive content and similarity between homoeologous chromosomes, hexaploid wheat completes meiosis in a shorter period than diploid species with a much smaller genome. Therefore, during wheat meiosis, mechanisms additional to the classical model based on DNA sequence homology, must facilitate more efficient homologous recognition. One such mechanism could involve exploitation of differences in chromosome structure between homologs and homoeologs at the onset of meiosis. In turn, these chromatin changes, can be expected to be linked to transcriptional gene activity. In this study, we present an extensive analysis of a large RNA-seq data derived from six different genotypes: wheat, wheat-rye hybrids and newly synthesized octoploid triticale, both in the presence and absence of the locus. Plant material was collected at early prophase, at the transition leptotene-zygotene, when the telomere bouquet is forming and synapsis between homologs is beginning. The six genotypes exhibit different levels of synapsis and chromatin structure at this stage; therefore, recombination and consequently segregation, are also different. Unexpectedly, our study reveals that neither synapsis, whole genome duplication nor the absence of the locus are associated with major changes in gene expression levels during early meiotic prophase. Overall wheat transcription at this meiotic stage is therefore highly resilient to such alterations, even in the presence of major chromatin structural changes. Further studies in wheat and other polyploid species will be required to reveal whether these observations are specific to wheat meiosis.
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http://dx.doi.org/10.3389/fpls.2018.01791DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6288783PMC
December 2018

Primula vulgaris (primrose) genome assembly, annotation and gene expression, with comparative genomics on the heterostyly supergene.

Sci Rep 2018 12 18;8(1):17942. Epub 2018 Dec 18.

School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom.

Primula vulgaris (primrose) exhibits heterostyly: plants produce self-incompatible pin- or thrum-form flowers, with anthers and stigma at reciprocal heights. Darwin concluded that this arrangement promotes insect-mediated cross-pollination; later studies revealed control by a cluster of genes, or supergene, known as the S (Style length) locus. The P. vulgaris S locus is absent from pin plants and hemizygous in thrum plants (thrum-specific); mutation of S locus genes produces self-fertile homostyle flowers with anthers and stigma at equal heights. Here, we present a 411 Mb P. vulgaris genome assembly of a homozygous inbred long homostyle, representing ~87% of the genome. We annotate over 24,000 P. vulgaris genes, and reveal more genes up-regulated in thrum than pin flowers. We show reduced genomic read coverage across the S locus in other Primula species, including P. veris, where we define the conserved structure and expression of the S locus genes in thrum. Further analysis reveals the S locus has elevated repeat content (64%) compared to the wider genome (37%). Our studies suggest conservation of S locus genetic architecture in Primula, and provide a platform for identification and evolutionary analysis of the S locus and downstream targets that regulate heterostyly in diverse heterostylous species.
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http://dx.doi.org/10.1038/s41598-018-36304-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6299000PMC
December 2018

Efficient and accurate detection of splice junctions from RNA-seq with Portcullis.

Gigascience 2018 12 1;7(12). Epub 2018 Dec 1.

Earlham Institute, Norwich Research Park, NR47UZ, Norwich, United Kingdom.

Next-generation sequencing technologies enable rapid and cheap genome-wide transcriptome analysis, providing vital information about gene structure, transcript expression, and alternative splicing. Key to this is the accurate identification of exon-exon junctions from RNA sequenced (RNA-seq) reads. A number of RNA-seq aligners capable of splitting reads across these splice junctions (SJs) have been developed; however, it has been shown that while they correctly identify most genuine SJs available in a given sample, they also often produce large numbers of incorrect SJs. Here, we describe the extent of this problem using popular RNA-seq mapping tools and present a new method, called Portcullis, to rapidly filter false SJs derived from spliced alignments. We show that Portcullis distinguishes between genuine and false-positive junctions to a high degree of accuracy across different species, samples, expression levels, error profiles, and read lengths. Portcullis is portable, efficient, and, to our knowledge, currently the only SJ prediction tool that reliably scales for use with large RNA-seq datasets and large, highly fragmented genomes, while delivering accurate SJs.
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http://dx.doi.org/10.1093/gigascience/giy131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302956PMC
December 2018

Biodiversity-function relationships in methanogenic communities.

Mol Ecol 2018 11 22;27(22):4641-4651. Epub 2018 Nov 22.

ESI and CEC, Biosciences, University of Exeter, Penryn, UK.

Methanogenic communities play a crucial role in carbon cycling and biotechnology (anaerobic digestion), but our understanding of how their diversity, or composition in general, determines the rate of methane production is very limited. Studies to date have been correlational because of the difficulty in cultivating their constituent species in pure culture. Here, we investigate the causal link between methanogenesis and diversity in laboratory anaerobic digesters by experimentally manipulating the diversity of cultures by dilution and subsequent equilibration of biomass. This process necessarily leads to the loss of the rarer species from communities. We find a positive relationship between methane production and the number of taxa, with little evidence of functional saturation, suggesting that rare species play an important role in methane-producing communities. No correlations were found between the initial composition and methane production across natural communities, but a positive relationship between species richness and methane production emerged following ecological selection imposed by the laboratory conditions. Our data suggest methanogenic communities show little functional redundancy, and hence, any loss of diversity-both natural and resulting from changes in propagation conditions during anaerobic digestion-is likely to reduce methane production.
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http://dx.doi.org/10.1111/mec.14895DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6282539PMC
November 2018

Shifting the limits in wheat research and breeding using a fully annotated reference genome.

Science 2018 08 16;361(6403). Epub 2018 Aug 16.

GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France.

An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.
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http://dx.doi.org/10.1126/science.aar7191DOI Listing
August 2018

Leveraging multiple transcriptome assembly methods for improved gene structure annotation.

Gigascience 2018 08 1;7(8). Epub 2018 Aug 1.

Earlham Institute, Norwich Research Park, NR47UZ, Norwich, United Kingdom.

Background: The performance of RNA sequencing (RNA-seq) aligners and assemblers varies greatly across different organisms and experiments, and often the optimal approach is not known beforehand.

Results: Here, we show that the accuracy of transcript reconstruction can be boosted by combining multiple methods, and we present a novel algorithm to integrate multiple RNA-seq assemblies into a coherent transcript annotation. Our algorithm can remove redundancies and select the best transcript models according to user-specified metrics, while solving common artifacts such as erroneous transcript chimerisms.

Conclusions: We have implemented this method in an open-source Python3 and Cython program, Mikado, available on GitHub.
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http://dx.doi.org/10.1093/gigascience/giy093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6105091PMC
August 2018

The ash dieback invasion of Europe was founded by two genetically divergent individuals.

Nat Ecol Evol 2018 06 23;2(6):1000-1008. Epub 2018 Apr 23.

John Innes Centre, Norwich Research Park, Norwich, UK.

Accelerating international trade and climate change make pathogen spread an increasing concern. Hymenoscyphus fraxineus, the causal agent of ash dieback, is a fungal pathogen that has been moving across continents and hosts from Asian to European ash. Most European common ash trees (Fraxinus excelsior) are highly susceptible to H. fraxineus, although a minority (~5%) have partial resistance to dieback. Here, we assemble and annotate a H. fraxineus draft genome, which approaches chromosome scale. Pathogen genetic diversity across Europe and in Japan, reveals a strong bottleneck in Europe, though a signal of adaptive diversity remains in key host interaction genes. We find that the European population was founded by two divergent haploid individuals. Divergence between these haplotypes represents the ancestral polymorphism within a large source population. Subsequent introduction from this source would greatly increase adaptive potential of the pathogen. Thus, further introgression of H. fraxineus into Europe represents a potential threat and Europe-wide biological security measures are needed to manage this disease.
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http://dx.doi.org/10.1038/s41559-018-0548-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5969572PMC
June 2018

A Single Community Dominates Structure and Function of a Mixture of Multiple Methanogenic Communities.

Curr Biol 2017 Nov 26;27(21):3390-3395.e4. Epub 2017 Oct 26.

Biosciences, University of Exeter, Penryn, Cornwall TR10 9FE, UK.

The ecology of microbes frequently involves the mixing of entire communities (community coalescence), for example, flooding events, host excretion, and soil tillage [1, 2], yet the consequences of this process for community structure and function are poorly understood [3-7]. Recent theory suggests that a community, due to coevolution between constituent species, may act as a partially cohesive unit [8-11], resulting in one community dominating after community coalescence. This dominant community is predicted to be the one that uses resources most efficiently when grown in isolation [11]. We experimentally tested these predictions using methanogenic communities, for which efficient resource use, quantified by methane production, requires coevolved cross-feeding interactions between species [12]. After propagation in laboratory-scale anaerobic digesters, community composition (determined from 16S rRNA sequencing) and methane production of mixtures of communities closely resembled that of the single most productive community grown in isolation. Analysis of each community's contribution toward the final mixture suggests that certain combinations of taxa within a community might be co-selected as a result of coevolved interactions. As a corollary of these findings, we also show that methane production increased with the number of inoculated communities. These findings are relevant to the understanding of the ecological dynamics of natural microbial communities, as well as demonstrating a simple method of predictably enhancing microbial community function in biotechnology, health, and agriculture [13].
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http://dx.doi.org/10.1016/j.cub.2017.09.056DOI Listing
November 2017

Exploiting the homologue within the wheat locus has identified two lines exhibiting homoeologous crossover in wheat-wild relative hybrids.

Mol Breed 2017 18;37(8):95. Epub 2017 Jul 18.

John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK.

Despite possessing related ancestral genomes, hexaploid wheat behaves as a diploid during meiosis. The wheat locus promotes accurate synapsis and crossover of homologous chromosomes. Interspecific hybrids between wheat and wild relatives are exploited by breeders to introgress important traits from wild relatives into wheat, although in hybrids between hexaploid wheat and wild relatives, which possess only homoeologues, crossovers do not take place during meiosis at metaphase I. However, in hybrids between deletion mutants and wild relatives, crossovers do take place. A single deletion () mutant has been exploited for the last 40 years for this activity. We show here that chemically induced mutant lines, selected for a mutation in within the locus, exhibit high levels of homoeologous crossovers when crossed with wild relatives. mutant lines may be more stable over multiple generations, as multivalents causing accumulation of chromosome translocations are less frequent. Exploitation of such mutants, rather than mutants with whole locus deletions, may therefore improve introgression of wild relative chromosome segments into wheat.
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http://dx.doi.org/10.1007/s11032-017-0700-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5515957PMC
July 2017

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.

Genome Res 2017 05;27(5):885-896

Earlham Institute, Norwich, NR4 7UZ, United Kingdom.

Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop.
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http://dx.doi.org/10.1101/gr.217117.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411782PMC
May 2017

Heterarchy of transcription factors driving basal and luminal cell phenotypes in human urothelium.

Cell Death Differ 2017 05 10;24(5):809-818. Epub 2017 Mar 10.

Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, UK.

Cell differentiation is affected by complex networks of transcription factors that co-ordinate re-organisation of the chromatin landscape. The hierarchies of these relationships can be difficult to dissect. During in vitro differentiation of normal human uro-epithelial cells, formaldehyde-assisted isolation of regulatory elements (FAIRE-seq) and RNA-seq was used to identify alterations in chromatin accessibility and gene expression changes following activation of the nuclear receptor peroxisome proliferator-activated receptor gamma (PPARγ) as a differentiation-initiating event. Regions of chromatin identified by FAIRE-seq, as having altered accessibility during differentiation, were found to be enriched with sequence-specific binding motifs for transcription factors predicted to be involved in driving basal and differentiated urothelial cell phenotypes, including forkhead box A1 (FOXA1), P63, GRHL2, CTCF and GATA-binding protein 3 (GATA3). In addition, co-occurrence of GATA3 motifs was observed within subsets of differentiation-specific peaks containing P63 or FOXA1. Changes in abundance of GRHL2, GATA3 and P63 were observed in immunoblots of chromatin-enriched extracts. Transient siRNA knockdown of P63 revealed that P63 favoured a basal-like phenotype by inhibiting differentiation and promoting expression of basal marker genes. GATA3 siRNA prevented differentiation-associated downregulation of P63 protein and transcript, and demonstrated positive feedback of GATA3 on PPARG transcript, but showed no effect on FOXA1 transcript or protein expression. This approach indicates that as a transcriptionally regulated programme, urothelial differentiation operates as a heterarchy, wherein GATA3 is able to co-operate with FOXA1 to drive expression of luminal marker genes, but that P63 has potential to transrepress expression of the same genes.
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http://dx.doi.org/10.1038/cdd.2017.10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5423105PMC
May 2017

Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species.

Genome Biol 2017 02 13;18(1):27. Epub 2017 Feb 13.

Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.

Background: The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a small number of closely related host species. Remarkably, the green peach aphid, Myzus persicae, colonises plant species across 40 families and single M. persicae clonal lineages can colonise distantly related plants. This remarkable ability makes M. persicae a highly destructive pest of many important crop species.

Results: To investigate the exceptional phenotypic plasticity of M. persicae, we sequenced the M. persicae genome and assessed how one clonal lineage responds to host plant species of different families. We show that genetically identical individuals are able to colonise distantly related host species through the differential regulation of genes belonging to aphid-expanded gene families. Multigene clusters collectively upregulate in single aphids within two days upon host switch. Furthermore, we demonstrate the functional significance of this rapid transcriptional change using RNA interference (RNAi)-mediated knock-down of genes belonging to the cathepsin B gene family. Knock-down of cathepsin B genes reduced aphid fitness, but only on the host that induced upregulation of these genes.

Conclusions: Previous research has focused on the role of genetic adaptation of parasites to their hosts. Here we show that the generalist aphid pest M. persicae is able to colonise diverse host plant species in the absence of genetic specialisation. This is achieved through rapid transcriptional plasticity of genes that have duplicated during aphid evolution.
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http://dx.doi.org/10.1186/s13059-016-1145-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5304397PMC
February 2017

Genome sequence and genetic diversity of European ash trees.

Nature 2017 01 26;541(7636):212-216. Epub 2016 Dec 26.

School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.

Ash trees (genus Fraxinus, family Oleaceae) are widespread throughout the Northern Hemisphere, but are being devastated in Europe by the fungus Hymenoscyphus fraxineus, causing ash dieback, and in North America by the herbivorous beetle Agrilus planipennis. Here we sequence the genome of a low-heterozygosity Fraxinus excelsior tree from Gloucestershire, UK, annotating 38,852 protein-coding genes of which 25% appear ash specific when compared with the genomes of ten other plant species. Analyses of paralogous genes suggest a whole-genome duplication shared with olive (Olea europaea, Oleaceae). We also re-sequence 37 F. excelsior trees from Europe, finding evidence for apparent long-term decline in effective population size. Using our reference sequence, we re-analyse association transcriptomic data, yielding improved markers for reduced susceptibility to ash dieback. Surveys of these markers in British populations suggest that reduced susceptibility to ash dieback may be more widespread in Great Britain than in Denmark. We also present evidence that susceptibility of trees to H. fraxineus is associated with their iridoid glycoside levels. This rapid, integrated, multidisciplinary research response to an emerging health threat in a non-model organism opens the way for mitigation of the epidemic.
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http://dx.doi.org/10.1038/nature20786DOI Listing
January 2017

Genetic architecture and evolution of the S locus supergene in Primula vulgaris.

Nat Plants 2016 12 2;2(12):16188. Epub 2016 Dec 2.

School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.

Darwin's studies on heterostyly in Primula described two floral morphs, pin and thrum, with reciprocal anther and stigma heights that promote insect-mediated cross-pollination. This key innovation evolved independently in several angiosperm families. Subsequent studies on heterostyly in Primula contributed to the foundation of modern genetic theory and the neo-Darwinian synthesis. The established genetic model for Primula heterostyly involves a diallelic S locus comprising several genes, with rare recombination events that result in self-fertile homostyle flowers with anthers and stigma at the same height. Here we reveal the S locus supergene as a tightly linked cluster of thrum-specific genes that are absent in pins. We show that thrums are hemizygous not heterozygous for the S locus, which suggests that homostyles do not arise by recombination between S locus haplotypes as previously proposed. Duplication of a floral homeotic gene 51.7 million years (Myr) ago, followed by its neofunctionalization, created the current S locus assemblage which led to floral heteromorphy in Primula. Our findings provide new insights into the structure, function and evolution of this archetypal supergene.
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http://dx.doi.org/10.1038/nplants.2016.188DOI Listing
December 2016

A stable genetic polymorphism underpinning microbial syntrophy.

ISME J 2016 12 3;10(12):2844-2853. Epub 2016 Jun 3.

School of Life Sciences, The University of Warwick, Coventry, UK.

Syntrophies are metabolic cooperations, whereby two organisms co-metabolize a substrate in an interdependent manner. Many of the observed natural syntrophic interactions are mandatory in the absence of strong electron acceptors, such that one species in the syntrophy has to assume the role of electron sink for the other. While this presents an ecological setting for syntrophy to be beneficial, the potential genetic drivers of syntrophy remain unknown to date. Here, we show that the syntrophic sulfate-reducing species Desulfovibrio vulgaris displays a stable genetic polymorphism, where only a specific genotype is able to engage in syntrophy with the hydrogenotrophic methanogen Methanococcus maripaludis. This 'syntrophic' genotype is characterized by two genetic alterations, one of which is an in-frame deletion in the gene encoding for the ion-translocating subunit cooK of the membrane-bound COO hydrogenase. We show that this genotype presents a specific physiology, in which reshaping of energy conservation in the lactate oxidation pathway enables it to produce sufficient intermediate hydrogen for sustained M. maripaludis growth and thus, syntrophy. To our knowledge, these findings provide for the first time a genetic basis for syntrophy in nature and bring us closer to the rational engineering of syntrophy in synthetic microbial communities.
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http://dx.doi.org/10.1038/ismej.2016.80DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5042321PMC
December 2016

The mucin-degradation strategy of Ruminococcus gnavus: The importance of intramolecular trans-sialidases.

Gut Microbes 2016 07 25;7(4):302-312. Epub 2016 May 25.

a Institute of Food Research, The Gut Health and Food Safety Institute Strategic Program, Norwich Research Park , Norwich , United Kingdom.

We previously identified and characterized an intramolecular trans-sialidase (IT-sialidase) in the gut symbiont Ruminococcus gnavus ATCC 29149, which is associated to the ability of the strain to grow on mucins. In this work we have obtained and analyzed the draft genome sequence of another R. gnavus mucin-degrader, ATCC 35913, isolated from a healthy individual. Transcriptomics analyses of both ATCC 29149 and ATCC 35913 strains confirmed that the strategy utilized by R. gnavus for mucin-degradation is focused on the utilization of terminal mucin glycans. R. gnavus ATCC 35913 also encodes a predicted IT-sialidase and harbors a Nan cluster dedicated to sialic acid utilization. We showed that the Nan cluster was upregulated when the strains were grown in presence of mucin. In addition we demonstrated that both R. gnavus strains were able to grow on 2,7-anyhydro-Neu5Ac, the IT-sialidase transglycosylation product, as a sole carbon source. Taken together these data further support the hypothesis that IT-sialidase expressing gut microbes, provide commensal bacteria such as R. gnavus with a nutritional competitive advantage, by accessing and transforming a source of nutrient to their own benefit.
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http://dx.doi.org/10.1080/19490976.2016.1186334DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4988440PMC
July 2016

An Improved microRNA Annotation of the Canine Genome.

PLoS One 2016 27;11(4):e0153453. Epub 2016 Apr 27.

Vertebrate and Health Genomics, The Genome Analysis Centre, Norwich, United Kingdom.

The domestic dog, Canis familiaris, is a valuable model for studying human diseases. The publication of the latest Canine genome build and annotation, CanFam3.1 provides an opportunity to enhance our understanding of gene regulation across tissues in the dog model system. In this study, we used the latest dog genome assembly and small RNA sequencing data from 9 different dog tissues to predict novel miRNAs in the dog genome, as well as to annotate conserved miRNAs from the miRBase database that were missing from the current dog annotation. We used both miRCat and miRDeep2 algorithms to computationally predict miRNA loci. The resulting, putative hairpin sequences were analysed in order to discard false positives, based on predicted secondary structures and patterns of small RNA read alignments. Results were further divided into high and low confidence miRNAs, using the same criteria. We generated tissue specific expression profiles for the resulting set of 811 loci: 720 conserved miRNAs, (207 of which had not been previously annotated in the dog genome) and 91 novel miRNA loci. Comparative analyses revealed 8 putative homologues of some novel miRNA in ferret, and one in microbat. All miRNAs were also classified into the genic and intergenic categories, based on the Ensembl RefSeq gene annotation for CanFam3.1. This additionally allowed us to identify four previously undescribed MiRtrons among our total set of miRNAs. We additionally annotated piRNAs, using proTRAC on the same input data. We thus identified 263 putative clusters, most of which (211 clusters) were found to be expressed in testis. Our results represent an important improvement of the dog genome annotation, paving the way to further research on the evolution of gene regulation, as well as on the contribution of post-transcriptional regulation to pathological conditions.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0153453PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4847789PMC
February 2017

The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract.

BMC Genomics 2015 Dec 1;16:1023. Epub 2015 Dec 1.

The Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK.

Background: Lactobacillus reuteri is a gut symbiont of a wide variety of vertebrate species that has diversified into distinct phylogenetic clades which are to a large degree host-specific. Previous work demonstrated host specificity in mice and begun to determine the mechanisms by which gut colonisation and host restriction is achieved. However, how L. reuteri strains colonise the gastrointestinal (GI) tract of pigs is unknown.

Results: To gain insight into the ecology of L. reuteri in the pig gut, the genome sequence of the porcine small intestinal isolate L. reuteri ATCC 53608 was completed and consisted of a chromosome of 1.94 Mbp and two plasmids of 138.5 kbp and 9.09 kbp, respectively. Furthermore, we generated draft genomes of four additional L. reuteri strains isolated from pig faeces or lower GI tract, lp167-67, pg-3b, 20-2 and 3c6, and subjected all five genomes to a comparative genomic analysis together with the previously completed genome of strain I5007. A phylogenetic analysis based on whole genomes showed that porcine L. reuteri strains fall into two distinct clades, as previously suggested by multi-locus sequence analysis. These six pig L. reuteri genomes contained a core set of 1364 orthologous gene clusters, as determined by OrthoMCL analysis, that contributed to a pan-genome totalling 3373 gene clusters. Genome comparisons of the six pig L. reuteri strains with 14 L. reuteri strains from other host origins gave a total pan-genome of 5225 gene clusters that included a core genome of 851 gene clusters but revealed that there were no pig-specific genes per se. However, genes specific for and conserved among strains of the two pig phylogenetic lineages were detected, some of which encoded cell surface proteins that could contribute to the diversification of the two lineages and their observed host specificity.

Conclusions: This study extends the phylogenetic analysis of L. reuteri strains at a genome-wide level, pointing to distinct evolutionary trajectories of porcine L. reuteri lineages, and providing new insights into the genomic events in L. reuteri that occurred during specialisation to their hosts. The occurrence of two distinct pig-derived clades may reflect differences in host genotype, environmental factors such as dietary components or to evolution from ancestral strains of human and rodent origin following contact with pig populations.
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http://dx.doi.org/10.1186/s12864-015-2216-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4667477PMC
December 2015

Lessons from Fraxinus, a crowd-sourced citizen science game in genomics.

Elife 2015 Jul 29;4:e07460. Epub 2015 Jul 29.

The Sainsbury Laboratory, Norwich, United Kingdom.

In 2013, in response to an epidemic of ash dieback disease in England the previous year, we launched a Facebook-based game called Fraxinus to enable non-scientists to contribute to genomics studies of the pathogen that causes the disease and the ash trees that are devastated by it. Over a period of 51 weeks players were able to match computational alignments of genetic sequences in 78% of cases, and to improve them in 15% of cases. We also found that most players were only transiently interested in the game, and that the majority of the work done was performed by a small group of dedicated players. Based on our experiences we have built a linear model for the length of time that contributors are likely to donate to a crowd-sourced citizen science project. This model could serve a guide for the design and implementation of future crowd-sourced citizen science initiatives.
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http://dx.doi.org/10.7554/eLife.07460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517073PMC
July 2015

Oakleaf: an S locus-linked mutation of Primula vulgaris that affects leaf and flower development.

New Phytol 2015 Oct 9;208(1):149-61. Epub 2015 Apr 9.

School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.

In Primula vulgaris outcrossing is promoted through reciprocal herkogamy with insect-mediated cross-pollination between pin and thrum form flowers. Development of heteromorphic flowers is coordinated by genes at the S locus. To underpin construction of a genetic map facilitating isolation of these S locus genes, we have characterised Oakleaf, a novel S locus-linked mutant phenotype. We combine phenotypic observation of flower and leaf development, with classical genetic analysis and next-generation sequencing to address the molecular basis of Oakleaf. Oakleaf is a dominant mutation that affects both leaf and flower development; plants produce distinctive lobed leaves, with occasional ectopic meristems on the veins. This phenotype is reminiscent of overexpression of Class I KNOX-homeodomain transcription factors. We describe the structure and expression of all eight P. vulgaris PvKNOX genes in both wild-type and Oakleaf plants, and present comparative transcriptome analysis of leaves and flowers from Oakleaf and wild-type plants. Oakleaf provides a new phenotypic marker for genetic analysis of the Primula S locus. We show that none of the Class I PvKNOX genes are strongly upregulated in Oakleaf leaves and flowers, and identify cohorts of 507 upregulated and 314 downregulated genes in the Oakleaf mutant.
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http://dx.doi.org/10.1111/nph.13370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973830PMC
October 2015

RAMPART: a workflow management system for de novo genome assembly.

Bioinformatics 2015 Jun 30;31(11):1824-6. Epub 2015 Jan 30.

The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK.

Motivation: The de novo assembly of genomes from whole- genome shotgun sequence data is a computationally intensive, multi-stage task and it is not known a priori which methods and parameter settings will produce optimal results. In current de novo assembly projects, a popular strategy involves trying many approaches, using different tools and settings, and then comparing and contrasting the results in order to select a final assembly for publication.

Results: Herein, we present RAMPART, a configurable workflow management system for de novo genome assembly, which helps the user identify combinations of third-party tools and settings that provide good results for their particular genome and sequenced reads. RAMPART is designed to exploit High performance computing environments, such as clusters and shared memory systems, where available.

Availability And Implementation: RAMPART is available under the GPLv3 license at: https://github.com/TGAC/RAMPART.
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http://dx.doi.org/10.1093/bioinformatics/btv056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443680PMC
June 2015
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