Natural variation in Arabidopsis shoot branching plasticity in response to nitrate supply affects fitness.

The capacity of organisms to tune their development in response to environmental cues is pervasive in nature. This phenotypic plasticity is particularly striking in plants, enabled by their modular and continuous development. A good example is the activation of lateral shoot branches in Arabidopsis, which develop from axillary meristems at the base of leaves. The activity and elongation of lateral shoots depends on the integration of many signals both external (e.g. light, nutrient supply) and internal (e.g. the phytohormones auxin, strigolactone and cytokinin). Here, we characterise natural variation in plasticity of shoot branching in response to nitrate supply using two diverse panels of Arabidopsis lines. We find extensive variation in nitrate sensitivity across these lines, suggesting a genetic basis for variation in branching plasticity. High plasticity is associated with extreme branching phenotypes such that lines with the most branches on high nitrate have the fewest under nitrate deficient conditions. Conversely, low plasticity is associated with a constitutively moderate level of branching. Furthermore, variation in plasticity is associated with alternative life histories with the low plasticity lines flowering significantly earlier than high plasticity lines. In Arabidopsis, branching is highly correlated with fruit yield, and thus low plasticity lines produce more fruit than high plasticity lines under nitrate deficient conditions, whereas highly plastic lines produce more fruit under high nitrate conditions. Low and high plasticity, associated with early and late flowering respectively, can therefore be interpreted alternative escape vs mitigate strategies to low N environments. The genetic architecture of these traits appears to be highly complex, with only a small proportion of the estimated genetic variance detected in association mapping.

Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases.

Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new data sets. We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver, a tool for running BLAST and visually inspecting BLAST results for biological interpretation. Sequenceserver uses simple algorithms to prevent potential analysis errors and provides flexible text-based and visual outputs to support researcher productivity. Our software can be rapidly installed for use by individuals or on shared servers.

Ultrasonic particle sizing in aqueous suspensions of solid particles of unknown density.

Estimates of particle size distributions (PSDs) in solid-in-liquid suspensions can be made on the basis of measurements of ultrasonic wave attenuation combined with a mathematical propagation model, which typically requires seven physical parameters to describe each phase of the mixture. The estimation process is insensitive to all of these except the density of the solid particles, which may not be known or difficult to measure. This paper proposes that an unknown density value is incorporated into the sizing computation as a free variable. It is shown that this leads to an accurate estimate of PSD, as well as the unknown density.

A role for more axillary growth1 (MAX1) in evolutionary diversity in strigolactone signaling upstream of MAX2.

Strigolactones (SLs) are carotenoid-derived phytohormones with diverse roles. They are secreted from roots as attractants for arbuscular mycorrhizal fungi and have a wide range of endogenous functions, such as regulation of root and shoot system architecture. To date, six genes associated with SL synthesis and signaling have been molecularly identified using the shoot-branching mutants more axillary growth (max) of Arabidopsis (Arabidopsis thaliana) and dwarf (d) of rice (Oryza sativa). Here, we present a phylogenetic analysis of the MAX/D genes to clarify the relationships of each gene with its wider family and to allow the correlation of events in the evolution of the genes with the evolution of SL function. Our analysis suggests that the notion of a distinct SL pathway is inappropriate. Instead, there may be a diversity of SL-like compounds, the response to which requires a D14/D14-like protein. This ancestral system could have been refined toward distinct ligand-specific pathways channeled through MAX2, the most downstream known component of SL signaling. MAX2 is tightly conserved among land plants and is more diverged from its nearest sister clade than any other SL-related gene, suggesting a pivotal role in the evolution of SL signaling. By contrast, the evidence suggests much greater flexibility upstream of MAX2. The MAX1 gene is a particularly strong candidate for contributing to diversification of inputs upstream of MAX2. Our functional analysis of the MAX1 family demonstrates the early origin of its catalytic function and both redundancy and functional diversification associated with its duplication in angiosperm lineages.

Effective viscosity in a wave propagation model for ultrasonic particle sizing in non-dilute suspensions.

Estimates of particle size distributions (PSDs) in solid-in-liquid suspensions can be obtained from measurements of ultrasonic wave attenuation. The technique is based on adaptively fitting theoretical wave propagation models to the measured data across a frequency range. These models break down at high solid concentrations and it is believed that this failure is due to the effective viscosity of the mixture in the vicinity of the particles being different from that of the continuous phase. This paper discusses PSD estimation when a number of different viscosity formulations are incorporated into the wave propagation model. The viscosity model due to Happel provides the best estimate of PSD in suspensions of medium concentration.

Genomes on a Tree (GoaT): A versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic tree of life.

As genomic data transform our understanding of biodiversity, the Earth BioGenome Project (EBP) has set a goal of generating reference quality genome assemblies for all ~1.9 million described eukaryotic taxa. Meeting this goal requires coordination among many individual regional and taxon-focussed projects working under the EBP umbrella. Large-scale sequencing projects require ready access to validated genome-relevant metadata, such as genome sizes and karyotypes, but these data are dispersed across the literature, and directly measured values are lacking for most taxa. To meet these needs, we have developed Genomes on a Tree (GoaT), an Elasticsearch-powered datastore and search index for genome-relevant metadata and sequencing project plans and statuses. GoaT indexes publicly available metadata for all eukaryotic species and interpolates missing values through phylogenetic comparison. GoaT also holds target priority and sequencing status information for many projects affiliated to the EBP to aid project coordination. Metadata and status attributes in GoaT can be queried through a mature API, a web front end, and a command line interface. The web front end additionally provides summary visualisations for data exploration and reporting (see https://goat.genomehubs.org). GoaT currently holds direct or estimated values for over 70 taxon attributes and over 30 assembly attributes across 1.5 million eukaryotic species. The depth and breadth of curated data, frequent updates, and a versatile query interface make GoaT a powerful data aggregator and portal to explore and report underlying data for the eukaryotic tree of life. We illustrate this utility through a series of use cases from planning through to completion of a genome-sequencing project.

Mitochondrial barcodes are diagnostic of shared refugia but not species in hybridizing oak gallwasps.

Mitochondrial DNA barcodes provide a simple taxonomic tool for systematic and ecological research, with particular benefit for poorly studied or species-rich taxa. Barcoding assumes genetic diversity follows species boundaries; however, many processes disrupt species-level monophyly of barcodes leading to incorrect classifications. Spatial population structure, particularly when shared across closely related and potentially hybridizing taxa, can invalidate barcoding approaches yet few data exist to examine its impacts. We test how shared population structure across hybridizing species impacts upon mitochondrial barcodes by sequencing the cytochrome b gene for 518 individuals of four well-delimited Western Palaearctic gallwasp species within the Andricus quercuscalicis species group. Mitochondrial barcodes clustered individuals into mixed-species clades corresponding to refugia, with no difference in within- and between-species divergence. Four nuclear genes were also sequenced from 4 to 11 individuals per refugial population of each species. Multi-locus analyses of these data supported established species, with no support for the refugial clustering across species seen in mitochondrial barcodes. This pattern is consistent with mitochondrial introgression among populations of species sharing the same glacial refugium, such that mitochondrial barcodes identify a shared history of population structure rather than species. Many taxa show phylogeographic structure across glacial refugia, suggesting that mitochondrial barcoding may fail when applied to other sets of co-distributed, closely related species. Robust barcoding approaches must sample extensively across population structure to disentangle spatial from species-level variation. Methods incorporating multiple unlinked loci are also essential to accommodate coalescent variation among genes and provide power to resolve recently diverged species.

Simulation of incoherent and coherent backscattered wave fields from cavities in a solid matrix.

This paper reports a study of the backscattered ultrasonic signal from a solid layer containing spherical cavities, to determine the conditions in which an effective medium model is a valid description of the response. The work is motivated by the need to model the response of porous composite materials for ultrasonic non-destructive evaluation (NDE) techniques. The numerical simulation predicts the response of a layer containing cavities at a single set of random locations, and compares it to the predicted response from a homogeneous layer with ensemble-averaged material properties (effective medium model). The study investigates the conditions in which the coherent (ensemble-averaged) response is obtained even from a single configuration of scatterers. Simulations are carried out for a range of cavity sizes and volume fractions. The deviation of the response from effective medium behavior is modeled, along with the trends as a function of cavity radius, volume fraction, and frequency, in order to establish an acceptability criterion for application of an effective medium model.

Acoustic scattering by a spherical obstacle: modification to the analytical long-wavelength solution for the zero-order coefficient.

Classical long wavelength approximate solutions to the scattering of acoustic waves by a spherical liquid particle suspended in a liquid (an emulsion) show small but significant differences from full solutions at very low k(c)a (typically k(c)a < 0.01) and above at k(c)a > 0.1, where k(c) is the compressional wavenumber and a the particle radius. These differences may be significant in the context of dispersed particle size estimates based on compression wave attenuation measurements. This paper gives an explanation of how these differences arise from approximations based on the significance of terms in the modulus of the complex zero-order partial wave coefficient, A(0). It is proposed that a more accurate approximation results from considering the terms in the real and imaginary parts of the coefficient, separately.

A comparison of stochastic and effective medium approaches to the backscattered signal from a porous layer in a solid matrix.

This paper reports a study of the backscattering behavior of a solid layer containing randomly spaced spherical cavities in the long wavelength limit. The motivation for the work arises from a need to model the responses of porous composite materials in ultrasonic NDE procedures. A comparison is made between models based on a summation over discrete scatterers, which show interesting emergent properties, and an integral formulation based on an ensemble average, and with a simple slab effective medium approximation. The similarities and differences between these three models are demonstrated. A simple quantitative criterion is established which sets the maximum frequency at which ensemble average or equivalent homogeneous medium models can represent echo signal generation in a porous layer for given interpore spacing, or equivalently, given pore size and concentration.

MolluscDB: a genome and transcriptome database for molluscs.

As sequencing becomes more accessible and affordable, the analysis of genomic and transcriptomic data has become a cornerstone of many research initiatives. Communities with a focus on particular taxa or ecosystems need solutions capable of aggregating genomic resources and serving them in a standardized and analysis-friendly manner. Taxon-focussed resources can be more flexible in addressing the needs of a research community than can universal or general databases. Here, we present MolluscDB, a genome and transcriptome database for molluscs. MolluscDB offers a rich ecosystem of tools, including an Ensembl browser, a BLAST server for homology searches and an HTTP server from which any dataset present in the database can be downloaded. To demonstrate the utility of the database and verify the quality of its data, we imported data from assembled genomes and transcriptomes of 22 species, estimated the phylogeny of Mollusca using single-copy orthologues, explored patterns of gene family size change and interrogated the data for biomineralization-associated enzymes and shell matrix proteins. MolluscDB provides an easy-to-use and openly accessible data resource for the research community. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.

The complete genome sequence of Eimeria tenella (Tyzzer 1929), a common gut parasite of chickens.

We present a genome assembly from a clonal population of Eimeria tenella Houghton parasites (Apicomplexa; Conoidasida; Eucoccidiorida; Eimeriidae). The genome sequence is 53.25 megabases in span. The entire assembly is scaffolded into 15 chromosomal pseudomolecules, with complete mitochondrion and apicoplast organellar genomes also present.

The genome sequence of the European water vole, Arvicola amphibius Linnaeus 1758.

We present a genome assembly from an individual male Arvicola amphibius (the European water vole; Chordata; Mammalia; Rodentia; Cricetidae). The genome sequence is 2.30 gigabases in span. The majority of the assembly is scaffolded into 18 chromosomal pseudomolecules, including the X sex chromosome. Gene annotation of this assembly on Ensembl has identified 21,394 protein coding genes.

The genome sequence of the brown trout, Salmo trutta Linnaeus 1758.

We present a genome assembly from an individual female Salmo trutta (the brown trout; Chordata; Actinopteri; Salmoniformes; Salmonidae). The genome sequence is 2.37 gigabases in span. The majority of the assembly is scaffolded into 40 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl has identified 43,935 protein coding genes.

The genome sequence of the Norway rat, Rattus norvegicus Berkenhout 1769.

We present a genome assembly from an individual male Rattus norvegicus (the Norway rat; Chordata; Mammalia; Rodentia; Muridae). The genome sequence is 2.44 gigabases in span. The majority of the assembly is scaffolded into 20 chromosomal pseudomolecules, with both X and Y sex chromosomes assembled. This genome assembly, mRatBN7.2, represents the new reference genome for R. norvegicus and has been adopted by the Genome Reference Consortium.

The genome sequence of the European golden eagle, Aquila chrysaetos chrysaetos Linnaeus 1758.

We present a genome assembly from an individual female Aquila chrysaetos chrysaetos (the European golden eagle; Chordata; Aves; Accipitridae). The genome sequence is 1.23 gigabases in span. The majority of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the W and Z sex chromosomes.

The genome sequence of the European turtle dove, Streptopelia turtur Linnaeus 1758.

We present a genome assembly from an individual female Streptopelia turtur (the European turtle dove; Chordata; Aves; Columbidae). The genome sequence is 1.18 gigabases in span. The majority of the assembly is scaffolded into 35 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled.

Phylogeny and DNA barcoding of inquiline oak gallwasps (Hymenoptera: Cynipidae) of the Western Palaearctic.

We examine phylogenetic relationships within the Synergus complex of herbivorous inquiline gallwasps (Hymenoptera; Cynipidae; Synergini) associated with cynipid host galls on oak, a biologically diverse group whose genus-level morphological taxonomy has long been considered stable but whose species level taxonomy is problematic. We incorporate data for over 70% of recognised Western Palaearctic species in five morphology-based genera (Ceroptres, Saphonecrus, Synergus, Synophrus, Ufo), comprising sequence for two mitochondrial loci (coxI, cytb) and one nuclear locus (28S D2). In particular, we assess the evidence for monophyly of two long-established, morphology-defined sections within the genus Synergus that differ in a range of biological traits. To aid analyses of ecological interactions within oak cynipid communities, we also consider the utility of cytochrome oxidase I (coxI) DNA barcodes in the oak inquilines. In this assessment, we do not assume that species are delineated at a single threshold value of sequence divergence for a single gene, but examine concordance in the composition of molecular operational Taxonomic units (MOTUs) across a range of sequence divergences in each gene and across genes. We also assess the impact of sampling effort on MOTU stability. Phylogenetic reconstructions for all three loci support monophyly for Synergus and Synophrus, but reject monophyly for Saphonecrus and for the two sections within Synergus. The suites of traits associated with the two sections of the genus Synergus are thus homoplasious. All three loci also reject monophyly for three Synergus species (S. hayneanus, S. pallipes, S. umbraculus). Sequences for each locus identify robust MOTUs that are largely concordant across loci for a range of cut-off values. Though many MOTU's correspond to recognised Linnean species, there is significant, multigene disagreement between groupings supported by morphology and sequence data, with both allocation of different morphospecies to the same MOTU and allocation of the same morphospecies to multiple MOTUs, regardless of cut-off value. Our results imply that while DNA barcoding has considerable utility within this group, morphology-based identification needs major revision at both genus and species levels. Further, lifehistory traits currently attributed to single morphospecies probably confound attributes of multiple lineages. Revealing patterns of character state evolution in Synergus requires collection of new host association and life history data explicitly linked to DNA barcode data for the specimens concerned.

Strigolactone regulation of shoot branching in chrysanthemum (Dendranthema grandiflorum).

Previous studies of highly branched mutants in pea (rms1-rms5), Arabidopsis thaliana (max1-max4), petunia (dad1-dad3), and rice (d3, d10, htd1/d17, d14, d27) identified strigolactones or their derivates (SLs), as shoot branching inhibitors. This recent discovery offers the possibility of using SLs to regulate branching commercially, for example, in chrysanthemum, an important cut flower crop. To investigate this option, SL physiology and molecular biology were studied in chrysanthemum (Dendranthema grandiflorum), focusing on the CCD8/MAX4/DAD1/RMS1/D10 gene. Our results suggest that, as has been proposed for Arabidopsis, the ability of SLs to inhibit bud activity depends on the presence of a competing auxin source. The chrysanthemum SL biosynthesis gene, CCD8 was cloned, and found to be regulated in a similar, but not identical way to known CCD8s. Expression analyses revealed that DgCCD8 is predominantly expressed in roots and stems, and is up-regulated by exogenous auxin. Exogenous SL can down-regulate DgCCD8 expression, but this effect can be overridden by apical auxin application. This study provides evidence that SLs are promising candidates to alter the shoot branching habit of chrysanthemum.

BlobToolKit - Interactive Quality Assessment of Genome Assemblies.

Reconstruction of target genomes from sequence data produced by instruments that are agnostic as to the species-of-origin may be confounded by contaminant DNA. Whether introduced during sample processing or through co-extraction alongside the target DNA, if insufficient care is taken during the assembly process, the final assembled genome may be a mixture of data from several species. Such assemblies can confound sequence-based biological inference and, when deposited in public databases, may be included in downstream analyses by users unaware of underlying problems. We present BlobToolKit, a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. BlobToolKit can be used to process assembly, read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility. We have been running an automated BlobToolKit pipeline on eukaryotic assemblies publicly available in the International Nucleotide Sequence Data Collaboration and are making the results available through a public instance of the Viewer at https://blobtoolkit.genomehubs.org/view We aim to complete analysis of all publicly available genomes and then maintain currency with the flow of new genomes. We have worked to embed these views into the presentation of genome assemblies at the European Nucleotide Archive, providing an indication of assembly quality alongside the public record with links out to allow full exploration in the Viewer.