Open Data Badge Research Articles

Transposable elements contribute to dynamic genome content in maize.

Transposable elements (TEs) are ubiquitous components of eukaryotic genomes and can create variation in genome organization and content. Most maize genomes are composed of TEs. We developed an approach to define shared and variable TE insertions across genome assemblies and applied this method to four maize genomes (B73, W22, Mo17 and PH207) with uniform structural annotations of TEs. Among these genomes we identified approximately 400000 TEs that are polymorphic, encompassing 1.6Gb of variable TE sequence. These polymorphic TEs include a combination of recent transposition events as well as deletions of older TEs. There are examples of polymorphic TEs within each of the superfamilies of TEs and they are found distributed across the genome, including in regions of recent shared ancestry among individuals. There are many examples of polymorphic TEs within or near maize genes. In addition, there are 2380 gene annotations in the B73 genome that are located within variable TEs, providing evidence for the role of TEs in contributing to the substantial differences in annotated gene content among these genotypes. TEs are highly variable in our survey of four temperate maize genomes, highlighting the major contribution of TEs in driving variation in genome organization and gene content. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://github.com/SNAnderson/maizeTE_variation; https://mcstitzer.github.io/maize_TEs.

Plasticity in Triticeae centromere DNA sequences: a wheat × tall wheatgrass (decaploid) model.

Centromeres mediate chromosome attachment to microtubules and maintain the integrity of chromosomes for proper segregation of the sister chromatids during cell division. Advances in the assembly of Triticeae genome sequences combined with the capacity to recover hybrid species derived from very distantly related species provides potential experimental systems for linking retrotransposon amplification and repositioning of centromeres via non-mendelian inheritance in partial amphiploid breeds. The decaploid tall wheatgrass (Thinopyrum ponticum) is one of the most successfully used perennial species in wheat breeding for generating translocation lines with valuable agronomic traits. We found that wheat centromere retrotransposons CRW and Quinta widely occur within the tall wheatgrass genome. In addition, one of the genome donors to Th. ponticum, Pseudoroegneria stipifolia (StSt), has been shown to have Abigail and a satellite repeat, CentSt. We also found two other centromeric retrotransposons, Abia and CL135 in Th. ponticum by ChIP-seq. Examination of partial amphiploid lines that were generated in the 1970s demonstrated extensive modification in centromere sequences using CentSt, Abigail and Abia as probes. We also detected that St-genome chromosomes were more enriched with Abigail and CentSt, whereas E-genome chromosomes were enriched with CRW and Quinta in tall wheatgrass and its closer relatives. It can be concluded that bursts of transposition of retrotransposons and repositioning of centromeres via non-mendelian segregation are common in partial amphiploids derived from interspecific hybrids. Practically speaking, our study reveals that the existence of homologous centromere functional sequences in both a donor and its receptor can substantially contribute to the successful transfer of alien genes into crop species. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://www.ncbi.nlm.nih.gov/sra/SRR9089557; https://www.ncbi.nlm.nih.gov/sra/SRR9089558; https://www.ncbi.nlm.nih.gov/sra/SRR9089559; https://www.ncbi.nlm.nih.gov/sra/SRR9089560; https://www.ncbi.nlm.nih.gov/sra/SRR9089561; https://www.ncbi.nlm.nih.gov/sra/SRR9089562; https://www.ncbi.nlm.nih.gov/sra/SRR9089563; https://www.ncbi.nlm.nih.gov/sra/SRR9089564; https://www.ncbi.nlm.nih.gov/nuccore/MK999394; https://www.ncbi.nlm.nih.gov/nuccore/MK999395; https://www.ncbi.nlm.nih.gov/nuccore/MK999396.

Linking pollen foraging of megachilid bees to their nest bacterial microbiota.

Solitary bees build their nests by modifying the interior of natural cavities, and they provision them with food by importing collected pollen. As a result, the microbiota of the solitary bee nests may be highly dependent on introduced materials. In order to investigate how the collected pollen is associated with the nest microbiota, we used metabarcoding of the ITS2 rDNA and the 16S rDNA to simultaneously characterize the pollen composition and the bacterial communities of 100 solitary bee nest chambers belonging to seven megachilid species. We found a weak correlation between bacterial and pollen alpha diversity and significant associations between the composition of pollen and that of the nest microbiota, contributing to the understanding of the link between foraging and bacteria acquisition for solitary bees. Since solitary bees cannot establish bacterial transmission routes through eusociality, this link could be essential for obtaining bacterial symbionts for this group of valuable pollinators.Open Research Badges This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at https://www.ebi.ac.uk/ena/data/view/PRJEB27223, https://www.ebi.ac.uk/ena/data/view/PRJEB31610, and https://doi.org/10.5061/dryad.qk36k8q

Transcription of specific auxin efflux and influx carriers drives auxin homeostasis in tobacco cells.

Auxin concentration gradients are informative for the transduction of many developmental cues, triggering downstream gene expression and other responses. The generation of auxin gradients depends significantly on cell-to-cell auxin transport, which is supported by the activities of auxin efflux and influx carriers. However, at the level of individual plant cell, the co-ordination of auxin efflux and influx largely remains uncharacterized. We addressed this issue by analyzing the contribution of canonical PIN-FORMED (PIN) proteins to the carrier-mediated auxin efflux in Nicotiana tabacum L., cv. Bright Yellow (BY-2) tobacco cells. We show here that a majority of canonical NtPINs are transcribed in cultured cells and in planta. Cloning of NtPIN genes and their inducible overexpression in tobacco cells uncovered high auxin efflux activity of NtPIN11, accompanied by auxin starvation symptoms. Auxin transport parameters after NtPIN11 overexpression were further assessed using radiolabelled auxin accumulation and mathematical modelling. Unexpectedly, these experiments showed notable stimulation of auxin influx, which was accompanied by enhanced transcript levels of genes for a specific auxin influx carrier and by decreased transcript levels of other genes for auxin efflux carriers. A similar transcriptional response was observed upon removal of auxin from the culture medium, which resulted in decreased auxin efflux. Overall, our results revealed an auxin transport-based homeostatic mechanism for the maintenance of endogenous auxin levels. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at http://osf.io/ka97b/.

An 'eFP-Seq Browser' for visualizing and exploring RNA sequencing data.

SummaryImprovements in next‐generation sequencing technologies have resulted in dramatically reduced sequencing costs. This has led to an explosion of ‘‐seq’‐based methods, of which RNA sequencing (RNA‐seq) for generating transcriptomic data is the most popular. By analysing global patterns of gene expression in organs/tissues/cells of interest or in response to chemical or environmental perturbations, researchers can better understand an organism's biology. Tools designed to work with large RNA‐seq data sets enable analyses and visualizations to help generate hypotheses about a gene's function. We present here a user‐friendly RNA‐seq data exploration tool, called the ‘eFP‐Seq Browser’, that shows the read map coverage of a gene of interest in each of the samples along with ‘electronic fluorescent pictographic’ (eFP) images that serve as visual representations of expression levels. The tool also summarizes the details of each RNA‐seq experiment, providing links to archival databases and publications. It automatically computes the reads per kilobase per million reads mapped expression‐level summaries and point biserial correlation scores to sort the samples based on a gene's expression level or by how dissimilar the read map profile is from a gene splice variant, to quickly identify samples with the strongest expression level or where alternative splicing might be occurring. Links to the Integrated Genome Browser desktop visualization tool allow researchers to visualize and explore the details of RNA‐seq alignments summarized in eFP‐Seq Browser as coverage graphs. We present four cases of use of the eFP‐Seq Browser for ABI3,SR34,SR45a and U2AF65B, where we examine expression levels and identify alternative splicing. The URL for the browser is https://bar.utoronto.ca/eFP-Seq_Browser/.Open research badges This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. Tool is at http://sps:urlprefix::https; RNA‐seq data at http://sps:urlprefix::https and http://sps:urlprefix::https. Code is available at http://sps:urlprefix::https

Lipid remodeling regulator 1 (LRL1) is differently involved in the phosphorus-depletion response from PSR1 in Chlamydomonas reinhardtii.

SummaryThe elucidation of lipid metabolism in microalgae has attracted broad interest, as their storage lipid, triacylglycerol (TAG), can be readily converted into biofuel via transesterification. TAG accumulates in the form of oil droplets, especially when cells undergo nutrient deprivation, such as for nitrogen (N), phosphorus (P), or sulfur (S). TAG biosynthesis under N‐deprivation has been comprehensively studied in the model microalga Chlamydomonas reinhardtii, during which TAG accumulates dramatically. However, the resulting rapid breakdown of chlorophyll restricts overall oil yield productivity and causes cessation of cell growth. In contrast, P‐deprivation results in oil accumulation without disrupting chloroplast integrity. We used a reverse genetics approach based on co‐expression analysis to identify a transcription factor (TF) that is upregulated under P‐depleted conditions. Transcriptomic analysis revealed that the mutants showed repression of genes typically associated with lipid remodeling under P‐depleted conditions, such as sulfoquinovosyl diacylglycerol 2 (SQD2), diacylglycerol acyltransferase (DGTT1), and major lipid droplet protein (MLDP). As accumulation of sulfoquinovosyl diacylglycerol and TAG were suppressed in P‐depleted mutants, we designated the protein as lipid remodeling regulator 1 (LRL1). LRL1 mutants showed slower growth under P‐depletion. Moreover, cell size in the mutant was significantly reduced, and TAG and starch accumulation per cell were decreased. Transcriptomic analysis also suggested the repression of several genes typically upregulated in adaptation to P‐depletion that are associated with the cell cycle and P and lipid metabolism. Thus, our analysis of LRL1 provides insights into P‐allocation and lipid remodeling under P‐depleted conditions in C. reinhardtii.Open Research Badges This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The sequencing data were made publicly available under the BioProject Accession number PRJDB6733 and an accession number LC488724 at the DNA Data Bank of Japan (DDBJ). The data is available at https://trace.ddbj.nig.ac.jp/BPSearch/bioproject?acc=PRJDB6733; http://getentry.ddbj.nig.ac.jp/getentry/na/LC488724. The metabolome data were made publicly available and can be accessed at http://metabolonote.kazusa.or.jp/SE195:/; http://webs2.kazusa.or.jp/data/nur/.

Bird species diversity in Altai riparian landscapes: Wood cover plays a key role for avian abundance.

AimsWe aim to understand bird richness and variation in species composition (beta diversity) along a 630 km riparian landscape in the Altai Mountains of China and to test whether vegetation cover is the main explanation of species diversity.MethodsWe selected nine regions along a gradient of natural vegetation change. Bird surveys and environmental measurements were conducted at 10 points in each of the nine regions. We collected environmental land cover variables such as wood cover (area proportion of trees and shrubs with saplings in habitats; here trees are woody plant with a single trunk and higher than 3 m, shrubs and saplings are distinguished from trees by their multiple trunks and shorter height) and tree cover, and two climate factors which were Annual Mean Temperature (AMT) and Annual Precipitation (AP). We used Liner Regression Models to explore the correlation between bird species richness and environmental variables. We used Sørensen's dissimilarity index to measure birds' beta diversity, and quantified the contribution of environmental variables to this pattern using a Canonical Correspondence Analysis (CCA).ResultsWood cover was the strongest predictor of overall, insectivore, and omnivore bird richness. Regions with wood cover contained more bird species. Beta diversity was overall high in the studied regions, and turnover components occupied a major part of beta diversity. Wood cover and AP were significant predictors of bird species composition explaining 33.24% of bird beta diversity together.ConclusionsWood vegetation including trees, shrubs, and saplings, rather than only trees, contains high bird richness. High beta diversity suggests that expansion of the existing nature reserves is needed in the riparian landscapes to capture the variation in bird species composition. Thus all wood cover in the overall riparian landscapes of Altai Mountains should be protected from farming and grazing to improve bird conservation outcomes.OPEN RESEARCH BADGES This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at Raw bird data in this study: osf.io/78qcw; Raw environment data: osf.io/qr5cw.

Functional divergence of the bitter receptor TAS2R38 in Sulawesi macaques.

Bitter perception is mediated by G protein‐coupled receptors TAS2Rs and plays an important role in avoiding the ingestion of toxins by inducing innate avoidance behavior in mammals. One of the best‐studied TAS2Rs is TAS2R38, which mediates the perception of the bitterness of synthetic phenylthiocarbamide (PTC). Previous studies of TAS2R38 have suggested that geographical separation enabled the independent divergence of bitter taste perception. The functional divergence of TAS2R38 in allopatric species has not been evaluated. We characterized the function of TAS2R38 in four allopatric species of Sulawesi macaques on Sulawesi Island. We found variation in PTC taste perception both within and across species. In most cases, TAS2R38 was sensitive to PTC, with functional divergence among species. We observed different truncated TAS2R38s that were not responsive to PTC in each species of Macaca nigra and M. nigrescens due to premature stop codons. Some variants of intact TAS2R38 with an amino acid substitution showed low sensitivity to PTC in M. tonkeana. Similarly, this intact TAS2R38 with PTC‐low sensitivity has also been found in humans. We detected a shared haplotype in all four Sulawesi macaques, which may be the ancestral haplotype of Sulawesi macaques. In addition to shared haplotypes among Sulawesi macaques, other TAS2R38 haplotypes were species‐specific. These results implied that the variation in TAS2R38 might be shaped by geographical patterns and local adaptation.OPEN RESEARCH BADGES This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.908jf3r.

Fitness costs and benefits vary for two facultative Burkholderia symbionts of the social amoeba, Dictyostelium discoideum.

Hosts and their associated microbes can enter into different relationships, which can range from mutualism, where both partners benefit, to exploitation, where one partner benefits at the expense of the other. Many host–microbe relationships have been presumed to be mutualistic, but frequently only benefits to the host, and not the microbial symbiont, have been considered. Here, we address this issue by looking at the effect of host association on the fitness of two facultative members of the Dictyostelium discoideum microbiome (Burkholderia agricolaris and Burkholderia hayleyella). Using two indicators of bacterial fitness, growth rate and abundance, we determined the effect of D. discoideum on Burkholderia fitness. In liquid culture, we found that D. discoideum amoebas lowered the growth rate of both Burkholderia species. In soil microcosms, we tracked the abundance of Burkholderia grown with and without D. discoideum over a month and found that B. hayleyella had larger populations when associating with D. discoideum while B. agricolaris was not significantly affected. Overall, we find that both B. agricolaris and B. hayleyella pay a cost to associate with D. discoideum, but B. hayleyella can also benefit under some conditions. Understanding how fitness varies in facultative symbionts will help us understand the persistence of host–symbiont relationships.OPEN RESEARCH BADGES This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at https://openscholarship.wustl.edu/data/15/

Children With Developmental Language Disorder Have an Auditory Verbal Statistical Learning Deficit: Evidence From an Online Measure

Successful language use requires the ability to process nonadjacent dependencies (NADs) that occur in linguistic input. Learning such structural regularities seems therefore crucial for children, and researchers have indeed proposed that language problems in children with developmental language disorder (DLD), especially problems with grammar, are due to their decreased sensitivity to NADs. Because the evidence supporting this claim is scarce, we compared children with DLD (n = 36; Mage = 9.1 years) and without DLD (n = 36; Mage = 9.1 years) performing a learning task with NADs. Using response times as an online measure of learning NADs, we observed that participants with DLD were less sensitive to NADs than were typically developing peers. The confidence intervals of the effect, however, indicated that the effect was probably small in size. We discuss clinical and theoretical implications of the present study in light of this effect size.Open PracticesThis article has been awarded Open Materials and Open Data badges. All data, materials, and analysis scripts for this study are publicly accessible via the Open Science Framework at https://osf.io/8a3yv. The study materials are also publicly available via the IRIS database at https://www.iris-database.org. Learn more about the Open Practices badges from the Center for Open Science: https://osf.io/tvyxz/wiki.

DNA metabarcoding adds valuable information for management of biodiversity in roadside stormwater ponds.

Stormwater ponds are used to compensate for the adverse effects that road runoff might have on the natural environment. Depending on their design and placement, stormwater ponds can act as both refugia and traps for local biodiversity. To evaluate the impact of stormwater ponds on biodiversity, it is critical to use effective and precise methods for identification of life associated with the water body. DNA metabarcoding has recently become a promising tool for identification and assessment of freshwater biodiversity.Using both morphology and DNA metabarcoding, we analyze species richness and biological composition of samples from 12 stormwater ponds and investigate the impact of pond size and pollution levels in the sediments and water column on the macroinvertebrate community structure.DNA metabarcoding captured and identified more than twice the number of taxa compared to morphological identification. The (dis)similarity of macroinvertebrate community composition in different ponds showed that the ponds appear better separated in the results obtained by DNA metabarcoding, but that the explained variation is higher for the results obtained by morphologically identification, since it provides abundance data.The reliance on morphological methods has limited our perception of the aquatic biodiversity in response to anthropogenic stressors, thereby providing inaccurate information for appropriate design and management of stormwater ponds; these drawbacks can be overcome by DNA metabarcoding. Synthesis and applications. The results indicate that DNA metabarcoding is a useful tool in identifying species, especially Diptera, which are difficult to determine. Application of DNA metabarcoding greatly increases the number of species identified at each sampling site, thereby providing a more accurate information regarding the way the ponds function and how they are affected by management. OPEN PRACTICES This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at https://www.ebi.ac.uk/ena/data/view/PRJEB30841.

Excuse Validation: A Cross-cultural Study.

If someone unintentionally breaks the rules, do they break the rules? In the abstract, the answer is obviously "yes." But, surprisingly, when considering specific examples of unintentional, blameless rule-breaking, approximately half of people judge that no rule was broken. This effect, known as excuse validation, has previously been observed in American adults. Outstanding questions concern what causes excuse validation, and whether it is peculiar to American moral psychology or cross-culturally robust. The present paper studies the phenomenon cross-culturally, focusing on Korean and American adults, and proposes a new explanation of why people engage in excuse validation, in terms of competing forces in human norm-psychology. The principal findings are that Americans and Koreans engaged in excuse validation at similar levels, and older adults were more likely to engage in excuse validation. OPEN RESEARCH BADGES: This article has been awarded Open Materials and Open Data badges. All materials and data are publicly accessible via the Open Science Framework at https://osf.io/8juyc/. Learn more about the Open Practices badges from the Center for Open Science: https://osf.io/tvyxz/wiki .

Even obligate symbioses show signs of ecological contingency: Impacts of symbiosis for an invasive stinkbug are mediated by host plant context.

Many species interactions are dependent on environmental context, yet the benefits of obligate, mutualistic microbial symbioses to their hosts are typically assumed to be universal across environments. We directly tested this assumption, focusing on the symbiosis between the sap‐feeding insect Megacopta cribraria and its primary bacterial symbiont Candidatus Ishikawaella capsulata. We assessed host development time, survival, and body size in the presence and absence of the symbiont on two alternative host plants and in the insects' new invasive range. We found that association with the symbiont was critical for host survival to adulthood when reared on either host plant, with few individuals surviving in the absence of symbiosis. Developmental differences between hosts with and without microbial symbionts, however, were mediated by the host plants on which the insects were reared. Our results support the hypothesis that benefits associated with this host–microbe interaction are environmentally contingent, though given that few individuals survive to adulthood without their symbionts, this may have minimal impact on ecological dynamics and current evolutionary trajectories of these partners.OPEN RESEARCH BADGES This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.kg4bc56

Geographic variation in opsin expression does not align with opsin genotype in Lake Victoria cichlid populations.

Sensory adaptation to the local environment can contribute to speciation. Aquatic environments are well suited for studying this process: The natural attenuation of light through water results in heterogeneous light environments, to which vision‐dependent species must adapt for communication and survival. Here, we study visual adaptation in sympatric Pundamilia cichlids from southeastern Lake Victoria. Species with blue or red male nuptial coloration co‐occur at many rocky islands but tend to be depth‐differentiated, entailing different visual habitats, more strongly at some islands than others. Divergent visual adaptation to these environments has been implicated as a major factor in the divergence of P. pundamilia and P. nyererei, as they show consistent differentiation in the long‐wavelength‐sensitive visual pigment gene sequence (LWS opsin). In addition to sequence variation, variation in the opsin gene expression levels may contribute to visual adaptation. We characterized opsin gene expression and LWS genotype across Pundamilia populations inhabiting turbid and clear waters, to examine how different mechanisms of visual tuning contribute to visual adaptation. As predicted, the short‐wavelength‐sensitive opsin (SWS2b) was expressed exclusively in a population from clear water. Contrary to prediction however, expression levels of the other opsins were species‐ and island‐dependent and did not align with species differences in LWS genotype. Specifically, in two locations with turbid water, the shallow‐water dwelling blue species expressed more LWS and less RH2A than the deeper‐dwelling red species, while the opposite pattern occurred in the two locations with clear water. Visual modeling suggests that the observed distribution of opsin expression profiles and LWS genotypes does not maximize visual performance, implying the involvement of additional visual tuning mechanisms and/or incomplete adaptation.OPEN RESEARCH BADGE This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at https://hdl.handle.net/10411/I1IUUQ.

Sympatric speciation in the Simulium arcticum s. l. complex (Diptera: Simuliidae): The Rothfels model updated.

We tested the Rothfels sympatric speciation model for black flies by comparing all available data for sex‐chromosome diversity with the geographic locations of larval collection sites within the Simulium arcticum complex of black flies (Diptera: Simuliidae). Five separate data sets equaling about 20,000 larvae were included from throughout the geographic range of this complex. We record a total of 31 taxa having unique sex chromosomes, all of which demonstrate linkage disequilibrium with most taxa sharing autosomal polymorphisms. All siblings share portions of their distributions with S. negativum, the presumed oldest member of the complex. Twenty‐one of 22 cytotypes have distributions within the ranges of siblings thus supporting the sympatric speciation model of Rothfels. Chromosomally diverse sites may require analysis of as many as 200 larvae to be properly described. There is no effect of any inversions influencing the occurrence of other inversions. Finally, we report a new cytotype, Simulium arcticum IIL‐6, which we originally discovered in Alaska. Aspects of future genomic research are discussed as they relate to the main chromosomal structural/functional tenants of the model.OPEN RESEARCH BADGE This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data are available at https://doi.org/10.6084/m9.figshare.7719398

The pleiotropic effects of Innexin genes expressed in Drosophila glia encompass wing chemosensory sensilla.

The neuroanatomy of Drosophila wing chemosensilla and the analysis of their sensory organ precursor cell lineage have demonstrated that they are surprisingly related to taste perception. The microarchitecture of wing bristles limits the use of electrophysiology methods to investigate wing chemosensory mechanisms. However, by monitoring the fluorescence of the complex calcium/GCaMP, calcium flux triggered upon tastant stimulation was observed within sensilla aligned along the wing anterior nerve. This string of fluorescent puncta was impaired in wings of Innexin 2 (Inx2) mutant flies; although it is unclear whether the Innexin proteins act at the level of the wing imaginal disc, adult wing and/or at both levels. Glial cells known to shelter Innexin(s) expression have no documented role in adult chemosensory sensilla. Our data suggest that Innexin(s) are likely required for the maturation of functional wing chemosensilla in adulthood. The unexpected presence of most Innexin transcripts in adult wing RNAseq data set argues for the expression of Innexin proteins in the larval imaginal wing disc that are continued in wing chemosensilla at adulthood. OPEN PRACTICES: This article has earned an Open Data badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available as supporting materials and includes the electronic lab notebook. Learn more about the Open Practices badges from the Center for Open Science: https://osf.io/tvyxz/wiki.

A review of protocols for the experimental release of kelp (Laminariales) zoospores.

Kelps (order Laminariales) are foundation species in temperate and arctic seas globally, but they are in decline in many places. Laminarian kelp have an alternation of generations and this poses challenges for experimental studies due to the difficulties in achieving zoospore release and gametophyte growth. Here, we review and synthesize the protocols that have been used to induce zoospore release in kelps to identify commonalities and provide guidance on best practices. We found 171 papers, where zoospore release was induced in four kelp families from 35 different ecoregions. The most commonly treated family was Laminariaceae, followed by Lessoniaceae and the most studied ecoregion was Central Chile, followed by the Southern California Bight. Zoospore release generally involved three steps: a pretreatment which included cleaning of the reproductive tissue to eliminate epiphytic organisms, followed by desiccation of the tissue, and finally a postdesiccation immersion of the reproductive material in a seawater medium for zoospore release. Despite these commonalities, there was a high degree of variation in the detail within each of these steps, even among studies within genera and from the same ecoregions. This suggests either that zoospore release may be relatively insensitive across the Laminariales or that little methods optimization has been undertaken. We suggest that greater attention to standardization of protocols and reporting of methodology and optimization would improve comparisons of kelp zoospore release across species and locations and facilitate a broader understanding of this key, but understudied life history stage.Open Research Badges This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.0kh1f8j.

Population structure of avian malaria parasites.

The geographic distribution of genetic diversity in malaria parasite populations (Apicomplexa: Haemosporida) presumably influences local patterns of virulence and the evolution of host‐resistance, but little is known about population genetic structure in these parasites. We assess the distribution of genetic diversity in the partial Domain I of apical membrane antigen 1 (AMA1) in three mtDNA‐defined lineages of avian Plasmodium to determine spatial population structure and host–parasite genetic relationships. We find that one parasite lineage is genetically differentiated in association with a single host genus and among some locations, but not with respect to other hosts. Two other parasite lineages are undifferentiated with respect to host species but exhibit geographic differentiation that is inconsistent with shared geographic barriers or with isolation‐by‐distance. Additional differentiation within two other lineages is unassociated with host species or location; in one case, we tentatively interpret this differentiation as the result of mitochondrial introgression from one of the lineages into a second lineage. More sampling of nuclear genetic diversity within populations of avian Plasmodium is needed to rule out coinfection as a possible confounding factor. If coinfections are not responsible for these findings, further assessment is needed to determine the frequency of mitonuclear discordance and its implications for defining parasite lineages based on mitochondrial genetic variation.OPEN RESEARCH BADGES This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at Genbank https://www.ncbi.nlm.nih.gov/genbank/, accession numbers MK965548‐MK965653 and MK929797‐MK930264.

Full-length mRNA sequencing and gene expression profiling reveal broad involvement of natural antisense transcript gene pairs in pepper development and response to stresses.

Pepper is an important vegetable with great economic value and unique biological features. In the past few years, significant development has been made toward understanding the huge complex pepper genome; however, pepper functional genomics has not been well studied. To better understand the pepper gene structure and pepper gene regulation, we conducted full-length mRNA sequencing by PacBio sequencing and obtained 57862 high-quality full-length mRNA sequences derived from 18362 previously annotated and 5769 newly detected genes. New gene models were built that combined the full-length mRNA sequences and corrected approximately 500 fragmented gene models from previous annotations. Based on the full-length mRNA, we identified 4114 and 5880 pepper genes forming natural antisense transcript (NAT) genes in-cis and in-trans, respectively. Most of these genes accumulate small RNAs in their overlapping regions. By analyzing these NAT gene expression patterns in our transcriptome data, we identified many NAT pairs responsive to a variety of biological processes in pepper. Pepper formate dehydrogenase 1 (FDH1), which is required for R-gene-mediated disease resistance, may be regulated by nat-siRNAs and participate in a positive feedback loop in salicylic acid biosynthesis during resistance responses. Several cis-NAT pairs and subgroups of trans-NAT genes were responsive to pepper pericarp and placenta development, which may play roles in capsanthin and capsaicin biosynthesis. Using a comparative genomics approach, the evolutionary mechanisms of cis-NATs were investigated, and we found that an increase in intergenic sequences accounted for the loss of most cis-NATs, while transposon insertion contributed to the formation of most new cis-NATs. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at http://bigd.big.ac.cn/gsa Accession number, CRA001412.

Genetic, epigenetic and genomic effects on variation of gene expression among grape varieties.

The transcriptional regulatory structure of plant genomes is still relatively unexplored, and little is known about factors that influence expression variation in plants. We used a genetic system consisting of 10 heterozygous grape varieties with high consanguinity and high haplotypic diversity to: (i) identify regions of haplotype sharing through whole-genome resequencing and single-nucleotide polymorphism (SNP) genotyping; (ii) analyse gene expression through RNA-seq in four stages of berry development; and (iii) associate gene expression variation with genetic and epigenetic properties. We found that haplotype sharing in and around genes was positively correlated with similarity in expression and was negatively correlated with the fraction of differentially expressed genes. Genetic and epigenetic properties of the gene and the surrounding region showed significant effects on the extent of expression variation, with negative associations for the level of gene body methylation and mean expression level, and with positive associations for nucleotide diversity, structural diversity and ratio of non-synonymous to synonymous nucleotide diversity. We also observed a spatial dependency of covariation of gene expression among varieties. These results highlight relevant roles for cis-acting factors, selective constraints and epigenetic features of the gene, and the regional context in which the gene is located, in the determination of expression variation. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA385116; https://www.ncbi.nlm.nih.gov/bioproject/PRJNA392287; https://www.ncbi.nlm.nih.gov/bioproject/PRJNA373967 (released upon publication); https://www.ncbi.nlm.nih.gov/bioproject/PRJNA490160 (released upon publication); https://www.ncbi.nlm.nih.gov/bioproject/PRJNA265039; https://www.ncbi.nlm.nih.gov/bioproject/PRJNA265040.