Find research datasets worth reusing

Data from: "De novo assembly transcriptome for the rostrum dace (Leuciscus burdigalensis, Cyprinidae: fish) naturally infected by a copepod ectoparasite" in Genomic Resources Notes accepted 1 December 2014 to 31 January 2015

The emergence of pathogens represents substantial threats to public health, livestock, domesticated animals, and biodiversity. How wild populations respond to emerging pathogens has generated a lot of interest in the last two decades. With the recent advent of high-throughput sequencing technologies it is now possible to develop large transcriptomic resources for non-model organisms, hence allowing new research avenues on the immune responses of hosts from a large taxonomic spectra. We here focused on a wild population of the rostrum dace (Leuciscus burgiladensis) that is infected by Tracheliastes polycolpus, an emerging freshwater ectoparasite copepod. We used next generation Illumina sequencing technology to sequence the transcriptome of eight L. burdigalensis adult individuals collected in natura from the same sampling site. Four individuals were non-infected and four individuals were infected by T. polycolpus. We specifically focused on the spleen, the head kidney and epithelial cells and mucus from the fins, three tissues known to be involved in the immune response of fish. We used the Trinity methodology to reconstruct a de novo full-length transcriptome for L. burdigalensis. The resulting transcriptome will serve as an important broad-scale genomic resource for further studying the response of local population of L. burdigalensis to T. polycolpus pressures.

opencc-zeroDec 2015View details →

Data from: Transcriptome modulation during host shift is driven by secondary metabolites in desert Drosophila

High-throughput transcriptome studies are breaking new ground to investigate the responses that organisms deploy in alternative environments. Nevertheless, much remains to be understood about the genetic basis of host plant adaptation. Here, we investigate genome-wide expression in the fly Drosophila buzzatii raised in different conditions. This species uses decaying tissues of cactus of the genus Opuntia as primary rearing substrate and secondarily, the necrotic tissues of the columnar cactus Trichocereus terscheckii. The latter constitutes a harmful host, rich in mescaline and other related phenylethylamine alkaloids. We assessed the transcriptomic responses of larvae reared in Opuntia sulphurea and T. terscheckii, with and without the addition of alkaloids extracted from the latter. Whole-genome expression profiles were massively modulated by the rearing environment, mainly by the presence of T. terscheckii alkaloids. Differentially expressed genes were mainly related to detoxification, oxidation–reduction and stress response; however, we also found genes involved in development and neurobiological processes. In conclusion, our study contributes new data onto the role of transcriptional plasticity in response to alternative rearing environments.

opencc-zeroDec 2011View details →

Data from: Characterization of transcriptomes from sexual and asexual lineages of a New Zealand snail (Potamopyrgus antipodarum)

Understanding the evolution and maintenance of sexual reproduction is one of the central challenges of evolutionary biology, yet we know very little about how sex influences molecular evolution. The New Zealand freshwater snail Potamopyrgus antipodarum is ideally suited to address this knowledge gap because obligately sexual individuals often coexist with multiple independently derived obligately asexual lineages. This unusual situation allows direct comparisons both between sexual and asexual P. antipodarum and across populations that differ in the relative frequency of sexual individuals. As such, P. antipodarum has received a great deal of attention as a model system for the maintenance of sex in nature and is also used as a model for environmental toxicology and biological invasions. Molecular genetic resources for P. antipodarum will thus be useful to investigators in a variety of biological fields. We used 454 sequencing of cDNA libraries to generate transcriptomes from two sexual and two asexual P. antipodarum lineages. A de novo assembly of 116.7 Mb of sequence reads produced 41 396 contigs, and sequence similarity-based Gene Ontology annotations were obtained for 3740 contigs. We detected 408 315 SNP loci and 7315 microsatellite loci, which together represent the first genome-scale resource available for P. antipodarum.

Data from: "Transcriptome resources for the oriental rat flea and primary plague vector, Xenopsylla cheopis" in Genomic Resources Notes Accepted 1 August 2015 to 31 September 2015

This article documents the public availability of raw transcriptome sequence data, 45,254 assembled unigenes as well as their functional annotations of a plague vector Xenopsylla cheopis.

Data from: eSnail: a transcriptome-based molecular resource of the central nervous system for terrestrial gastropods

To expand on emerging terrestrial gastropod molecular resources, we have undertaken transcriptome-based sequencing of the central nervous system (CNS) from six ecologically invasive terrestrial gastropods. Focusing on snail species Cochlicella acuta and Helix aspersa, and reticulated slugs Deroceras invadens, Deroceras reticulatum, Lehmannia nyctelia, and Milax gagates, we obtained a total of 367,869,636 high quality reads and compared them with existing CNS transcript resources for the invasive Mediterranean snail, Theba pisana. In total we obtained, 419,289 unique transcripts (unigenes) from 1,410,569 assembled contigs, with BLAST search analysis of multiple protein databases leading to the annotation of 124,268 unigenes, of which 92,544 mapped to NCBI non-redundant protein databases. We found that these transcriptomes have representatives in most biological functions, based on comparison of gene ontology, KEGG pathway, and protein family contents, demonstrating a high range of transcripts responsible for regulating metabolic activities and molecular functions occurring within the CNS. To provide an accessible genetic resource, we also demonstrate the presence of 66,687 microsatellites and 304,693 single nucleotide variants, which can be used for the design of potentially thousands of unique primers for functional screening. An online 'eSnail' database with a user-friendly web interface was implemented to query all the information obtained herein (http://soft.bioinfo-minzhao.org/esnail). We demonstrate the usefulness of the database through the mining of molluscan neuropeptides. As the most comprehensive CNS transcriptome resource for terrestrial gastropods, eSnail may serve as a useful gateway for researchers to explore gastropod CNS function for multiple purposes, including for the development of biocontrol approaches.

Data from: Transcriptomic characterization of the immunogenetic repertoires of heteromyid rodents

Background: When populations evolve under disparate environmental conditions, they experience different selective pressures that shape patterns of sequence evolution and gene expression. These may be manifested in genetic and phenotypic differences such as a diverse immunogenetic repertoire in species from tropical latitudes that have greater and/or different parasite burdens than more temperate species. To test this idea, we compared the transcriptomes of one tropical species (Heteromys desmarestianus) and two species from temperate latitudes (Dipodomys spectabilis and Chaetodipus baileyi) from the Heteromyidae. We did so in a search for positive selection on sequences and/or differential expression, while controlling for phylogenetic history in our choice of species. Results: We identified 127,812 contigs and annotated 34,878 of these, identifying immune genes associated with interleukins, cytokines, and the production of mast cells. We identified 632 genes that were upregulated in H. desmarestianus (8.7% of genes tested) and 492 (6.7%) that were downregulated. Gene ontology terms including "immune response" were associated with 31 (4.9%) of the 632 upregulated genes. We found preliminary evidence for positive selection on three genes (Palmitoyltransferase ZDHHC5 Ubiquitin-conjugating enzyme E2 N, Krueppel-like factor 10, and Spindle and kinetochore-associated protein 1) along the H. desmarestianus lineage. Conclusions: Overall our findings pinpoint genes in species from disparate environments that are on different evolutionary trajectories in terms of expression levels and/or nucleotide sequence. Our data indicate there are significant differences in the expression of genes among the spleen transcriptomes of these species and that a number of these differentially expressed genes do not show the same pattern of differential expression in another tissue type. This points to the possibility of expression differences between these species specific to the spleen transcriptome.

Data from: Comparative transcriptomics support evolutionary convergence of diapause responses across Insecta

Diapause is a common phenotype that is broadly phylogenetically dispersed across Insecta and appears to have multiple evolutionary origins. Nevertheless, there are clear commonalities in diapause regulation across insect taxa. In the present study, we report a meta-analysis of diapause whole transcriptomic data sets from 11 different insect species that addresses three questions: (i) how similar are whole-transcriptome diapause responses across species within and across different diapause life-cycle stages; (ii) do the most closely-related species demonstrate the most similar diapause responses within and across diapause life-cycle stages (the existence of phylogenetic signal); and (iii) is there a core set of regulatory genes that universally associate with insect diapause at the transcript level? The included species are mostly Dipterans (n = 9), plus one species each from Lepidoptera and Hymenoptera. The group includes multiple species that enter diapause as either larvae, pupae or adults. We establish a set of 4791 orthologous transcript sequences with expression data acquired from published studies of diapause transcriptomes. We find no support for phylogenetic signal. Transcriptomic responses of nondipterans clustered within rather than outside of Dipteran responses. However, expression profiles do tend to cluster with the diapause stage of developmental arrest, although this pattern is only moderately supported. We identify a statistically significant set of 542 orthologues (11% of all orthologues) that are commonly differentially regulated during diapause across all included species. From this core set, we identify candidate genes participating in circadian rhythmicity, insulin signalling and Wnt signalling, which are pathways previously associated with insect diapause development. Clustering relationships among species are most consistent with evolutionary convergence of the shared transcriptomic response, although we are unable to determine whether this reflects convergence of the diapause initiation, maintenance or termination phases.

Data from: Venom-gland transcriptome and venom proteome of the Malaysian king cobra (Ophiophagus hannah)

Background: The king cobra (Ophiophagus hannah) is widely distributed throughout many parts of Asia. This study aims to investigate the complexity of Malaysian Ophiophagus hannah (MOh) venom for a better understanding of king cobra venom variation and its envenoming pathophysiology. The venom gland transcriptome was investigated using the Illumina HiSeq™ platform, while the venom proteome was profiled by 1D-SDS-PAGE-nano-ESI-LCMS/MS. Results: Transcriptomic results reveal high redundancy of toxin transcripts (3357.36 FPKM/transcript) despite small cluster numbers, implying gene duplication and diversification within restricted protein families. Among the 23 toxin families identified, three-finger toxins (3FTxs) and snake-venom metalloproteases (SVMPs) have the most diverse isoforms. These 2 toxin families are also the most abundantly transcribed, followed in descending order by phospholipases A 2 (PLA 2 s), cysteine-rich secretory proteins (CRISPs), Kunitz-type inhibitors (KUNs), and L-amino acid oxidases (LAAOs). Seventeen toxin families exhibited low mRNA expression, including hyaluronidase, DPP-IV and 5'-nucleotidase that were not previously reported in the venom-gland transcriptome of a Balinese O. hannah. On the other hand, the MOh proteome includes 3FTxs, the most abundantly expressed proteins in the venom (43 % toxin sbundance). Within this toxin family, there are 6 long-chain, 5 short-chain and 2 non-conventional 3FTx. Neurotoxins comprise the major 3FTxs in the MOh venom, consistent with rapid neuromuscular paralysis reported in systemic envenoming. The presence of toxic enzymes such as LAAOs, SVMPs and PLA 2 would explain tissue inflammation and necrotising destruction in local envenoming. Dissimilarities in the subtypes and sequences between the neurotoxins of MOh and Naja kaouthia (monocled cobra) are in agreement with the poor cross-neutralization activity of N. kaouthia antivenom used against MOh venom. Besides, the presence of cobra venom factor, nerve growth factors, phosphodiesterase, 5'-nucleotidase, and DPP-IV in the venom proteome suggests its probable hypotensive action in subduing prey. Conclusion: This study reports the diversity and abundance of toxins in the venom of the Malaysian king cobra (MOh). The results correlate with the pathophysiological actions of MOh venom, and dispute the use of Naja cobra antivenoms to treat MOh envenomation. The findings also provide a deeper insight into venom variations due to geography, which is crucial for the development of a useful pan-regional antivenom.

opencc-zeroDec 2015View details →

Data from: Antennal transcriptome analysis and expression profiles of odorant binding proteins in Eogystia hippophaecolus (Lepidoptera: Cossidae)

Background: Eogystia hippophaecolus (Hua et al.) (Lepidoptera: Cossidae) is the major threat to seabuckthorn plantations in China. Specific and highly efficient artificial sex pheromone traps was developed and used to control it. However, the molecular basis for the pheromone recognition is not known. So we established the antennal transcriptome of E. hippophaecolus and characterized the expression profiles of odorant binding proteins. These results establish and improve the basis knowledge of the olfactory receptive system, furthermore provide a theoretical basis for the development of new pest control method. Results: We identified 29 transcripts encoding putative odorant-binding proteins (OBPs), 18 putative chemosensory proteins (CSPs), 63 odorant receptors (ORs), 13 gustatory receptors (GRs), 12 ionotropic receptors (IRs), and two sensory neuron membrane proteins (SNMPs). Based on phylogenetic analysis, we found one Orco and three pheromone receptors of E. hippophaecolus and found that EhipGR13 detects sugar, EhipGR11 and EhipGR3 detect bitter. Nine OBPs expression profile indicated that most were the highest expression in antennae, consistent with functions of OBPs in binding and transporting odors during the antennal recognition process. OBP6 was external expressed in male genital-biased in, and this locus may be responsible for pheromone binding and recognition as well as mating. OBP1 was the highest and biased expressed in the foot and may function as identification of host plant volatiles. Conclusions: One hundred thirty-seven chemosensory proteins were identified and the accurate functions and groups of part proteins were obtained by phylogenetic analysis. The most OBPs were antenna-biased expressed, which are involved in antennal recognition. However, few OBP was detected biased expression in the foot and external genitalia, and these loci may function in pheromone recognition, mating, and the recognition of plant volatiles.

Data from: Stress response or beneficial temperature acclimation: transcriptomic signatures in Antarctic fish (Pachycara brachycephalum)

Research on the thermal biology of Antarctic marine organisms has increased awareness of their vulnerability to climate change, as a flipside of their adaptation to life in the permanent cold and their limited capacity to acclimate to variable temperatures. Here, we employed a species–specific microarray of the Antarctic eelpout, Pachycara brachycephalum to identify long-term shifts in gene expression after 2 months of acclimation to six temperatures between -1°C and 9°C. Changes in cellular processes comprised signalling, post-translational modification, cytoskeleton remodelling, metabolic shifts and alterations in the transcription as well as translation machinery. The magnitude of transcriptomic responses paralleled the change in whole animal performance. Optimal growth at 3°C occurred at a minimum in gene expression changes indicative of a balanced steady state. The up–regulation of ribosomal transcripts at 5°C and above was accompanied by the transcriptomic activation of differential protein degradation pathways, from proteasome-based degradation in the cold towards lysosomal protein degradation in the warmth. From 7°C upwards increasing transcript levels representing heat shock proteins and an acute inflammatory response indicate cellular stress. Such patterns may contribute to a warm-induced energy deficit and a strong weight loss at temperatures above 6°C. Together, cold or warm acclimation led to specific cellular rearrangements and the progressive development of functional imbalances beyond the optimum temperature. The observed temperature–specific expression profiles reveal the molecular basis of thermal plasticity and refine present understanding of the shape and positioning of the thermal performance curve of ectotherms on the temperature scale.

Data from: Transcriptome comparative analysis of two Camellia species reveals lipid metabolism during mature seed natural drying

Camellia seed oil has been used as high quality and healthy food for over two thousand years. Seed drying management effects oil quality and quantity. however, the molecular mechanisms of fatty acid biosynthesis and accumulation during the drying process remain unknown. In this study, the transcriptomes of Camellia meiocarpa and C. oleifera seed were characterized at five moisture content levels (10 - 50%) to identify the major processes and reveal genes affecting lipid metabolism in response to nature drying. We found a total of 111,156 unigenes by de novo assembled from RNA-Seq libraries of five moisture content levels during after-ripening of C. meiocarpa (74,016) and C. oleifera (76,374). Ten pathways were closely linked to changes in oil content and composition with 244 genes involved in fatty acid synthesis and accumulation. Gene Ontology enrichment of differentially expressed genes (DEGs) indicated that fatty acid synthesis and accumulation are essential in C. meiocarpa while fatty acid accumulation in C. oleifera during nature drying process. Comparative analyses of DEGs between any two consecutive moisture contents, identified six and three key unigenes in C. Meiocarpa and C. oleifera seeds, respectively, and one additional unigene responsible for the difference between the two species' fatty acid synthesis and accumulation. Natural drying has improved the quality and quantity of the camellia seed oil. The study provided: a) global transcriptional profiles at five moisture content levels during seed nature drying, b) insights into highlighting transcripts putatively involved in the regulation of the gene expression program and in specific processes likely essential for lipid metabolism, and c) an opportunity to discovering genes associated with oil seed quantity and quality improvement for the studied two camellia species.

opencc-zeroDec 2012View details →

Data from: Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach

Despite the recent advances in generating molecular data, reconstructing species-level phylogenies for non-models groups remains a challenge. The use of a number of independent genes is required to resolve phylogenetic relationships, especially for groups displaying low polymorphism. In such cases, low-copy nuclear exons and non-coding regions, such as 3′ untranslated regions (3′-UTRs) or introns, constitute a potentially interesting source of nuclear DNA variation. Here, we present a methodology meant to identify new nuclear orthologous markers using both public-nucleotide databases and transcriptomic data generated for the group of interest by using next generation sequencing technology. To identify PCR primers for a non-model group, the genus Leucadendron (Proteaceae), we adopted a framework aimed at minimizing the probability of paralogy and maximizing polymorphism. We anchored when possible the right-hand primer into the 3′-UTR and the left-hand primer into the coding region. Seven new nuclear markers emerged from this search strategy, three of those included 3′-UTRs. We further compared the phylogenetic potential between our new markers and the ribosomal internal transcribed spacer region (ITS). The sequenced 3′-UTRs yielded higher polymorphism rates than the ITS region did. We did not find strong incongruences with the phylogenetic signal contained in the ITS region and the seven new designed markers but they strongly improved the phylogeny of the genus Leucadendron. Overall, this methodology is efficient in isolating orthologous loci and is valid for any non-model group given the availability of transcriptomic data.

opencc-zeroDec 2010View details →

Data from: Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome

Next-generation sequencing provides a powerful new approach for developing functional genomic tools for nonmodel species, helping to narrow the gap between studies of model organisms and those of natural populations. Consequently, massively parallel 454 sequencing was used to characterize a normalized cDNA library derived from skin biopsy samples of twelve Antarctic fur seal (Arctocephalus gazella) individuals. Over 412 Mb of sequence data were generated, comprising 1.4 million reads of average length 286 bp. De novo assembly using Newbler 2.3 yielded 156 contigs plus 22 869 isotigs, which in turn clustered into 18 576 isogroups. Almost half of the assembled transcript sequences showed significant similarity to the nr database, revealing a functionally diverse array of genes. Moreover, 97.9% of these mapped to the dog (Canis lupis familiaris) genome, with a strong positive relationship between the number of sequences locating to a given chromosome and the length of that chromosome in the dog indicating a broad genomic distribution. Average depth of coverage was also almost 20-fold, sufficient to detect several thousand putative microsatellite loci and single nucleotide polymorphisms. This study constitutes an important step towards developing genomic resources with which to address consequential questions in pinniped ecology and evolution. It also supports an earlier but smaller study showing that skin tissue can be a rich source of expressed genes, with important implications for studying the genomics not only of marine mammals, but also more generally of species that cannot be destructively sampled.

Data from: "De novo assembled transcriptome of organs involved in reproduction in an endangered endemic Iberian cyprinid fish (Squalius pyrenaicus)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015

Sex determination systems are diverse, especially among fish, and include genetic and/or environmental components. Unexpectedly for such a basic aspect of development, sex determination systems change rapidly during evolution and gonadal fate is not ultimate, being actively maintained lifelong. Here, sequences of expressed genes involved in maintenance of gonad identity and reproduction processes were obtained through transcriptome assembly of the brain-gonadal axis tissues of a freshwater fish inhabiting highly variable environments, the gonochoristic Iberian fish Squalius pyrenaicus. Through Illumina total RNA-sequencing, male and female transcriptomes of brain and gonad tissues were assembled with Trans-ABySS software and merged to produce a more comprehensive S. pyrenaicus transcriptome. Coding sequences (CDS) predicted by TransDecoder were annotated using blastx. By means of read mapping against the reference transcriptome and CDS datasets, using Bowtie2, the accuracy of read mapping was assessed. This first endemic Iberian cyprinid transcriptome of organs involved in reproduction processes may serve as a valuable genomic resource for studying sexual mechanisms and other aspects of evolution, such as speciation and responses to environmental changes, and may be a useful tool for conservation studies since S. pyrenaicus is an endangered species.

Data from: Machine learning-based differential network analysis: a study of stress-responsive transcriptomes in Arabidopsis thaliana

Machine learning (ML) is an intelligent data mining technique that builds a prediction model based on the learning of prior knowledge to recognize patterns in large-scale data sets. We present an ML-based methodology for transcriptome analysis via comparison of gene coexpression networks, implemented as an R package called machine learning–based differential network analysis (mlDNA) and apply this method to reanalyze a set of abiotic stress expression data in Arabidopsis thaliana. The mlDNA first used a ML-based filtering process to remove nonexpressed, constitutively expressed, or non-stress-responsive "noninformative" genes prior to network construction, through learning the patterns of 32 expression characteristics of known stress-related genes. The retained "informative" genes were subsequently analyzed by ML-based network comparison to predict candidate stress-related genes showing expression and network differences between control and stress networks, based on 33 network topological characteristics. Comparative evaluation of the network-centric and gene-centric analytic methods showed that mlDNA substantially outperformed traditional statistical testing–based differential expression analysis at identifying stress-related genes, with markedly improved prediction accuracy. To experimentally validate the mlDNA predictions, we selected 89 candidates out of the 1784 predicted salt stress–related genes with available SALK T-DNA mutagenesis lines for phenotypic screening and identified two previously unreported genes, mutants of which showed salt-sensitive phenotypes.

Data from: Transcriptome sequencing reveals both neutral and adaptive genome dynamics in a marine invader

Species invasions cause significant ecological and economic damage, and genetic information is important to understanding and managing invasive species. In the ocean, many invasive species have high dispersal and gene flow, lowering the discriminatory power of traditional genetic approaches. High-throughput sequencing holds tremendous promise for increasing resolution and illuminating the relative contributions of selection and drift in marine invasion, but has not yet been used to compare the diversity and dynamics of a high-dispersal invader in its native and invaded ranges. We test a transcriptome-based approach in the European green crab (Carcinus maenas), a widespread invasive species with high gene flow and a well-known invasion history, in two native and five invasive populations. A panel of 10 809 transcriptome-derived nuclear SNPs identified significant population structure among highly bottlenecked invasive populations that were previously undifferentiated with traditional markers. Comparing the full data set and a subset of 9246 putatively neutral SNPs strongly suggested that non-neutral processes are the primary driver of population structure within the species' native range, while neutral processes appear to dominate in the invaded range. Non-neutral native range structure coincides with significant differences in intraspecific thermal tolerance, suggesting temperature as a potential selective agent. These results underline the importance of adaptation in shaping intraspecific differences even in high geneflow marine invasive species. They also demonstrate that high-throughput approaches have broad utility in determining neutral structure in recent invasions of such species. Together, neutral and non-neutral data derived from high-throughput approaches may increase the understanding of invasion dynamics in high-dispersal species.

opencc-zeroDec 2012View details →

Data from: Stronger transferability but lower variability in transcriptomic- than in anonymous microsatellites: evidence from Hylid frogs.

A simple way to quickly optimize microsatellites in non-model organisms is to re-use loci available in closely related taxa; however, this approach can be limited by the stochastic and low cross-amplification success experienced in some groups (e.g. amphibians). An efficient alternative is to develop loci from transcriptome sequences. Transcriptomic microsatellites have been found to vary in their levels of cross-species amplification and variability, but this has to date never been tested in amphibians. Here, we compare the patterns of cross-amplification and levels of polymorphism of 18 published anonymous microsatellites isolated from genomic DNA versus 17 loci derived from a transcriptome, across nine species of tree frogs (Hyla arborea and Hyla cinerea group). We established a clear negative relationship between divergence time and amplification success, which was much steeper for anonymous than transcriptomic markers, with half-lives (time at which 50% of the markers still amplify) of 1.1 and 37 My respectively. Transcriptomic markers are significantly less polymorphic than anonymous loci, but remain variable across diverged taxa. We conclude that the exploitation of amphibian transcriptomes for developing microsatellites is an optimal approach for multi-species surveys (e.g. analyses of hybrid zones, comparative linkage mapping), while anonymous microsatellites may be more informative for fine-scale analyses of intraspecific variation. Moreover, our results confirm the pattern that microsatellite cross-amplification is greatly variable among amphibians, and should be assessed independently within target lineages. Finally, we provide a bank of microsatellites for Palearctic tree frogs (so far only available for H. arborea), which will be useful for conservation and evolutionary studies in this radiation.

Data from: Design of a 9K SNP chip for polar bears (Ursus maritimus) from RAD and transcriptome sequencing

Single-nucleotide polymorphisms (SNPs) offer numerous advantages over anonymous markers such as microsatellites, including improved estimation of population parameters, finer-scale resolution of population structure and more precise genomic dissection of quantitative traits. However, many SNPs are needed to equal the resolution of a single microsatellite, and reliable large-scale genotyping of SNPs remains a challenge in nonmodel species. Here, we document the creation of a 9K Illumina Infinium BeadChip for polar bears (Ursus maritimus), which will be used to investigate: (i) the fine-scale population structure among Canadian polar bears and (ii) the genomic architecture of phenotypic traits in the Western Hudson Bay subpopulation. To this end, we used restriction-site associated DNA (RAD) sequencing from 38 bears across their circumpolar range, as well as blood/fat transcriptome sequencing of 10 individuals from Western Hudson Bay. Six-thousand RAD SNPs and 3000 transcriptomic SNPs were selected for the chip, based primarily on genomic spacing and gene function respectively. Of the 9000 SNPs ordered from Illumina, 8042 were successfully printed, and – after genotyping 1450 polar bears – 5441 of these SNPs were found to be well clustered and polymorphic. Using this array, we show rapid linkage disequilibrium decay among polar bears, we demonstrate that in a subsample of 78 individuals, our SNPs detect known genetic structure more clearly than 24 microsatellites genotyped for the same individuals and that these results are not driven by the SNP ascertainment scheme. Here, we present one of the first large-scale genotyping resources designed for a threatened species.

Data from: Transcriptomic basis of genome by genome variation in a legume-rhizobia mutualism

In the legume-rhizobia mutualism, the benefit each partner derives from the other depends on the genetic identity of both host and rhizobial symbiont. To gain insight into the extent of genome x genome interactions on hosts at the molecular level and to identify potential mechanisms responsible for the variation, we examined host gene expression within nodules (the plant organ where the symbiosis occurs) of four genotypes of Medicago truncatula grown with either Ensifer meliloti or E. medicae symbionts. These host x symbiont combinations show significant variation in nodule and biomass phenotypes. Likewise, combinations differ in their transcriptomes: host, symbiont, and host x symbiont affected the expression of 70%, 27% and 21%, respectively, of the approximately 27,000 host genes expressed in nodules. Genes with the highest levels of expression often varied between hosts and/or symbiont strain and include leghemoglobins that modulate oxygen availability and hundreds of Nodule Cysteine-Rich (NCR) peptides involved in symbiont differentiation and viability in nodules. Genes with host x symbiont dependent expression were enriched for functions related to resource exchange between partners (sugar/sulfate/iron/amino acid transport and dicarboxylate/amino acid synthesis). These enrichments suggest mechanisms for host control of the currencies of the mutualism. The transcriptome of M. truncatula accession HM101 (A17), the reference genome used for most molecular research, was less affected by symbiont identity than the other hosts. These findings underscore the importance of assessing the molecular basis of variation in ecologically important traits, particularly those involved in biotic interactions, in multiple genetic contexts.