SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population

International audienceBackground - Progress in genetics and breeding in pea still suffers from the limited availability of molecular resources. SNP markers that can be identified through affordable sequencing processes, without the need for prior genome reduction or a reference genome to assemble sequencing data would allow the discovery and genetic mapping of thousands of molecular markers. Such an approach could significantly speed up genetic studies and marker assisted breeding for non-model species. Results - A total of 419,024 SNPs were discovered using HiSeq whole genome sequencing of four pea lines, followed by direct identification of SNP markers without assembly using the discoSnp tool. Subsequent filtering led to the identification of 131,850 highly designable SNPs, polymorphic between at least two of the four pea lines. A subset of 64,754 SNPs was called and genotyped by short read sequencing on a subpopulation of 48 RILs from the cross 'Baccara' x 'PI180693'. This data was used to construct a WGGBS-derived pea genetic map comprising 64,263 markers. This map is collinear with previous pea consensus maps and therefore with the Medicago truncatula genome. Sequencing of four additional pea lines showed that 33 % to 64 % of the mapped SNPs, depending on the pairs of lines considered, are polymorphic and can therefore be useful in other crosses. The subsequent genotyping of a subset of 1000 SNPs, chosen for their mapping positions using a KASP™ assay, showed that almost all generated SNPs are highly designable and that most (95 %) deliver highly qualitative genotyping results. Using rather low sequencing coverages in SNP discovery and in SNP inferring did not hinder the identification of hundreds of thousands of high quality SNPs. Conclusions - The development and optimization of appropriate tools in SNP discovery and genetic mapping have allowed us to make available a massive new genomic resource in pea. It will be useful for both fine mapping within chosen QTL confidence intervals and marker assisted breeding for important traits in pea improvement

Colib'read on galaxy : a tools suite dedicated to biological information extraction from raw NGS reads

Background: With next-generation sequencing (NGS) technologies, the life sciences face a deluge of raw data. Classical analysis processes for such data often begin with an assembly step, needing large amounts of computing resources, and potentially removing or modifying parts of the biological information contained in the data. Our approach proposes to focus directly on biological questions, by considering raw unassembled NGS data, through a suite of six command-line tools. Findings: Dedicated to 'whole-genome assembly-free' treatments, the Colib'read tools suite uses optimized algorithms for various analyses of NGS datasets, such as variant calling or read set comparisons. Based on the use of a de Bruijn graph and bloom filter, such analyses can be performed in a few hours, using small amounts of memory. Applications using real data demonstrate the good accuracy of these tools compared to classical approaches. To facilitate data analysis and tools dissemination, we developed Galaxy tools and tool shed repositories. Conclusions: With the Colib'read Galaxy tools suite, we enable a broad range of life scientists to analyze raw NGS data. More importantly, our approach allows the maximum biological information to be retained in the data, and uses a very low memory footprint.Peer reviewe

AskoR, A R Package for Easy RNASeq Data Analysis

International audienceFor facilitating the process of transcriptomics data, and to guarantee the reproducibility of our analyses, we developed AskoR, which is a R library for performing a suite of statistical analysisand graphical output from gene expression data obtained by sequencing (RNA-Seq). From raw counts, it makes it possible to filter and normalize the data, to check the consistency of the samples,and to carry out differential expression tests, GO terms enrichments, and clusters of co-expression, with a large number of figures in the output. AskoR can be downloaded and used in your favoriteR environment or directly accessible through a Galaxy portal like the one which is hosted by the BioInformatics Platform for the Agroecosystems Arthropods (BIPAA)

Reference-free high-throughput SNP detection in pea: an example of discoSnp usage for a non-model complex genome

International audienceBackground / Purpose:Detecting Single Nucleotide Polymorphisms (SNPs) between genomes is a routine task with Next Generation Sequencers (NGS) data. SNP detection methods generally need a reference genome. As non-model organisms are increasingly investigated, reference-free methods are needed. The discoSnp method detects SNPs directly from raw NGS data set(s) without using any third-party information. The pea non-model organism has a 4.5 GB complex genome without reference. We compared, on the same set of low depth pea sequences, the SNPs generated by discoSnp with those published with a previous SNP discovery pipeline, and those generated using classical mapping approach with the association of Bowtie2 and GATK tools.Main conclusion:The quality of discoSnp results in association with its very low memory needs and low time footprints led us to choose this software for a SNP discovery and direct Genotypin. By Sequencing project on a set of 48 pea genomic DNA libraries from a recombinant inbred lines subpopulation sequenced with Illumina HiSeq2000 technology. The analysis enabled to identify 88,851 SNP polymorphs on this population, from which around 60k SNPs will be genetically mapped

A 69-year-old man with a painful vesicular rash

Additional file 3. Evolution of the number and the size of the de novo genomics contigs as a function of the iterations

SNP discovery in pea: a powerful tool for academic research and breeding

absen

MOESM2 of De novo construction of a “Gene-space” for diploid plant genome rich in repetitive sequences by an iterative Process of Extraction and Assembly of NGS reads (iPEA protocol) with limited computing resources

Additional file 2. Mapping of genomics HiSeq 2000 reads against the pea Unigene at the first iteration

Rhizocarpon geographicum Lichen Discloses a Highly Diversified Microbiota Carrying Antibiotic Resistance and Persistent Organic Pollutant Tolerance

International audienceAs rock inhabitants, lichens are exposed to extreme and fluctuating abiotic conditions associated with poor sources of nutriments. These extreme conditions confer to lichens the unique ability to develop protective mechanisms. Consequently, lichen-associated microbes disclose highly versatile lifestyles and ecological plasticity, enabling them to withstand extreme environments. Because of their ability to grow in poor and extreme habitats, bacteria associated with lichens can tolerate a wide range of pollutants, and they are known to produce antimicrobial compounds. In addition, lichen-associated bacteria have been described to harbor ecological functions crucial for the evolution of the lichen holobiont. Nevertheless, the ecological features of lichen-associated microbes are still underestimated. To explore the untapped ecological diversity of lichen-associated bacteria, we adopted a novel culturomic approach on the crustose lichen Rhizocarpon geographicum. We sampled R. geographicum in French habitats exposed to oil spills, and we combined nine culturing methods with 16S rRNA sequencing to capture the greatest bacterial diversity. A deep functional analysis of the lichen-associated bacterial collection showed the presence of a set of bacterial strains resistant to a wide range of antibiotics and displaying tolerance to Persistent Organic Pollutants (POPs). Our study is a starting point to explore the ecological features of the lichen microbiota

Localisation / Globalisation: Diversity of processes in eight Dairy Basins

The Changes affecting farming, operating between local and global, are important concerning milk processing. How these changes express themselves locally? What consequences concerning strategies of processing firms and concerning livestock farming systems? Developing diachronic studies we analyze interactions between marketing strategies of milk processing factories, livestock farming systems and consequences of these changes at local scales. Comparing contrasted situations (France, South America, Vietnam and Senegal), we found mostly two contrated dynamics : - a process of globalisation ( concentration of operators, increasing importance of long food chains, location of farm in high productivity areas, intensification of farming practices) - a process of strengthening relationship between product and local specificity (emphasizing local image and the link between product and the « terroir », handicraft processes of transformation), increasing of local marketing channels, farming practices valorizing a diversity of local resources. Intermediating between production and distribution, dairy factories are at the core of these two dynamics. We will present the methodologies employed to characterize the studied situations. From examples we will illustrate how are emerging and operate these two dynamics. We will discuss then how in a same place it may appear complementarity, tensions or exclusions between these two dynamics

Comparative transcriptome analysis at the onset of speciation in a mimetic butterfly—The Ithomiini Melinaea marsaeus

Plateforme bioinformatique pour les arthropodes des agroécosystèmes : BIPAAInternational audienceEcological speciation entails divergent selection on specific traits, and ultimately on the developmental pathways responsible for these traits. Selection can act on gene sequences, but also on regulatory regions responsible for gene expression. Mimetic butterflies are a relevant system for speciation studies because wing color pattern (WCP) often diverges between closely related taxa, and is thought to drive speciation through assortative mating and increased predation on hybrids. Here we generate the first transcriptomic resources for a mimetic butterfly of the tribe Ithomiini, Melinaea marsaeus, to examine patterns of differential expression between two subspecies and between tissues that express traits that likely drive reproductive isolation; WCP and chemosensory genes. We sequenced whole transcriptomes of three life stages to cover a large catalogue of transcripts and we investigated differential expression between subspecies in pupal wing discs and antennae. Eighteen known WCP genes were expressed in wing discs and 115 chemosensory genes were expressed in antennae, with a remarkable diversity of chemosensory protein genes. Many transcripts were differentially expressed between subspecies, including two WCP genes and one odorant receptor. Our results suggest that in M. marsaeus the same genes as in other mimetic butterflies are involved in traits causing reproductive isolation, and point at possible candidates for the differences in those traits between subspecies. Differential expression analyses of other developmental stages and body organs and functional studies are needed to confirm and expand these results. Our work provides key resources for comparative genomics in mimetic butterflies, and more generally in Lepidoptera