Development of Picea abies SNPs catalog
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PROVIDER: PRJEB27336 | ENA |
REPOSITORIES: ENA
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Project description:Development of a Picea abies SNPs catalog. A bioinformatics pipeline was developed and allowed to detect 61,771 in silico SNPs distributed among 13,543 genes. A bioinformatics pipeline was developed and allowed to detect 61,771 in silico SNPs distributed among 13,543 genes The true positive rate for this set of SNPs was estimated using a sample of 5571 predicted SNPs by genotyping 1130 P. abies trees using an Illumina Infinium iSelect SNP array. The true positive rate for the set of in silico SNPs was 84.2% and was comparable to the genotyping success rate of 85.4% for a set of 89 P. abies control SNPs successfully genotyped on previous Illumina GoldenGate genotyping arrays. Nucleotide diversity was analyzed across functional categories
2018-12-15 | PRJEB27427 | EVA
Project description:BACKGROUND:Norway spruce [Picea abies (L.) Karst.] is ecologically and economically one of the most important conifer worldwide. Our main goal was to develop a large catalog of annotated high confidence gene SNPs that should sustain the development of genomic tools for the conservation of natural and domesticated genetic diversity resources, and hasten tree breeding efforts in this species. RESULTS:Targeted sequencing was achieved by capturing P. abies exome with probes previously designed from the sequenced transcriptome of white spruce (Picea glauca (Moench) Voss). Capture efficiency was high (74.5%) given a high level of exome conservation between the two species. Using stringent criteria, we delimited a set of 61,771 high-confidence SNPs across 13,543 genes. To validate SNPs, a high-throughput genotyping array was developed for a subset of 5571 predicted SNPs representing as many different gene loci, and was used to genotype over 1000 trees. The estimated true positive rate of the resource was 84.2%, which was comparable with the genotyping success rate obtained for P. abies control SNPs recycled from previous genotyping efforts. We also analyzed SNP abundance across various gene functional categories. Several GO terms and gene families involved in stress response were found over-represented in highly polymorphic genes. CONCLUSION:The annotated high-confidence SNP catalog developed herein represents a valuable genomic resource, being representative of over 13?K genes distributed across the P. abies genome. This resource should serve a variety of population genomics and breeding applications in Norway spruce.
| S-EPMC6296092 | biostudies-literature
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Picea abies tissues (including needles, immature cones and lateral bud meristem). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.
2011-05-10 | GSE28983 | GEO
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Picea abies tissues (including needles, immature cones and lateral bud meristem). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study. Small RNA libraries were derived from needles, immature female cones and lateral bud meristem of Picea abies. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank David Neale for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.
2011-05-09 | E-GEOD-28983 | biostudies-arrayexpress
Project description:Picea abies embryogenic tissue Raw sequence reads
| PRJNA818083 | ENA