https://researchdata.se/sv/catalogue Search results sv RNA-Seq data was generated from stages of somatic (SE) and zygotic embryogenesis (ZE). The developing zygotes (Zem) were isolated from the female megagametyophyte (FG) tissue at later stages. Differential expression analysis was performed for each dataset and the results were compared to identify common and contrasting expression changes. The somatic embryogenesis data was used to predict long intergenic RNAs and a co-expression network was generated. The network was used to assign putative functional annotation to the lincRNAs using a guilt-by-association approach. The normalised expression values, results of differential expression test, results of functional enrichment of gene sets and figures representing these are included. The sequences of identified lncRNAs are included as well as annotation information. The data is structured in three folders: SE = Somatic Embryogenesis ZE = Zygotic Embryogenesis SE_ZE = All files related to the comparison of differentially expressed genes between the two datasets. Some of the file names or figures can contain abbreviations different from the ones in the original publications. A conversion table is provided in the README file. More information on the folder and file content can be found in the manifest file. Tue, 01 Oct 2024 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-25315867-v1 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-25315867-v1 Umeå universitet Nathaniel Street Katja Stojkovič Ulrika Egertsdotter Kim-Cuong Le Nicolas Delhomme Camilla Canovi RNA-Seq data was generated from stages of somatic (SE) and zygotic embryogenesis (ZE). The developing zygotes (Zem) were isolated from the female megagametyophyte (FG) tissue at later stages. Differential expression analysis was performed for each dataset and the results were compared to identify common and contrasting expression changes. The somatic embryogenesis data was used to predict long intergenic RNAs and a co-expression network was generated. The network was used to assign putative functional annotation to the lincRNAs using a guilt-by-association approach. The normalised expression values, results of differential expression test, results of functional enrichment of gene sets and figures representing these are included. The sequences of identified lncRNAs are included as well as annotation information. The data is structured in three folders: SE = Somatic Embryogenesis ZE = Zygotic Embryogenesis SE_ZE = All files related to the comparison of differentially expressed genes between the two datasets. Some of the file names or figures can contain abbreviations different from the ones in the original publications. A conversion table is provided in the README file. More information on the folder and file content can be found in the manifest file. Tue, 01 Oct 2024 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-25315867 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-25315867 Umeå universitet Nathaniel Street Katja Stojkovič Ulrika Egertsdotter Kim-Cuong Le Nicolas Delhomme Camilla Canovi Background to the study: We have produced a chromosome-scale genome assembly generated using long-read sequencing, optical and high-density genetic maps containing 39,894 annotated genes with functional annotations for 73,765 transcripts in 37,184 genes. We conducted whole-genome resequencing of the Umeå Aspen (UmAsp) collection comprising 227 aspen individuals. We utilised the assembly and existing whole genome re-sequencing data to perform genome-wide association analyses (GWAS) using Single Nucleotide Polymorphisms (SNPs) in the UmAsp, Swedish Aspen (SwAsp) and Scottish Aspen (ScotAsp) collections for leaf physiognomy phenotypes. We conducted Assay of Transposase Accessible Chromatin sequencing (ATAC-Seq) and identified genomic regions of accessible chromatin, and subset SNPs to these regions, which improved the GWAS detection rate. We identified candidate long non-coding RNAs in leaf samples and quantified their expression in an updated co-expression network, which we used to explore the functions of candidate genes identified from the GWAS. This data set comprises: the ATAC-Seq peaks from the ATAC-Sequencing of aspen leaves, 'Aspen leaf ATAC_Seq peaks.zip'; and the gene expression matrix of mean values per aspen genotype from the SwAsp collection, 'Gene_Expression_matrix_genotype_mean.tsv'. We provide a zipped directory for each of 'ScotAsp.zip', 'SwAsp.zip' and 'UmAsp.zip' providing the raw leaf image scans, the cropped leaf images and raw data files from the LAMINA leaf shape analyses of these images, and the processed data files and genotypic BLUP values for each of these ScotAsp, SwAsp and UmAsp collections. We provide the GWAS associations of SNPs ranked by decreasing P-value until the 1000th gene for each of the 26 leaf physiognomy traits for each collection, i.e. 'ScotAsp top-ranked GWAS results', 'SwAsp top-ranked GWAS results' and 'UmAsp top-ranked GWAS results'. The single nucleotide polymorphism (SNP) data for each of the aspen collections is in 'ScotAsp_biallelic_Het.HWE.recode.vcf.gz', 'SwAsp_AfterBatchRemoval_biallelic_Het.HWE.recode.vcf.gz' and 'UmAsp_biallelic_Het.MAF.HWE.recode_.vcf.gz'. Thu, 22 Aug 2024 00:00:00 GMT https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-25335448 https://researchdata.se/sv/catalogue/dataset/doi-10-17044-scilifelab-25335448 Umeå universitet Kathryn Robinson Bastian Schiffthaler Hui Liu Sara Westman Martha Rendon Anaya Teitur Kalman Vikash Kumar Camilla Canovi Carolina Bernhardsson Nicolas Delhomme Jerry Jenkins Jing Wang Niklas Mähler Kerstin Richau Victoria Stokes Stuart A'Hara Joan Cottrell Kizi Coeck Tim Diels Klaas Vandepoele Chanaka Mannapperuma Eung-Jun Park Stephane Plaisance Stefan Jansson Pär Ingvarsson Nathaniel Street Work on the Lake Victoria cichlids Pundamilia nyererei (red dorsum males, deeper water), Pundamilia pundamilia (blue males, shallower water) and related species pairs has provided insights into processes of speciation. Here, we investigate female mating behaviour of five Pundamilia species and four of their F1-hybrids through mate choice trials and paternity testing. We discuss the results in the context of the geography of speciation and coexistence. Complete assortative mating was observed among all sympatric species. Parapatric species with similar depth habitat distributions interbred whereas other parapatric and allopatric species showed complete assortative mating. F1-hybrids mated exclusively with species accepted by females of the parental species. Although consistent with reinforcement in sympatry, a closer look at our results suggests otherwise and it is more likely that pre-existing female preferences influence which taxa can co-exist in sympatry. Regardless of the mechanism, mating preferences may influence species distribution in potentially hybridizing taxa, such as in the adaptive radiations of cichlid fish. We suggest that this at least partly explains why some species fail to establish breeding populations in locations where they are occasionally recorded. Our result support the notion that mating preferences of potentially cross-breeding species ought to be included in coexistence theory. Supplementary tables S1-S3The supplementary tables contain all microsatellite paternity analyses of the wild type females and F1-females used in the present study.Table S1 contains a summary of the spawning decisions of all females, including their IDs. Table S2 includes the microsatellite genotype of all males used in the experiment as well as in which experimental round they were used. The experimental rounds were approximately four weeks each. The experiment was carried out over two years, from August 2006 to July 2008. Table S3 includes microsatellite raw data of the offspring of the females, as well as the paternity analyses. The first row with the ID shows the genotype of the females whereas the following rows with the same ID show the IDs of the offspring. Brood No is the ID of the brood and the rows below, until the next Brood number, are siblings from the same brood. When available, number of eggs in the brood, the size of the brooding female, the date when the female was stripped of eggs/fry and the number and starting date of the experimental round are given on the same row as Brood No. A slash between potential fathers of the same species show that it was not possible to dettermine parentage between the two conspecific males. Fathers within brackets show that the conspecific male is a potential father. However, it is a less likely father e.g. because short time in the experimental setup. Note that all offspring were 100% assigned to one species only. Empty cells are marked with n/a. Species included in the present study:P. azurea, Ruti IslandP. igneopinnis, Igombe IslandP. nyererei, Makobe IslandP. pundamilia, Makobe IslandP. sp. red head, Zue Island Table S1. Spawning decisions of wild type females and F1 hybrid femalesTable S2. Microsatellite genotypes and experimental round of malesTable S3. Microsatellite genotypes and paternity analyses Supplementary figures S1-S2Supplemental figure S2a. ‘melanic’ v. ‘red dorsum’ and ‘blue’ F1-crosses. In the P. azurea x P. nyererei cross (both directions) approximately three fourth were ‘red dorsum’ morphs and one fourth of the crosses were ‘blue’ morphs. The same was true for the P. igneopinnis x P. nyererei cross (both directions). In the latter we followed 26 randomly picked males to old age and the ratio did not change (20 ‘red dorsum’ v. 6 ‘blue’). One male and one female produced the cross except where noted (mother 1, mother 2). We do not have a photo of the P. igneopinnis x P. nyererei, ‘blue’ morph. Photos: Katie Woodhouse. Supplemental figure S2a. ‘melanic’ v. ‘red dorsum’ and ‘blue’ F1-crosses. In the P. azurea x P. nyererei cross (both directions) approximately three fourth were ‘red dorsum’ morphs and one fourth of the crosses were ‘blue’ morphs. The same was true for the P. igneopinnis x P. nyererei cross (both directions). In the latter we followed 26 randomly picked males to old age and the ratio did not change (20 ‘red dorsum’ v. 6 ‘blue’). One male and one female produced the cross except where noted (mother 1, mother 2). We do not have a photo of the P. igneopinnis x P. nyererei, ‘blue’ morph. Photos: Katie Woodhouse. Supplemental figure S2b. ‘blue’ v. ‘red chest’ and ‘red dorsum’ F1-crosses. One male and one female produced the cross except where noted (mother 1, mother 2). We do not have photos of the P. pundamilia x P. nyererei and P. sp. ‘red head’ x P. pundamilia crosses. Photos: Katie Woodhouse and Ola Svensson. Figures S1-2. Experimental set-up and photos of F1 hybrid males Datasetet har ursprungligen publicerats i DiVA och flyttades över till SND 2024. Mon, 24 Jun 2024 13:41:08 GMT https://researchdata.se/sv/catalogue/dataset/2024-407 https://researchdata.se/sv/catalogue/dataset/2024-407 Högskolan i Borås Ola Svensson Katie Woodhouse Alan Smith Ole Seehausen George F Turner Datasetet utgörs av en TSV-fil bestående av 209 rader och 48 kolumner innehållande följande information: information om flocken och dess lokalisation (typ av by, bynummer, hushållsnummer), information om tackan (pseudonymiserad ID, ålder, totalantal födda lamm, antal lamm i kullen, hullskala, förekomst av ullkontamination och förekomst av kliniska symtom på sjukdom), information om lammet (kön, pseudonymiserad ID, ålder vid första vägning, antal syskon, vikt vid första vägning och förekomst av kliniska symtom på sjukdom) samt lammets vikt vid ett, två, tre, fyra och fem månaders ålder. Tackans body condition score är baserad på en femgradig skala från 1 (kraftigt avmagrad) till 5 (kraftigt överviktig). Tackans grad av ullkontamination är baserad på en skala fyrgradig skala från 0 (helt ren) till 3 (kraftigt nedsmutsad). Datasetet beskriver samma flockar som datasetet SND-ID: 2020-185. Thu, 15 Jun 2023 13:14:48 GMT https://researchdata.se/sv/catalogue/dataset/2023-115-1 https://researchdata.se/sv/catalogue/dataset/2023-115-1 Sveriges lantbruksuniversitet Sara Lysholm Elisabeth Genfors Data samlades in i Uppsala, Sverige, mellan 2019 och 2021. Bikupor med varroaresistenta bidrottningar från Oslo, Norge (n=3), Gotland, Sverige (n=5), och Avignon, Frankrike (n=4), samt icke-resistenta kontrollpopulationer från Uppsala, Sverige (n=5) etablerades och placerades vid SLU Lövsta fältforskningsstation (GPS-koordinater: 59° 50’ 2.544”N, 17° 48’ 47.447”E). Reproduktionsframgången för varroakvalster mättes i yngelramar som antingen varit tillgängliga eller otillgängliga för arbetsbina. Avskiljare till ramarna installerades direkt efter täckning och nio dagar senare dissekerades yngelramarna. Cellernas lock avlägsnades med skalpell, och därefter avlägsnades försiktigt bipuppan och kvalstren från varje cell med pincett och pensel. Antalet framgångsrika reproduktionsförsök, definierat som att ett moderkvalster gett upphov till en hane och minst ett nytt honkvalster, räknades. Om detta kriterium inte uppfylldes bedömdes detta som ett misslyckat reproduktionsförsök, och orsaken till detta noterades. Data analyserades i R version 4.0.1, i R Studio 1.3.959. En linjär blandad modell användes för att jämföra kvalstrets fekunditet och effekten av behandlingarna mellan de olika bipopulationerna, där varroakvalstrets reproduktionsframgång användes som responsvariabel, populationens ursprung och om bina haft eller inte haft tillgång till yngelramarna användes som oberoende variabel, och koloni och år som slumpvariabel. Minstakvadratmetoden användes för att jämföra behandlingar mellan individuella populationer. Scaramella_et_al_2023_Data.tsv - Datauppsättning består av 34 rader och 21 kolumner. Bisamhällets demografi och behandling är listade. All insamlad data är räknedata och förklaras mer detaljerat i README-filen. Det R-skript som använts i analysen bifogas. Det är uppdelat i två sektioner där den första använts för den statistiska analysen och den andra för att göra de grafer som ingår i artikeln. Se SECTION 1 - ANALYSIS och SECTION 2 – PLOTs Scaramella_et_al_2023_Analysis_Code_log.txt och Rplots.pdf kan, givet att skriptet finns i samma katalog som datafilerna och nödvändiga paket installerats (se sessionInfo.txt), återskapas genom att köra: Rscript Scaramella_et_al_2023_Analysis_Code.R > \ Scaramella_et_al_2023_Analysis_Code_log.txt Scaramella_et_al_2023_Bar_Graph_Data.tsv - Datauppsättning bestående av 8 rader och 5 kolumner. Kolonidemografi och utsedd behandling listas. All data är genererad från räkningsdata i Scaramella_et_al_2023_Data.tsv och förklaras mer i detalj i read me-filen. Scaramella_et_al_2023_Stacked_Bar_Graph_Data.tsv - Datauppsättning bestående av 102 rader & 8 kolumner. Kolonidemografi och utsedd behandling listas. All data är Scaramella_et_al_2023_Data.tsv omstrukturerad för att inkludera "reason failed" som en kolumn. Uppgifterna förklaras mer i detalj i read me-filen. Thu, 01 Jun 2023 11:09:57 GMT https://researchdata.se/sv/catalogue/dataset/2023-79-1 https://researchdata.se/sv/catalogue/dataset/2023-79-1 Sveriges lantbruksuniversitet Nicholas Scaramella Ashley Burke Melissa Oddie Barbara Locke I den här tvärsnittsstudien undersökte vi prevalensen av Mycoplasma bovis i tankmjölk och besättningsfaktorer associerade med ett positivt antikroppstest hos svenska mjölkkobesättningar. Tankmjölksprover från alla svenska mjölkkobesättningar (n=3144) samlades in och analyserades med ID Screen antikropps-ELISA och PCR. Information om besättningsfaktorer hämtades från den Nationella kodatabasen. För att identifiera besättningsfaktorer associerade med antikroppar i tankmjölken användes logistisk regression i fyra olika modeller. För mer information, se "Description of data" och den publicerade artikeln. Variabler använda i studien (kategoriserade) återfinns i filen "M_bovis_dataset_csv". Beskrivning från Växa Sverige hur vissa data beräknats återfinns i filen "Berakningsprinciper_valfardsindikatorer" (enbart på svenska). Kodning av parametrar i datasetet återfinns i filerna "Coding_of_variables_M_bovis" och "Coding_of_continuous _variables_into_4_groups". Beskrivning av studien, urval och datakällor i "Description_of_data_M_bovis" Fri, 26 Aug 2022 12:26:57 GMT https://researchdata.se/sv/catalogue/dataset/2021-319-1 https://researchdata.se/sv/catalogue/dataset/2021-319-1 Sveriges lantbruksuniversitet Madeleine Tråven Emma Hurri Anna Ohlson Åsa Lundberg Anna Aspán Karl Pedersen