Data from: What causes mating system shifts in plants? Arabidopsis lyrata as a case study

Mable BK, Hagmann J, Kim S, Adam A, Kilbride E, Weigel D, Stift M

Date Published: August 23, 2016

DOI: http://dx.doi.org/10.5061/dryad.832t8

 

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Title SISCpools_consensus_chr5
Downloaded 2 times
Description SNP calls for chromosome 5 from bulked segregant analysis. F1s were generated from crosses between a self-incompatible and a self-compatible parent of Arabidopsis lyrata, sampled from the Great Lakes region of Eastern North America, which were then crossed amongst themselves to create F2s. Pools were created from: 1) 10 individuals that were phenotypically self-incompatible; and 2) 10 individuals that were phenotypically self-compatible. Three lanes of separate runs (two 150 bp and one 100 bp paired-end read run) were sequenced on an Illumina GAII instrument for each pool. The Illumina quality-filtered reads were mapped against the A. lyrata reference genome sequence MN47 (Hu et al. 2011) using GenomeMapper (Schneeberger et al. 2009), allowing for up to 10% mismatches/gaps relative to the read length. All alternative alleles relative to the reference base with a minimum frequency within each pool of 10% and a score of at least 25 were called by SHORE, as described (Ossowski et al. 2008). SNP calls (in genes only) were made using SHORE and compared for the two pools against the MN47 reference and for a reference genome constructed from two self-compatible individuals (AL4). These individuals were created by hybridisation between individuals sampled from the same population used for the self-compatible parent of the pools with the MN47 reference strain. The genomic sequence thus was determined by subtraction from the MN47 reference. The data file shows the SNP calls, % of reads with the variant and read coverage for that position. See readme file for complete details. References Hu TT, Pattyn P, Bakker EG, et al. (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genetics 43, 476-481. doi: 10.1038/ng.807 Ossowski S, Schneeberger K, Clark RM, et al. (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Research 18, 2024-2033. 10.1101/gr.080200.108 Schneeberger K, Hagmann J, Ossowski S, et al. (2009) Simultaneous alignment of short reads against multiple genomes. Genome Biology 10, 1-12. 10.1186/gb-2009-10-9-r98
Download SISCpools_consensus_chr5.xls (17.92 Mb)
Download README.docx (71.14 Kb)
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Title SISCpools_consensus_chr7
Downloaded 3 times
Description SNP calls for chromosome 5 from bulked segregant analysis. F1s were generated from crosses between a self-incompatible and a self-compatible parent of Arabidopsis lyrata, sampled from the Great Lakes region of Eastern North America, which were then crossed amongst themselves to create F2s. Pools were created from: 1) 10 individuals that were phenotypically self-incompatible; and 2) 10 individuals that were phenotypically self-compatible. Three lanes of separate runs (two 150 bp and one 100 bp paired-end read run) were sequenced on an Illumina GAII instrument for each pool. The Illumina quality-filtered reads were mapped against the A. lyrata reference genome sequence MN47 (Hu et al. 2011) using GenomeMapper (Schneeberger et al. 2009), allowing for up to 10% mismatches/gaps relative to the read length. All alternative alleles relative to the reference base with a minimum frequency within each pool of 10% and a score of at least 25 were called by SHORE, as described (Ossowski et al. 2008). SNP calls (in genes only) were made using SHORE and compared for the two pools against the MN47 reference and for a reference genome constructed from two self-compatible individuals (AL4). These individuals were created by hybridisation between individuals sampled from the same population used for the self-compatible parent of the pools with the MN47 reference strain. The genomic sequence thus was determined by subtraction from the MN47 reference. The data file shows the SNP calls, % of reads with the variant and read coverage for that position. See readme file for complete details. References Hu TT, Pattyn P, Bakker EG, et al. (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genetics 43, 476-481. doi: 10.1038/ng.807 Ossowski S, Schneeberger K, Clark RM, et al. (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Research 18, 2024-2033. 10.1101/gr.080200.108 Schneeberger K, Hagmann J, Ossowski S, et al. (2009) Simultaneous alignment of short reads against multiple genomes. Genome Biology 10, 1-12. 10.1186/gb-2009-10-9-r98
Download README.docx (71.14 Kb)
Download SISCpools_consensus_chr7.xls (20.96 Mb)
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Title B70haplotypes
Downloaded 1 time
Description Alignment of haplotypes from the gene B70 (Ethylene-responsive protein related; At4g21340). Individual sequences have also been uploaded to Genbank.
Download B70haplotypes.fa (13.26 Kb)
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Title b80haplotypes
Downloaded 1 time
Description Alignment of haplotypes found at B80 (U-box domain protein; At4g21350). Sequences had been uploaded to Genbank for a previous paper (Popset accession 374282218).
Download b80haplotypes.fa (56.98 Kb)
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Title b120haplotypes
Downloaded 1 time
Description Alignment of haplotypes found at B120 (S-locus lectin kinase 9; At4g21390). Individual sequences have been deposited to Genbank.
Download b120haplotypes.fa (59.20 Kb)
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Title b160haplotypes
Downloaded 1 time
Description Alignment of haplotypes at B160 (transcription factor; At4g21430). Sequences were deposited to Genbank for a previous project (Popset accession: 374282986).
Download b160haplotypes.fa (34.78 Kb)
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When using this data, please cite the original publication:

Mable BK, Hagmann J, Kim S, Adam A, Kilbride E, Weigel D, Stift M (2016) What causes mating system shifts in plants? Arabidopsis lyrata as a case study. Heredity 118(1): 52-63. http://dx.doi.org/10.1038/hdy.2016.99

Additionally, please cite the Dryad data package:

Mable BK, Hagmann J, Kim S, Adam A, Kilbride E, Weigel D, Stift M (2016) Data from: What causes mating system shifts in plants? Arabidopsis lyrata as a case study. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.832t8
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