DOI: 10.5061/dryad.832t8
title: Data from: What causes mating system shifts in plants? Arabidopsis lyrata as a case study

description: The genetic breakdown of self-incompatibility (SI) and subsequent mating
 system shifts to inbreeding has intrigued evolutionary geneticists for
 decades. Most of our knowledge is derived from interspecific comparisons
 between inbreeding species and their outcrossing relatives, where
 inferences may be confounded by secondary mutations that arose after the
 initial loss of SI. Here, we study an intraspecific breakdown of SI and
 its consequences in North American Arabidopsis lyrata to test whether: (1)
 particular S-locus haplotypes are associated with the loss of SI and/or
 the shift to inbreeding; (2) a population bottleneck may have played a
 role in driving the transition to inbreeding; and (3) the mutation(s)
 underlying the loss of SI are likely to have occurred at the S-locus.
 Combining multiple approaches for genotyping, we found that outcrossing
 populations on average harbour 5 to 9 S-locus receptor kinase (SRK)
 alleles, but only two, S1 and S19, are shared by most inbreeding
 populations. Self-compatibility (SC) behaved genetically as a recessive
 trait, as expected from a loss-of-function mutation. Bulked segregant
 analysis in SC × SI F2 individuals using deep sequencing confirmed that
 all SC plants were S1 homozygotes but not all S1 homozygotes were SC. This
 was also revealed in population surveys, where only a few S1 homozygotes
 were SC. Together with crossing data, this suggests that there is a
 recessive factor that causes SC that is physically unlinked to the
 S-locus. Overall, our results emphasise the value of combining classical
 genetics with advanced sequencing approaches to resolve long outstanding
 questions in evolutionary biology.
description: SISCpools_consensus_chr5SNP 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-r98SISCpools_consensus_chr7SNP 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-r98B70haplotypesAlignment of haplotypes from the gene B70 (Ethylene-responsive protein related; At4g21340). Individual sequences have also been uploaded to Genbank.b80haplotypesAlignment of haplotypes found at B80 (U-box domain protein; At4g21350). Sequences had been uploaded to Genbank for a previous paper (Popset accession 374282218).b120haplotypesAlignment of haplotypes found at B120 (S-locus lectin kinase 9; At4g21390). Individual sequences have been deposited to Genbank.b160haplotypesAlignment of haplotypes at B160 (transcription factor; At4g21430). Sequences were deposited to Genbank for a previous project (Popset accession: 374282986).