DOI: 10.6084/m9.figshare.22567558
title: SRK and SCR reference sequences for running the NGSgenotyp pipeline

description: These datasets are attached to the publication:T. Duan, Z. Zhang, M. Genete, C. Poux, A. Sicard, M. Lascoux, V. Castric & X. Vekemans, 2024. Dominance between self-incompatibility alleles determines the mating system of Capsella allopolyploids. <b>Evolution Letters</b>, qrae011, https://doi.org/10.1093/evlett/qrae011<b><i>Reference SRK and SCR sequences from Arabidopsis and Capsella</i></b>Obtaining S-locus genotypes using the NGSgenotyp pipeline (Genete et al. 2020) requires a series of reference <i>SRK </i>and/or <i>SCR </i>sequences. Here we post fasta files with reference sequences for SRK and SCR, separately. These were obtained by assembling data from the literature. For <i>A. halleri</i>, the reference <i>SRK</i> sequences were taken from Table S1 of Genete et al. (2020). For <i>A. lyrata</i> they were taken from Table S14 of Mable et al. (2018) and from Takou et al. (2021). For <i>C. grandiflora </i>we used a set of partial S-domain sequences obtained by Paetsch et al. (2006), Bechsgaard & Paetsch 2020, Guo et al. 2009, Bachmann et al. 2019, Nasrallah et al. 2007 and Neuffer et al. 2023. Reference sequences of <i>SCR</i> from <i>A. halleri </i>and <i>A. lyrata</i> were taken from Guo et al. (2011), Goubet et al. (2012), and Durand et al. (2014).Each file of reference sequences is accompanied by an Excel file with Genbank accession numbers of the data. When the sequences were obtained from de novo assembly made by previous runs of the NGSgenotyp pipeline, we give the SRA accession number of the raw reads individual data used to prduce the corresponding SRK or SCR sequence.<br><b><i>New SRK and SCR sequences from Capsella species obtained with the NGSgenotyp pipeline</i></b>We also post the new or extended sequences of SRK and SCR obtained in Capsella grandiflora or C. bursa-pastoris by applying the NGSgenotyp pipelline on RNAseq or genomic raw Illumina datasets.<br><br>ReferencesBachmann, J.A., Tedder, A., Laenen, B., Fracassetti, M., Désamoré, A., Lafon-Placette, C., et al. (2019) Genetic basis and timing of a major mating system shift in Capsella. New Phytologist, 224, 505–517.Genete, M., Castric, V. & Vekemans, X. (2020) Genotyping and De Novo Discovery of Allelic Variants at the Brassicaceae Self-Incompatibility Locus from Short-Read Sequencing Data. Molecular Biology and Evolution, 37, 1193–1201.Goubet, P.M., Bergès, H., Bellec, A., Prat, E., Helmstetter, N., Mangenot, S., et al. (2012) Contrasted Patterns of Molecular Evolution in Dominant and Recessive Self-Incompatibility Haplotypes in Arabidopsis. PLOS Genetics, 8, e1002495.Guo, Y.L., Bechsgaard, J.S., Slotte, T., Neuffer, B., Lascoux, M., Weigel, D., et al. (2009) Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck. Proceedings of the National Academy of Sciences of the United States of America, 106, 5246–5251.Guo, Y.L., Zhao, X., Lanz, C. & Weigel, D. (2011) Evolution of the S-Locus Region in Arabidopsis Relatives. Plant Physiology, 157, 937–946.Neuffer, B., Bechsgaard, J., Paetsch, M., Titel, C., Wesse, C., Bona, E., et al. (2023) S-alleles and mating system in natural populations of Capsella grandiflora (Brassicaceae) and its congeneric relatives. Flora, 299, 152206.Mable, B.K., Brysting, A.K., Jørgensen, M.H., Carbonell, A.K.Z., Kiefer, C., Ruiz-Duarte, P., et al. (2018) Adding complexity to complexity: Gene family evolution in polyploids. Frontiers in Ecology and Evolution, 6, 114.Nasrallah, J.B., Liu, P., Sherman-Broyles, S., Schmidt, R. & Nasrallah, M.E. (2007) Epigenetic Mechanisms for Breakdown of Self-Incompatibility in Interspecific Hybrids. Genetics, 175, 1965.Paetsch, M., Mayland-Quellhorst, S. & Neuffer, B. (2006) Evolution of the self-incompatibility system in the Brassicaceae: identification of S-locus receptor kinase (SRK) in self-incompatible Capsella grandiflora. Heredity 2006 97:4, 97, 283–290.Takou, M., Hämälä, T., Koch, E.M., Steige, K.A., Dittberner, H., Yant, L., et al. (2021) Maintenance of Adaptive Dynamics and No Detectable Load in a Range-Edge Outcrossing Plant Population. Molecular Biology and Evolution, 38, 1820–1836.