Plant genomic archaeology: whole‐genome sequencing reveals the pedigree of a classical trisomic line

Patrice A. Salomé 1,2 and Detlef Weigel

Department of Molecular , Max Planck Institute for Developmental Biology, Spemannstraße 37‐39, D‐ Downloaded from https://academic.oup.com/g3journal/article/5/2/253/6025315 by guest on 27 September 2021 72076 Tübingen, D‐72076 Tübingen,

1 Corresponding author. Email: [email protected]

2 Current address: UCLA, Department of and Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095, USA

DOI: 10.1534/g3.114.015156

chr 1 chr 2

chr 3 Downloaded from https://academic.oup.com/g3journal/article/5/2/253/6025315 by guest on 27 September 2021

gi-1 CS3227

chr 4gi-2 chr 5

Figure S1 SNP frequency in gi‐1, gi‐2 and CS3227. Scaled Venn diagrams for SNP number in the genotypes gi‐1, gi‐2 and CS3227 for each of the five Arabidopsis chromosomes. Note that diagram areas between chromosomes should not be compared, as scaling was not applied between chromosomes. Number of SNPs for each genotype is given in Table 3.

2 SI P. A. Salomé and D. Weigel

chr1 chr2 chr3 7 6 4 10 GI 10 10 5 5 10 3 10 104 10 3 2 3 10 10 10 102 10 10 10 1

1 inter-SNP distance inter-SNP distance inter-SNP distance 0 5 10 15 20 25 30 0 5 10 15 20 0 5 10 15 20 25 position (Mbp) position (Mbp) position (Mbp) chr4 chr5 106 107 5 10 5 104 10 3 10 3 2 10

10 Downloaded from https://academic.oup.com/g3journal/article/5/2/253/6025315 by guest on 27 September 2021 10 10

inter-SNP distance 1 inter-SNP distance 0 5 10 15 20 0 5 10 15 20 25 30 position (Mbp) position (Mbp)

Figure S2 SNP distribution in CS3227 is not random. Inter‐SNP distance between consecutives SNPs is plotted as a function of the mid‐position between consecutive SNPs. Clear haplotype blocks appear along all CS3227 chromosomes, with the exception of chromosome 5, which also exhibits the lowest SNP count for this genotype.

P. A. Salomé and D. Weigel 3 SI

A

CS3227 An-1 CS3227 Er-0 CS3227 Est Salk CS3227 Gr-1

CS3227 La-0 CS3227 Ler-0 CS3227 Li-2:1 Downloaded from https://academic.oup.com/g3journal/article/5/2/253/6025315 by guest on 27 September 2021 B

CS3227Est Salk CS3227 Est MPI Est MPI Est Salk

Figure S3 SNP sharing between chosen accessions and CS3227. Note SNP numbers are not corrected for the un‐ sequenced portion of the compared genomes. All SNP data downloaded from 1001genomes.org on August 2013. A. SNP sharing between CS3227 and accessions An‐1, Er‐0, Est, Gr‐1, La‐0, Ler‐0 and Li‐2:1 used by George Redeí, for the interval 10‐20 Mbp of chromosome 1. B. SNP sharing between CS3227 and Est accessions (from Salk, CS 67485, or MPI, CS22683), for, after re‐ sequencing as PCR‐free DNA Truseq libraries. Note that SNP numbers are not corrected for the un‐ mapped portion of the compared genomes.

4 SI P. A. Salomé and D. Weigel

Tables S1‐S5 Available for download at http://www.g3journal.org/lookup/suppl/doi:10.1534/g3.114.015156/‐/DC1

Table S1. SNP data for CS3227. Table S2. SNP data for EstMPI. Table S3.SNP data for EstSalk. Table S4. SNP data for gi‐1. Table S5. SNP data for gi‐2.

Tables S1‐S5 are provided in Shore output format: Genotype Chromosome: chromosome identifier Position: position of a base in the reference sequence

Reference: nucleotide found in Col‐0 Downloaded from https://academic.oup.com/g3journal/article/5/2/253/6025315 by guest on 27 September 2021 Non‐reference: nucleotide (or deletion) in the sequenced genome Quality: Highest base quality supporting the base change, between 0‐40. Cut‐off was chosen >25. Support: Number of reads supporting the base change Concordance: concordance of all short reads overlapping the position Copy: copy number of the target sequence

P. A. Salomé and D. Weigel 5 SI