Brassica_ABC_genomes.fasta_all_oligos_selected

Zenodo (CERN European Organization for Nuclear Research)

Abstract

Brassica_ABC_genomes.fasta_all_oligos_selected.bed – BED format file with all 1.4M identified (Chorus2: filtered and selected) 45nt oligonucleotide-based probes. Use with Chorus2 “ChorusPBGUI”. Figure S1 Brassica ABC genomes.fasta: all oligos selected, Chorus2 plot: Localization of all 1.4M identified oligonucleotide sequences along chromosomes based on the B. rapa, B. nigra, and B. oleracea genomes as seen in Chorus2 “ChorusPBGUI”. For each chromosome pair, the top plot shows the whole chromosome in Mb and the bottom plot the zoomed-in regions in Kb. Figure S2 Evaluation ABC-genomes A01-C1 oligos: Localization of oligonucleotide sequences along chromosomes based on the B. rapa, B. nigra, and B. oleracea genomes. Chromosomes were divided into 50 kb windows, and the number of unique oligos recovered was calculated for each window. The distribution of the number of oligos is shown in the line plot. The x-axis is the position of the chromosome in megabase pair. The y-axis is the number of oligos in each 50 kb window. A01-specific oligos are shown in green, C1-specific oligos in pink. Top plots show overlay between A01 and C1 oligos; bottom plots show the specific distribution for each chromosome pair. Figure S3 Evaluation AB-AC-BC-genomes A01-C1 oligos: Localization of oligonucleotide sequences along chromosomes based on the B. juncea (CM031925.1- CM031942.1), B. napus (A01/A10-C01/C09), and B. carinata (CM028687.1- CM028703.1) genomes. Chromosomes were divided into 50 kb windows, and the number of unique oligos recovered was calculated for each window. The distribution of the number of oligos is shown in the line plot. The x-axis is the position of the chromosome in megabase pair. The y-axis is the number of oligos in each 50 kb window. A01-specific oligos are shown in green, C1-specific oligos in pink. Top plots show A01-specific oligos and middle plots the C1-specific oligos; bottom plots show the A01/C1 overlay distribution for each chromosome pair.

Authors 6

1. Mariana Alejandra Baez

   University of Bonn

   Affiliation as printed

   University of Bonn

2. Ludwig Mann Aachen

   RWTH Aachen University

   Affiliation as printed

   RWTH Aachen University

3. Daniela Quezada-Martinez

   Justus-Liebig-Universität Gießen

   Affiliation as printed

   Justus-Liebig-Universität Gießen

4. Vinita Ramtekey

   Indian Council of Agricultural Research

   Affiliation as printed

   ICAR - Indian Institute of Seed Science

5. Tony Heitkam Aachen

   Technische Universität Dresden · RWTH Aachen University

   Affiliation as printed

   RWTH Aachen University

   TU Dresden Fakultät Biologie

6. Annaliese S. Mason

   University of Bonn

   Affiliation as printed

   University of Bonn