Tripal File

The assembled sequences from the 2020 Nantaise transcriptome assembly were mapped to the carrot genome assembly DCARv2 using blastn. Resulting hits were converted to gff3 format for use in the CarrotOmics JBrowse. This file can be downloaded from the download link.

A de novo transcriptome assembly containing 63,164 contigs from supplemental table S9 of the publication. This file has been converted from the Excel format used in the publication to standard FASTA format. For further details see the referenced analysis below.

NCBI FTP Download link for NCBI assembly GCA_001625215.1

NCBI FTP Download link for NCBI assembly GCA_003724115.1

NCBI FTP Download link for NCBI assembly GCA_008931105.1

NCBI FTP Download link for NCBI assembly GCA_009905375.1

NCBI FTP Download link for NCBI assembly GCA_014296215.1

NCBI FTP Download link for NCBI assembly GCA_014636745.1

NCBI FTP Download link for NCBI assembly GCA_016801055.1

NCBI FTP Download link for NCBI assembly GCA_902728035.1

Accessions in the Eukaryota that are not full genome projects.

A subset of the Pathogen Receptor Genes Database (PRGdb) containing annotations for the DCAR v2 genome assembly. This file contains correspondences between DCAR gene annotations and PRGdb accession numbers. For further details see the referenced analysis below.

Supplementary Figures S1–S22.

Supplementary Tables S1–S51.

Supplementary Notes (including legends).

Supplementary Figs. 1‐34.

Supplementary Tables 1‐52.

Supplementary Notes 1‐6.

FASTA file with peptide sequence of the gene annotations of the DCARv2 genome assembly (LNRQ01, GCA_001625215.1, ASM162521v1)

Mainlab Chado Loader Excel file derived from supplemental table S1, used to load phenotype data into CarrotOmics. This file is not part of the publication.

Final report for SCRI Project 2016-51181-25400 "Identifying phenotypes, markers, and genes in carrot germplasm to deliver improved carrots to growers
and consumers"

SUPPLEMENTARY MATERIAL – FIGURES S1-S15

List of tables included in this file
Supplementary Table S1. Characteristics of the plant materials and sequencing libraries used for transcriptome (RNA-seq) analysis, and number of reads obtained for each sample
Supplementary Table S2. Normalization factors for pair-wise transcriptome comparison
Supplementary Table S3: Observed phenotypic frequencies of purple pigmentation in the root phloem (A) and xylem (B), and in leaf petioles (C), in F2, and F4 carrot families
Supplementary Table S4. Concentration of individual and combined anthocyanin pigments in purple root phloem and xylem tissues of population 3242 (A) and concentration of individual and combined anthocyanin pigments in roots…