Tripal File

Supplemental files and figures from the publication "Carotenoid Presence Is Associated with the Or Gene in Domesticated Carrot"

T. Kotlinska, left, and M. Kotlinska, right, visit with a Polish gardener who is helping to maintain local vegetable land races, including carrots.

Authors' original file for this image.

Carrot seed production in Poland.

Authors' original file for this image.

Typical site for finding wild carrot varieties in Turkey.

Authors' original file for this image.

A. Kucuk (right) in a Turkish carrot field with agriculture specialist A. Apa (left).

Authors' original file for this image.

T. Kotlinska and S. Samaras collecting wild carrot varieties in Greece.

Authors' original file for this image.

Web site containing the whole-genome sequences of 'DC-27' carrot, published in 2014.

This web site appears to no longer be available.

Sequences used to assess coverage of the carrot DH1 v3.0 genome assembly. This file contains 18,137 sequences. Carrot EST sequences were obtained from NCBI with the query:
esearch -db nuccore -query '(EST AND "Daucus carota"[porgn:__txid4039])' | efetch -format fasta

This FASTA file contains the sequence of the DCAR version 1 de-novo genome assembly. This represents a preliminary assembly and was not published, however it is presented here simply for historical reasons. When published, the genome assembly was improved and integrated with linkage maps and designated version 2.

This file contains the carrot genome assembly sequences with the authors' original naming scheme, and is the version used for the JBrowse instance available here. See the referenced analysis below for more details.

This file contains the carrot genome assembly sequences with the authors' original naming scheme, and is the version used for the JBrowse instance available here. See the referenced analysis below for more details.

Genome assembly LNRQ01 FASTA file. For details see the linked analysis below.

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

Correspondences between LNRQ01 and DCARv2 sequence names, sequence lengths, and numbers of proteins.

Supplemental table S1 contains geolocation data and phenotypic scores

Supplemental Table S2. Pearson’s correlation coefficients for canopy height and harsh flavor in collection of 433
carrot accessions and in core sets. None of the correlations are significantly different from zero as determined by
a t-test for differences in means.

Supplemental Fig. S1: Average silhouette width of genotypic clusters. Silhouette width was calculated for K=2-10
clusters of accessions based on their genetic distances. The vertical dotted line indicates the most appropriate
number of clusters.

Supplemental Fig. S2. Distribution of phenotypes for collection of 433 carrot accessions. Four hundred thirty-
three accessions were grown over two years in Hancock, Wisconsin in a randomized…

DcSto insertions with designed primers. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

A published collection of 55,386 SSR primer pairs. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

2019 Stowaway miniature inverted repeat transposable elements. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

Mobile Element Annotation performed by BGI. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

Tandem repeats were detected by BGI using Tandem Repeats Finder. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

CarrotOmics unpublished SSR detection in the DCARv2 Genome Assembly using MISA. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

Filled gaps in the genome assembly. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

Gaps in the genome assembly. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

DCARv2 Gene annotation V1.0 locations on the DCARv3 assembly. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

Collection of 1,393,425 SNP variants from the genome publication. This is the VCF file used for JBrowse. See the linked analysis below for further details.

L8708 × Z020 Linkage Map Variants. This is the VCF file used for JBrowse. See the linked analysis below for further details.

Gene annotations by the NCBI Eukaryotic Genome Annotation Pipeline. This is the GFF3 file used for JBrowse. See the linked Genome Annotation analysis below for further details.

A RepeatExplorer analysis performed on Illumina reads of the carrot doubled haploid line used for genome assembly. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

Population 70796, plants with dark orange (yyy2y2) and pale orange (YYy2y2) genotypes. Normalized counts of the mapped RNA sequences were used to calculate the relative abundances of transcripts expressed as Fragments Per Kilobase of exon per Million fragments mapped (FPKM).

Population 97837, plants with yellow (yyY2Y2) and white (YYY2Y2) genotypes. Normalized counts of the mapped RNA sequences were used to calculate the relative abundances of transcripts expressed as Fragments Per Kilobase of exon per Million fragments mapped (FPKM).

Gene prediction V1.0 for the DCARv2 genome assembly. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

Gene annotation from the DCARv3 genome gene prediction version 3.0. See the referenced analysis for more details.

78,850 SNP variants from the F4 population 74,146. This is the VCF file used for JBrowse. See the linked analysis below for further details.

Note that this set of 78,850 SNPs was submitted to dbSNP at NCBI under BioProject PRJNA348698, however dbSNP dropped support for non-human genomes after publication, and the variants were not archived, and are not available there.

Gaps in the DCARv3 genome assembly. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

PlantTFcat was used to predict the transcription factors and regulatory genes. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

De novo identification of carrot repetitive DNA. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

PRGdb 3.0 was used to predict disease resistant genes. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

SSRs were detected in the Daucus carota V.3 assembly using misa, and when possible primers were designed with primer3. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

Tandem repeats detection using Tandem Repeats Finder. This is the GFF3 file used for JBrowse. See the linked analysis below for further details.

Genome assembly LNRQ01 GenBank flatfile. For details see the linked analysis below.