Journal: bioRxiv

Article Title: Solanum galapagense -derived purple tomato fruit color is conferred by novel alleles of the Anthocyanin fruit and atroviolacium loci

doi: 10.1101/2021.11.09.467926

Figure Lengend Snippet: Composite interval mapping (CIM) of fruit color measured as hue (violet), chroma (pink), and L* (green, dotted) in the LA1141 x OH8245 BC 2 S 3 inbred backcross population. The y-axis is the logarithm of the odds (LOD). The horizontal lines are the resampled LOD significance cutoff (α=0.05, N=1000 permutations) for hue (violet), chroma (pink) and L* (green, dotted). The x-axis represents the 12 chromosomes in tomato and chromosome distance in cM was calculated using the Kosambi function to correct for multiple crossovers.

Article Snippet: Genomes from 84 unique cultivated and wild tomato accessions published as part of the 100 Tomato Genome Sequencing Consortium (The 100 Tomato Genome Sequencing Consortium, et al., 2014) and a reference quality whole genome sequence for OH8245 generated as part of a collaboration between the Tomato Pan Genome Consortium and NRGene (Ness-Ziona, Israel; see: https://www.nrgene.com/solutions/consortia/tomato/ ) were stored on the Ohio Supercomputer Center (OSC) ( ) computing environment and a nucleotide BLAST database was created using the function “makeblastdb” in the Basic Local Alignment Search Tool (BLAST) version/2020-04 ( ) program.

Techniques:

Journal: bioRxiv

Article Title: Solanum galapagense -derived purple tomato fruit color is conferred by novel alleles of the Anthocyanin fruit and atroviolacium loci

doi: 10.1101/2021.11.09.467926

Figure Lengend Snippet: Box plots represent interactions between the Anthocyanin fruit and atroviolacium loci. The x-axis is marker-locus genotypic class, and the y-axis is degrees of hue. (A) The interaction is shown in the BC 2 S 3 population and ( B) the combined F 2 validation populations. For the Anthocyanin fruit locus: homozygous LA1141 alleles are abbreviated as Aft/Aft , heterozygous alleles as AFT/aft , and homozygous OH8245 AFT / AFT . For the atroviolacium locus: homozygous LA1141 alleles are abbreviated as atv/atv , heterozygous alleles as ATV/atv , and homozygous OH8245 ATV/ATV . Different letters indicate statistically significant differences among groups (Tukey’s Honest Significant Difference (HSD), P<0.05). Marker-locus genotypic class notation follows previous pblications (Cao at al. 2017).

Article Snippet: Genomes from 84 unique cultivated and wild tomato accessions published as part of the 100 Tomato Genome Sequencing Consortium (The 100 Tomato Genome Sequencing Consortium, et al., 2014) and a reference quality whole genome sequence for OH8245 generated as part of a collaboration between the Tomato Pan Genome Consortium and NRGene (Ness-Ziona, Israel; see: https://www.nrgene.com/solutions/consortia/tomato/ ) were stored on the Ohio Supercomputer Center (OSC) ( ) computing environment and a nucleotide BLAST database was created using the function “makeblastdb” in the Basic Local Alignment Search Tool (BLAST) version/2020-04 ( ) program.

Techniques: Marker, Biomarker Discovery

Journal: bioRxiv

Article Title: Solanum galapagense -derived purple tomato fruit color is conferred by novel alleles of the Anthocyanin fruit and atroviolacium loci

doi: 10.1101/2021.11.09.467926

Figure Lengend Snippet: Sequence polymorphism of selected genomic regions of the atv locus. A novel 18 bp insertion/deletion (INDEL) found in the first intron in LA1141 is highlighted (arrow). The causal 4 bp INDEL ( slmybatv ) previously characterized in the tomato cultivar Indigo Rose (Cao et al., 2017) is also highlighted (arrow). Two G to A SNPs in the coding region of the 2 nd exon ( boxed ) are labeled ( bold ) in a region identified by CRISPR/CAS9 as important for the function of the conserved R3 domain . Sequences were aligned using MUSCLE using default settings. Conserved nucleotides are starred. The Heinz reference sequence (Heinz1706), OH8245, LA1141 and Indigo Rose genomic atv sequences are represented.

Article Snippet: Genomes from 84 unique cultivated and wild tomato accessions published as part of the 100 Tomato Genome Sequencing Consortium (The 100 Tomato Genome Sequencing Consortium, et al., 2014) and a reference quality whole genome sequence for OH8245 generated as part of a collaboration between the Tomato Pan Genome Consortium and NRGene (Ness-Ziona, Israel; see: https://www.nrgene.com/solutions/consortia/tomato/ ) were stored on the Ohio Supercomputer Center (OSC) ( ) computing environment and a nucleotide BLAST database was created using the function “makeblastdb” in the Basic Local Alignment Search Tool (BLAST) version/2020-04 ( ) program.

Techniques: Sequencing, Labeling, CRISPR

Journal: bioRxiv

Article Title: Solanum galapagense -derived purple tomato fruit color is conferred by novel alleles of the Anthocyanin fruit and atroviolacium loci

doi: 10.1101/2021.11.09.467926

Figure Lengend Snippet: Midpoint rooted phylogenetic tree for MYB transcription factors underlying the Aft locus. The tree represents clustering of genomic sequences underlying Aft 84 unique tomato accessions from the 100 Tomato genome sequencing consortium, LA1996 (purple), OH8245 and LA1141 (purple) are clustered. A maximum likelihood midpoint rooted tree was constructed in the phangorn R package using the G.T.R model. Data resampling using 1000 rapid bootstrap replications was performed using the boostrap.pml function and bootstrap values are given for each branch. There are 47 identical S. lycopersicum sequences are condensed under the name “Cultivated tomato Aft (47 accessions) ( red triangle ).

Article Snippet: Genomes from 84 unique cultivated and wild tomato accessions published as part of the 100 Tomato Genome Sequencing Consortium (The 100 Tomato Genome Sequencing Consortium, et al., 2014) and a reference quality whole genome sequence for OH8245 generated as part of a collaboration between the Tomato Pan Genome Consortium and NRGene (Ness-Ziona, Israel; see: https://www.nrgene.com/solutions/consortia/tomato/ ) were stored on the Ohio Supercomputer Center (OSC) ( ) computing environment and a nucleotide BLAST database was created using the function “makeblastdb” in the Basic Local Alignment Search Tool (BLAST) version/2020-04 ( ) program.

Techniques: Genomic Sequencing, Sequencing, Construct

Journal: bioRxiv

Article Title: Solanum galapagense -derived purple tomato fruit color is conferred by novel alleles of the Anthocyanin fruit and atroviolacium loci

doi: 10.1101/2021.11.09.467926

Figure Lengend Snippet: Outgroup rooted phylogenetic tree for MYB transcription factors underlying Ant1 and An2-like coding sequence (CDS) at the Aft locus. Arabidopsis thaliana, Salvia miltiorrhiza, S. tuberosome Phureja, C. annum, S. lycopersicum ty Indigo Rose [MN433087 ], S. chilense accession LA1996 [ MN242011.1 , EF433417.1 (Sapir et 008; )], S. chilense (Dunal) Reiche (formerly Lycopersicon chilense Dunal) accession LA1930 42012.1 ], 84 tomato accessions published as part of The 100 Tomato Genome Sequencing ortium (The 100 Tomato Genome Sequencing Consortium, et al., 2014), S. lycopersicum variety OH8245, and S. agense accession LA1141 are clustered. Identical S. lycopersicum sequences are condensed ( red triangles ). A mum likelihood tree was constructed in the phangorn R package using the G.T.R model. Data mpling using 1000 rapid bootstrap replications was performed using the boostrap.pml function and bootstrap s are given for each branch. Trees were rooted at Arabidopsis thaliana MYB-encoding genes as the outgroup.

Article Snippet: Genomes from 84 unique cultivated and wild tomato accessions published as part of the 100 Tomato Genome Sequencing Consortium (The 100 Tomato Genome Sequencing Consortium, et al., 2014) and a reference quality whole genome sequence for OH8245 generated as part of a collaboration between the Tomato Pan Genome Consortium and NRGene (Ness-Ziona, Israel; see: https://www.nrgene.com/solutions/consortia/tomato/ ) were stored on the Ohio Supercomputer Center (OSC) ( ) computing environment and a nucleotide BLAST database was created using the function “makeblastdb” in the Basic Local Alignment Search Tool (BLAST) version/2020-04 ( ) program.

Techniques: Sequencing, Construct