Additional file 1 of Long-read sequencing of extrachromosomal circular DNA and genome assembly of a Solanum lycopersicum breeding line revealed active LTR retrotransposons originating from S. Peruvianum L. introgressions

Supplementary Material

Divergence among members of <i>PAL</i>, <i>P5CS</i>, <i>OOMT</i> orthologous genes of <i>Fragaria</i> and their similarity to <i>Rosa wichurana</i> gene fragments used in this study.

<p>Genes that were selected for the comparative analysis are highlighted.</p>z<p>: Not significant: according to BLAST search.</p

Integration of the gene position on the genetic map (RwLG) (partially) obtained by regression mapping in Joinmap 4.0 showing the consensus linkage groups with indication of the map position of <i>P5CS</i> (green), <i>OOMT</i> (red), <i>PAL</i> (blue) and the physical chromosomes of <i>Rosa wichurana</i> (RwChr) and the pseudochromosomes of <i>Fragaria vesca</i> (FvChr).

<p>Framework of the genetic linkage map follows Moghaddam et al. (2012).</p

HRM melting profiles for <i>P5CS</i>.

<p>The melting curve for <i>Rosa wichurana</i> is part of the green cluster; <i>Rosa</i> ‘Yesterday’ is part of the red cluster. Both clusters also contain curves of the siblings. Blue and pink clusters contain only the melting curves of siblings.</p

Overview of HRM primers for PAL (Phenylalanine Ammonia Lyase), OOMT (Orcinol O-Methyl Transferase) and P5CS (Pyrroline-5-Carboxylate Synthase).

<p>Amplicon length, amount of introns present in the amplicon and the number of SNPs in the amplicon are indicated.</p>z<p>no sequence information is available for <i>Rosa wichurana</i>.</p

Overview of the primers used to isolate the genes PAL (Phenylalanine Ammonia Lyase), OOMT (Orcinol O-Methyl Transferase) and P5CS (Pyrroline-5-Carboxylate Synthase).

<p>The length of the obtained amplicons is indicated as well as the Tm and source sequence.</p

Additional file 3: of Evolution of blue-flowered species of genus Linum based on high-throughput sequencing of ribosomal RNA genes

Consensus sequences of 5S rRNA genes of the studied flax samples. For flax specimens possessing different classes of 5S rRNA genes sequences, the numbers of corresponding classes (cl) are shown below the name abbreviations. (TXT 31 kb

Additional file 2: of Evolution of blue-flowered species of genus Linum based on high-throughput sequencing of ribosomal RNA genes

Consensus ITS1-5.8S rDNA-ITS2 sequences of the studied flax samples. (TXT 27 kb