<i>Nicotiana</i> section <i>Repandae</i> flavonoid biosynthetic pathway gene alignments

Consensus sequences of flavonoid biosynthetic pathway (FBP) genes from <i>Nicotiana</i> section <i>Repandae</i> allotetraploids (<i>N. nudicaulis</i>, <i>N. repanda</i>, and <i>N. stocktonii</i>) and their diploid progenitors, <i>N. sylvestris</i> and <i>N. obtusifolia</i> obtained by mapping RNA-seq reads to a concatenated FBP reference including FBP gene sequences from the <i>N. sylvestris</i> and <i>N. obtusifolia</i> genomes. Briefly, we used bwa-mem2 v.2.2.1 to map reads (pooling reads from corolla tissue from buds at 60%, 85%, and 95% of anthesis length) from each individual biological replicate to the FBP reference, sorted and indexed the resulting BAM files with samtools v.1.15.1, split each FBP sequence into separate fasta files with bamtools v.2.5.1, and used darkmatter (https://github.com/acorg/dark-matter), BCFtools v.1.15, and iVar v.1.3.1 to extract a consensus sequence for each FBP homeolog. These sequences were concatenated into a single fasta file for each FBP gene homeolog. The sequence names in each fasta file include an abbreviated species name and the biological replicate number. The abbreviated species names are as follows: Sylv = <i>N. sylvestris</i>, Obtus = <i>N. obtusifolia</i>, Nudi = <i>N. nudicaulis</i>, Repa = <i>N. repanda</i>, Stock = <i>N. stocktonii</i>. Seed stocks for the corolla material were obtained from the USDA <i>Nicotiana</i> Germplasm Bank: <i>N. sylvestris</i> (TW136), <i>N. obtusifolia</i> (TW143), <i>N. nudicaulis</i> (TW90), <i>N. repanda</i> (TW110), and <i>N. stocktonii </i>(TW86).