The Cassandra retrotransposon landscape in sugar beet (Beta vulgaris): Recombination and re-shuffling leads to a high structural variability

Here we provide supplementary data for our study of non-autonomous Cassandra terminal-repeat retrotransposons in miniature (TRIMs) in sugar beet and related genomes.

Cassandra sequences are distributed across the plant kingdom and share a unique feature: conserved 5S rDNA promoter motifs within their long terminal repeats (LTRs). This dataset contains two multiple sequence alignments and a sequence list of tandemly-arranged (TA) Cassandra sequences in FASTA format. Alignments cover LTR and internal regions of all Amaranthaceae Cassandra (Ama-Cassandra) from our study. This includes Cassandra full-length sequences from B. vulgaris (Ama_Cassandra_Beet_full-length) and C. quinoa (Ama_Cassandra_Quinoa_full-length). Sequence names include information on host plant, subfamily classification, localisation (scaffold), start and stop position, a Lab-unique TE identifier and sequence orientation. For the tandemly-arranged Cassandra sequences from sugar beet, we provide a sequence list of twelve sequences (Ama_Cassandra_TA_Beet_list). Here, sequence names refer to TA copy number, host, localisation (scaffold), start and stop position, a Lab-unique TE identifier and sequence orientation.

All sequences were identified in the recent genome assemblys of B. vulgaris (RefBeet1.2; Dohm et al. 2014) and C. quinoa (ASM168347v1; Jarvis et al., 2017).