Seeds of a rye (Secale cereale L.) self-fertile inbred line 7415 with and without Bs were grown under long-day conditions (16 h light, 22°C day/16°C night), and all experimental materials from different tissues were collected during this period. Illumina paired-end RNAseq reads obtained from generative (anther) and vegetative (root and leave) tissues with (4B) and without (0B) B chromosomes.. Rye B chromosomes encode a functional genes

Comparative transcriptome analysis (RNAseq) confirmed that B chromosomes of rye (Secale cereal) contribute to the transcriptome. In total, 1,954 and 1,218 B-derived transcripts with an open reading frame were expressed in generative and vegetative tissues, respectively. Beside B derived transposable element transcripts a high percentage of short transcripts without detectable similarity to known proteins and gene fragments from A chromosomes were found (41.2% and 54.4% in generative and vegetative tissue, respectively) suggesting an ongoing gene erosion process. 15.8% of the transcripts that derived from anthers and 20.3% that derived from vegetative tissues showed similarities with potential protein coding genes from the Bs. Thus, we conclude that rye B chromosomes carry functional genes and B- derived transcripts provide an additional layer of genetic complexity in combination with their related A-located genes.