Integrative analysis of genome‐wide lnc RNA and mRNA expression in newly synthesized Brassica hexaploids

Abstract Polyploidization, as a significant evolution force, has been considered to facilitate plant diversity. The expression levels of lnc RNA s and how they control the expression of protein‐coding genes in allopolyploids remain largely unknown. In this study, lnc RNA expression profiles were compared between Brassica hexaploid and its parents using a high‐throughput sequencing approach. A total of 2,725, 1,672, and 2,810 lnc RNA s were discovered in Brassica rapa , Brassica carinata , and Brassica hexaploid, respectively. It was also discovered that 725 lnc RNA s were differentially expressed between Brassica hexaploid and its parents, and 379 lnc RNA s were nonadditively expressed in this hexaploid. Lnc RNA s have multiple expression patterns between Brassica hexaploid and its parents and show paternal parent‐biased expression. These lnc RNA s were found to implement regulatory functions directly in the long‐chain form, and acted as precursors or targets of mi RNA s. According to the prediction of the targets of differentially expressed lnc RNA s, 109 lnc RNA s were annotated, and their target genes were involved in the metabolic process, pigmentation, reproduction, exposure to stimulus, biological regulation, and so on. Compared with the paternal parent, differentially expressed lnc RNA s between Brassica hexaploid and its maternal parent participated in more regulation pathways. Additionally, 61 lnc RNA s were identified as putative targets of known mi RNA s, and 15 other lnc RNA s worked as precursors of mi RNA s. Some conservative motifs of lnc RNA s from different groups were detected, which indicated that these motifs could be responsible for their regulatory roles. Our findings may provide a reference for the further study of the function and action mechanisms of lnc RNA s during plant evolution.