The lncRNA Landscape of Diploid vs. Allotetraploid Cotton Genomes

Eukaryote genomes are composed of protein-coding regions, replicated regions and non-coding regions. The non-coding regions can also be transcribed and processed into small RNAs (19-30nt) and long transcripts. Those long transcripts are known as long non-coding RNAs (lncRNAs). Noncoding regions have been demonstrated to play regulatory roles in coding gene expression in both animal and plant kingdoms. Compared to coding sequences, the non-coding regions evolve quickly. It is well known that polyploidization is a key driving force behind plant genome evolution, but the relationship between lncRNA and polyploidization remains largely unknown. Using strand-specific total RNA sequencing, we examined lncRNA of diploid and tetraploid cotton (Gossypium) species, including accession Texas Marker-1 (TM-1), a genetic standard of the allotetraploid cultivated upland cotton species (G. hirsutum, 2n = 4x = 52, 2(AD)₁), and two extant species closely related to G. hirsutum A- and D-subgenome progenitors, namely G. arboreum (A₂A₂) acc. Shixiya and G. raimondii (D₅D₅). We examined the landscape and dynamic of lncRNA behavior relative to hybridization and polyploidization. The expression level of lncRNA in cotton genome is lower than that of mRNA. Both the length and exon number are less than that of mRNA. Most of the lncRNAs overlap with transposon elements (TE), which indicates a correlation between lncRNA and TE in genome polyploidization. Our study provides the insights of lncRNA roles in genome duplication and evolution.