Transcriptomic repertoires depict the initiation of lint and fuzz fibres in cotton (<italic>Gossypium hirsutum</italic> L.).

Summary: Cotton fibre is an important natural fibre for the textile industry. The number of fibre initials determines the lint percentage, which is an important factor for cotton fibre yield. Although fibre development has been described by transcriptomic analysis, the mechanism by which the long noncoding RNA manipulates the initiation of lint and fuzz fibres remains unknown. In this study, three lines with different lint percentages were developed by crossing Xu142 with its fibreless mutant Xu142 <italic>fl</italic>. We collected the epidermal cells from the ovules with attached fibres at 0 and 5 days post anthesis (DPA) from Xu142, the fibreless mutant Xu142 <italic>fl</italic> and the three lint percent diversified lines for deep transcriptome sequencing. A total of 2641 novel genes, 35 802 long noncoding RNAs (lncRNAs) and 2262 circular RNAs (circRNAs) were identified, of which 645 lncRNAs were preferentially expressed in the fibreless mutant Xu142 <italic>fl</italic> and 651 lncRNAs were preferentially expressed in the fibre‐attached lines. We demonstrated the functional roles of the three lncRNAs in fibre development via a virus‐induced gene silencing (VIGS) system. Our results showed that silencing XLOC_545639 and XLOC_039050 in Xu142 <italic>fl</italic> increased the number of fibre initials on the ovules, but silencing XLOC_079089 in Xu142 resulted in a short fibre phenotype. This study established the transcriptomic repertoires in cotton fibre initiation and provided evidence for the potential functions of lncRNAs in fibre development. [ABSTRACT FROM AUTHOR]