Genome-wide analysis of small RNAs reveals eight fiber elongation-related and 257 novel microRNAs in elongating cotton fiber cells

Abstract

BackgroundMicroRNAs (miRNAs) and other types of small regulatory RNAs play critical roles in the regulation of gene expression at the post-transcriptional level in plants. Cotton is one of the most economically important crops, but little is known about the roles of miRNAs during cotton fiber elongation.ResultsHere, we combined high-throughput sequencing with computational analysis to identify small RNAs (sRNAs) related to cotton fiber elongation in Gossypium hirsutum L. (G. hirsutum). The sequence analysis confirmed the expression of 79 known miRNA families in elongating fiber cells and identified 257 novel miRNAs, primarily derived from corresponding specific loci in the Gossypium raimondii Ulbr. (G. raimondii) genome. Furthermore, a comparison of the miRNAomes revealed that 46 miRNA families were differentially expressed throughout the elongation period. Importantly, the predicted and experimentally validated targets of eight miRNAs were associated with fiber elongation, with obvious functional relationships with calcium and auxin signal transduction, fatty acid metabolism, anthocyanin synthesis and the xylem tissue differentiation. Moreover, one tasiRNA was also identified, and its target, ARF4, was experimentally validated in vivo.ConclusionThis study not only facilitated the discovery of 257 novel low-abundance miRNAs in elongating cotton fiber cells but also revealed a potential regulatory network of nine sRNAs important for fiber elongation. The identification and characterization of miRNAs in elongating cotton fiber cells might promote the further study of fiber miRNA regulation mechanisms and provide insight into the importance of miRNAs in cotton.

High-throughput sequencing-based genome-wide identification of microRNAs expressed in developing cotton seeds

“…The miRNA data from the 15 DPA small RNA libraries in our previous study were used as a reference to gain insight into the miRNA expression profiles [4]. The relative abundances of known and novel miRNAs in these two libraries were reported as normalized reads (reads per ten million, RPTM).…”

“…Small RNA library from cotton fibers at 15-DPA used in our previous study [4] was used as a reference. The Minimum Folding free Energy Index (MFEI) is one of the most important parameters to distinguish miRNAs from other small RNAs.…”

“…The mature fiber is the world's most important natural textile fiber, whereas the high-quality oil and proteins can further increase the agronomic and economic importance of cotton as a crop plant. Although the growth process of cotton fiber has been intensively studied [2][3][4], as an integral part of the seed, increasing evidence shows that fiber growth is indeed regulated by seed development [5]. Therefore, it is necessary to have an in-depth investigation into the regulatory molecules of cotton seed development.…”

“…In our previous studies, seven fiber initiation-related miRNAs were characterized by comparative miRNAome analysis in developing cotton ovules [3]. Subsequently, from four small RNA libraries constructed from upland cotton fibers ranging from 5-to 20-DPA, eight miRNAs were found to be related to cotton fiber elongation [4]. Recently, 21 novel miRNA candidates were found to be expressed in secondary wall thickening fiber cells [10].…”

Recent Developments in Fiber Genomics of Tetraploid Cotton Species

“…Among 79 and 46 miRNA families identified in G. hirsutum and G. raimondii, respectively, eight miRNAs were specifically related to fiber elongation and associated pathways such as calcium and auxin signal transduction, fatty acid metabolism and anthocyanin biosynthesis, and xylem tissue differentiation. In addition, one tasiRNA was identified and its target, ARF4, was experimentally validated in vivo [104].…”