Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development

Abstract

Background Whilst information regarding small RNAs within agricultural crops is increasing, the miRNA composition of the nutritionally valuable pulse narrow-leafed lupin ( Lupinus angustifolius ) remains unknown. Results By conducting a genome- and transcriptome-wide survey we identified 7 Dicer-like and 16 Argonaute narrow-leafed lupin genes, which were highly homologous to their legume counterparts. We identified 43 conserved miRNAs belonging to 16 families, and 13 novel narrow-leafed lupin-specific miRNAs using high-throughput sequencing of small RNAs from foliar and root and five seed development stages. We observed up-regulation of members of the miRNA families miR167, miR399, miR156, miR319 and miR164 in narrow-leafed lupin seeds, and confirmed expression of miR156, miR166, miR164, miR1507 and miR396 using quantitative RT-PCR during five narrow-leafed lupin seed development stages. We identified potential targets for the conserved and novel miRNAs and were able to validate targets of miR399 and miR159 using 5′ RLM-RACE. The conserved miRNAs are predicted to predominately target transcription factors and 93% of the conserved miRNAs originate from intergenic regions. In contrast, only 43% of the novel miRNAs originate from intergenic regions and their predicted targets were more functionally diverse. Conclusion This study provides important insights into the miRNA gene regulatory networks during narrow-leafed lupin seed development. Electronic supplementary material The online version of this article (10.1186/s12864-019-5521-8) contains supplementary material, which is available to authorized users.

Integrated microRNA and transcriptome profiling reveal key miRNA-mRNA interaction pairs associated with seed development in Tartary buckwheat (Fagopyrum tataricum)

“…In plants, the biosynthesis of miRNAs is a multistep pathway that is involved in many genes and enzymes [ 5 ]. Plant miRNA genes are initially transcribed into primary miRNAs (pri-miRNAs) by RNA polymerase II in the nucleus [ 5 , 6 ]. Then, the pri-miRNAs are processed into miRNA precursors (pre-miRNAs) with stem-loop structures by the DICER-LIKE1 (DCL1), HYPONASTIC LEAVES1 (HYL1) and SERRATE (SE) protein complex [ 5 – 7 ].…”

Integrated Analysis of Small RNA, Transcriptome and Degradome Sequencing Provides New Insights into Floral Development and Abscission in Yellow Lupine (Lupinus luteus L.)

“…Only three studies on miRNAs have been conducted so far using only two species of Lupinus genus: Lupinus albus (white lupine) and Lupinus angustifolius (narrow-leafed lupine). These studies were focused on small RNA sequences isolated from phloem exudate [43], global expression of miRNAs during phosphate deficiency [44], and gene regulatory networks during seed development [45]. Unfortunately, the knowledge on the roles of mi- and siRNAs function during flower development in leguminous plants is still incomplete [43].…”

MicroRNAs expression dynamics reveal post-transcriptional mechanisms regulating seed development in Phaseolus vulgaris L.

“…With the release miRBase 22.1, these miRNAs were rechecked and a final list of 72 known and 39 new miRNAs were obtained (Tables 1 and 2 and Supplementary Tables 4 and 5). Among predicted miRNAs, only miRNAs that presented the following secondary structure prediction criteria as: (1) number of basepair (bp) in stem region (≥22), (2) free energy (dG in kcal/mol ≤ −17), (3) length of hairpin (up and down stem + terminal loop ≥56), (4) length of terminal loop (≤82), (5) number of allowed biased bulges in mature region (≤2), (6) number of basepair (bp) in mature or mature* region (≥14), (7) percentage of small RNA in stem region (pm) (≥80), and (8) minimal folding energy index (MFEI ≥ 0.80) were considered as new miRNAs (Supplementary Table 3). Additionally, MFE and secondary structure of the extended sequences ( Supplementary Fig.…”

“…Post-transcriptional regulation mediated by microRNAs (miRNAs) controls numerous developmental processes in plants, including SD in legumes 6 , 7 . MiRNAs are small noncoding RNAs (sRNAs, ~21–22 nt) that act as negative post-transcriptional regulators of gene expression, either by transcript cleavage or translation repression 8 .…”