Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening

Abstract

In plants there are several classes of 21-24-nt short RNAs that regulate gene expression. The most conserved class is the microRNAs (miRNAs), although some miRNAs are found only in specific species. We used high-throughput pyrosequencing to identify conserved and nonconserved miRNAs and other short RNAs in tomato fruit and leaf. Several conserved miRNAs showed tissue-specific expression, which, combined with target gene validation results, suggests that miRNAs may play a role in fleshy fruit development. We also identified four new nonconserved miRNAs. One of the validated targets of a novel miRNA is a member of the CTR family involved in fruit ripening. However, 62 predicted targets showing near perfect complementarity to potential new miRNAs did not validate experimentally. This suggests that target prediction of plant short RNAs could have a high false-positive rate and must therefore be validated experimentally. We also found short RNAs from a Solanaceae-specific foldback transposon, which showed a miRNA/miRNA*-like distribution, suggesting that this element may function as a miRNA gene progenitor. The other Solanaceae-specific class of short RNA was derived from an endogenous pararetrovirus sequence inserted into the tomato chromosomes. This study opens a new avenue in the field of fleshy fruit biology by raising the possibility that fruit development and ripening may be under miRNA regulation.

miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns

“…We have been able to predict 30 novel miRNA, some of them tissue specific. The level of expression of these new miRNAs was lower in comparison with the levels observed for the conserved miRNA which is consistent with previous studies reporting that non-conserved miRNAs were expressed at lower levels and were usually characteristic of a tissue or developmental stage Moxon et al 2008a;Rajagopalan et al 2006;Yao et al 2007). Despite their lower expression, 4 new miRNAs were validated by northern blotting, two of them phellem-specific (miR-3P and miR-13P).…”

MicroRNAs in tomato plants

“…With emergence of deep sequencing, 454 pyrosequencing was first employed by Moxon et al [27] in tomato, and is the only deep sequencing study so far proved to be unsaturated. More effective platforms such as Solexa can be used to explore a greater number of miRNAs, but the lack of a complete genome sequence is a limiting factor for miRNA research in tomato.…”

“…The 454 sequencing platform was used to sequence tomato sRNAs from young leaves and a mixture of young green fruits of the Micro-Tom cultivar [27]. Most known conserved miRNAs were found in their sRNA libraries, and many of them showed differential expression levels between leaves and fruit.…”

“…Moxon Simon et al [27] analyzed the expression levels of 13 additional known miRNAs that were present in their libraries and that had not been examined in their previous study using Northern blot [26]. All tested miRNAs showed differential expression patterns in these tissues except for miR165/166, miR403, and miR472.…”

“…An epigenetic mutation in a tomato SBP-box gene (COLO-RLESS NON-RIPENING; CNR) resulted in colorless non-ripening fruits [62]. Cleavage of CNR by miR156 was also demonstrated by 5′-RACE analysis [27], but in the transgenic plants, the fruit color was slightly lighter red than that of the wild type. This could be because overexpression of miR156 down-regulated, but did not eliminate expression of CNR genes.…”