Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type

Qiang Xu,Andan Zhu,Xiaomeng Wu,Xiuxin Deng,Wenwu Guo,Junli Ye,Keqin Yu,Yuanlong Liu

doi:10.1186/1471-2164-11-246

Abstract

BackgroundRed-flesh fruit is absent from common sweet orange varieties, but is more preferred by consumers due to its visual attraction and nutritional properties. Our previous researches on a spontaneous red-flesh mutant revealed that the trait is caused by lycopene accumulation and is regulated by both transcriptional and post-transcriptional mechanisms. However, the knowledge on post-transcriptional regulation of lycopene accumulation in fruits is rather limited so far.ResultsWe used Illumina sequencing method to identify and quantitatively profile small RNAs on the red-flesh sweet orange mutant and its wild type. We identified 85 known miRNAs belonging to 48 families from sweet orange. Comparative profiling revealed that 51 known miRNAs exhibited significant expression differences between mutant (MT) and wild type (WT). We also identified 12 novel miRNAs by the presence of mature miRNAs and corresponding miRNA*s in the sRNA libraries. Comparative analysis showed that 9 novel miRNAs are differentially expressed between WT and MT. Target predictions of the 60 differential miRNAs resulted 418 target genes in sweet orange. GO and KEGG annotation revealed that high ranked miRNA-target genes are those implicated in transcription regulation, protein modification and photosynthesis. The expression profiles of target genes involved in carotenogenesis and photosynthesis were further confirmed to be complementary to the profiles of corresponding miRNAs in WT and MT.ConclusionThis study comparatively characterized the miRNAomes between the red-flesh mutant and the wild type, the results lay a foundation for unraveling the miRNA-mediated molecular processes that regulate lycopene accumulation in the sweet orange red-flesh mutant.

Highlights

Red-flesh fruit is absent from common sweet orange varieties, but is more preferred by consumers due to its visual attraction and nutritional properties
Sequencing and annotation of sweet orange small RNAs Our previous studies showed that the stage of 170 days after flowering (DAF) is the critical stage for the phenotype of color break and global gene expression changes during fruit development in the mutant (Figure 1) [11,13]
Further analysis using the small RNA (sRNA) sequences searching against Rfam database revealed that 1.7%, and 1.5% of the sequences for wild type (WT) and MT, respectively, matched noncoding RNAs including Ribosomal RNA (rRNA), transfer RNA (tRNA), Small nuclear RNA (snRNA) and Small nucleolar RNA (snoRNA) (Additional file 3 and 4)

Summary

Introduction

Red-flesh fruit is absent from common sweet orange varieties, but is more preferred by consumers due to its visual attraction and nutritional properties. We found that lycopene in the 'Hong Anliu' mutant was 1000-fold higher than that in its wild type fruits, and in juice sacs the lycopene accumulation was coincided with increased expression of upstream carotenogenic genes and reduced expression of downstream genes [11]. The proteomic data, when considered in combination with transcriptional data, suggest that post-transcriptional regulations are involved in shaping the redflesh trait of the orange mutant [14]. It remains largely unknown what kind of post-transcriptional mechanism was involved in the red-flesh mutant. Very little is known about miRNAs or miRNA-mediated molecular processes that regulate lycopene accumulation in plant fruits

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Results

Discussion

Conclusion