Characterization of the small RNA component of leaves and fruits from four different cucurbit species

Guru Jagadeeswaran,Ramanjulu Sunkar,Umesh K Reddy,Yun Zheng,Padma Nimmakayala,Kanchana Gowdu

doi:10.1186/1471-2164-13-329

Guru Jagadeeswaran, Ramanjulu Sunkar + Show 4 more

Open Access

https://doi.org/10.1186/1471-2164-13-329

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Abstract

BackgroundMicroRNAs (miRNAs) are a class of non-coding small RNAs involved in post-transcriptional regulation of gene expression critical for plant growth and development, stress responses and other diverse biological processes in plants. The Cucurbitaceae or cucurbit family represents some of economically important species, particularly those with edible and medicinal fruits. Genomic tools for the molecular analysis of members of this family are just emerging. Partial draft genome sequence became available recently for cucumber and watermelon facilitating investigation of the small RNA component of the transcriptomes in cucurbits.ResultsWe generated four small RNA libraries from bottle gourd (Lagenaria siceraria), Cucurbita moschata, Cucurbita pepo, and, watermelon (Citrullus lanatus var. lanatus) in order to identify conserved and novel lineage specific miRNAs in these cucurbits. Deep sequencing of small RNA libraries from these species resulted in 1,597,263, 532,948, 601,388, and 493,384 unique sRNA reads from bottle gourd, moschata, pepo and watermelon, respectively. Sequence analysis of these four libraries resulted in identification of 21 miRNA families that are highly conserved and 8 miRNA families that are moderately conserved in diverse dicots. We also identified 4 putative novel miRNAs in these plant species. Furthermore, the tasiRNAs were identified and their biogenesis was determined in these cucurbits. Small RNA blot analysis or q-PCR analyses of leaf and fruit tissues of these cucurbits showed differential expression of several conserved miRNAs. Interestingly, the abundance of several miRNAs in leaves and fruits of closely related C. moschata and C. pepo was also distinctly different. Target genes for the most conserved miRNAs are also predicted.ConclusionHigh-throughput sequencing of small RNA libraries from four cucurbit species has provided a glimpse of small RNA component in their transcriptomes. The analysis also showed considerable variation within four cucurbit species with regards to expression of individual miRNAs.

Highlights

MicroRNAs are a class of non-coding small RNAs involved in post-transcriptional regulation of gene expression critical for plant growth and development, stress responses and other diverse biological processes in plants
The duplex is exported to the cytosol, where it can be loaded into RNA-Induced Silencing Complex (RISC)
Besides conserved miRNAs, a large number of miRNA families have been identified in diverse plant species, some of which are conserved in closely related species or speciesspecific, which are referred to as ‘young miRNAs’ [12]

Summary

Introduction

MicroRNAs (miRNAs) are a class of non-coding small RNAs involved in post-transcriptional regulation of gene expression critical for plant growth and development, stress responses and other diverse biological processes in plants. Because of the sequence conservation, identification of conserved miRNAs is not a difficult task provided sufficient genomic/EST resources are available for a plant species in question [13,14]. A minor portion of these young miRNAs appears to be functional, whereas the majority of them appear to be non-functional and eventually dissipate, and only few of them will be integrating into gene regulatory networks [12,15]. Functionally such nonconserved miRNAs seem less significant, their identification is important to trace the birth and death of miRNAs in a specific plant lineage [12]

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