Identification of microRNAs and transcript targets in Camelina sativa by deep sequencing and computational methods.

Saroj Poudel,Niranjan Aryal,Chaofu Lu,Tai Wang

doi:10.1371/journal.pone.0121542

Abstract

Camelina sativa is an annual oilseed crop that is under intensive development for renewable resources of biofuels and industrial oils. MicroRNAs, or miRNAs, are endogenously encoded small RNAs that play key roles in diverse plant biological processes. Here, we conducted deep sequencing on small RNA libraries prepared from camelina leaves, flower buds and two stages of developing seeds corresponding to initial and peak storage products accumulation. Computational analyses identified 207 known miRNAs belonging to 63 families, as well as 5 novel miRNAs. These miRNAs, especially members of the miRNA families, varied greatly in different tissues and developmental stages. The predicted miRNA target genes are involved in a broad range of physiological functions including lipid metabolism. This report is the first step toward elucidating roles of miRNAs in C. sativa and will provide additional tools to improve this oilseed crop for biofuels and biomaterials.

Highlights

Camelina [Camelina sativa (L.) Crantz], known as false flax or gold of pleasure, is a temperate climate oilseed crop belonging to the mustard family, Brassicaceae [1]
To identify the known and potential novel miRNAs in C. sativa, small RNA libraries prepared from young leaves, flower buds and developing seeds at 13 and 19 days after flowering (DAF) were sequenced by Illumina technology, resulting in a total of 39,459,118 reads (Table 1)
This is lower than expected miRNAs present in camelina given its close relation to Arabidopsis and the strong conservation of miRNAs in plants [35], partly because we have only investigated young leaves, flower buds and two stages of developing seeds of camelina plants grown under normal conditions

Summary

Introduction

Camelina [Camelina sativa (L.) Crantz], known as false flax or gold of pleasure, is a temperate climate oilseed crop belonging to the mustard family, Brassicaceae [1]. Today camelina is generating renewed interest as a second generation oilseed crop for biofuels and there is some limited interest in it for an omega-3 fatty acid source as well due to its high content of α-linolenic acid [2,3]. Camelina can be found growing in a wide range of climatic and soil conditions including low fertility or saline soils, and is relatively tolerant of cold weather and drought [1,4]. The oil content of camelina seeds can vary considerably between genotypes from 30–45% leading to a wide range of potential oil yields reported [5,6]. Camelina is considered to be a low input crop compared to other oilseeds for water usage, fertilizer and pesticide requirements [1,4]. The short life cycle of camelina at 85–100 days allows it to fit into rotation with crops like winter wheat without disrupting existing planting times

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Conclusion