Investigation of the microRNAs in safflower seed, leaf, and petal by high-throughput sequencing

Abstract

Safflower (Carthamus tinctorius L.) is one of the most important crop plants that has been utilized for production of oleosins. miRNAs (microRNAs) are a class of small and non-coding RNAs that negatively regulate gene expression at post-transcriptional level thus playing a role in plant growth, development, and stress response. In this study, high-throughput Illumina sequencing technology has been used to comprehensively investigate the small RNA transcriptomes of safflower seed, flower, and leaf. It is found that there are at least 236 known miRNAs expressed in safflower, of which 100 miRNAs with relatively high expression abundance exhibited evolutionary conservation across multiple plants. Comparison of their expression abundance among different tissues shows that a total of 116, 133, and 128 miRNAs are significantly differentially expressed with higher abundance or lower abundance between safflower seed/leaf, seed/petal, and leaf/petal. The majority of the most significant differences in miRNA abundance between tissues are tissue-specific miRNAs. In addition, 13 putative novel miRNAs have been identified in safflower. The small RNA transcriptomes obtained in this study provide a basis for further investigation of the physiological roles of identified miRNAs in safflower.

Discovery of precursor and mature microRNAs and their putative gene targets using high-throughput sequencing in pineapple (Ananas comosus var. comosus)

“…Besides that, the miRNAs in plants are normally 21 nt and 22 nt in animals, thus this data is also in agreement with this theory. In contrast, libraries constructed from Brachypodium and safflowers Li et al, 2010) were dominated by 24 nt miRNAs. Because DCL3, which generates 24 nt miRNAs, has been reported to be involved in the formation of newly evolved MIR genes, the presence of 23 to 25 nt miRNAs suggests the evolution and biogenesis of the miRNAs in these libraries.…”

Salt and drought stresses in safflower: a review

“…The results can act as a basis for unraveling the miRNA-mediated molecular processes that control gene expression of safflower at a post-transcriptional level. Finally, Li et al (2011) reported 236 known miRNAs, of which 100 miRNAs exhibited evolutionary conservation across multiple plants. Furthermore, experimental validation of plant miRNAs showed that miRNAs expression varied upon cold, drought, and other stress responses (Song et al 2010;Sunkar and Zhu 2004;Zhang et al 2009), indicating that miRNAs possibly have a dynamic regulation role in plants.…”

“…Furthermore, experimental validation of plant miRNAs showed that miRNAs expression varied upon cold, drought, and other stress responses (Song et al 2010;Sunkar and Zhu 2004;Zhang et al 2009), indicating that miRNAs possibly have a dynamic regulation role in plants. Hence, a comprehensive study of miRNAs in the safflower could provide supplementary evidence in order to elucidate their physiological functions and evolutionary roles in plants and stress responses (Li et al 2011). …”

Identification and validation of Asteraceae miRNAs by the expressed sequence tag analysis

“…In this study, we designed stem-loop primers based on the newly identified potential miRNAs in sunflower and previously identified conserved miRNA of safflower (Li et al, 2010). We adopted this technique to validate and measure the expression levels of eight potential conserved miRNAs (miR156, miR159, miR160, miR162, miR166, miR396, miR398 and miR477) in both safflower and sunflower seedlings.…”

“…A number of major and minor crops, such as Lactuca sativa, Helianthus annuus, carthamus tinctorius, Cynara cardunculus, and Cichorium intybus, as well as numerous ecologically-important taxa including many weedy and invasive species (Funk et al, 2005), are members of the Asteraceae. To date, miRNAs within the Asteraceae have been identified only in lettuce (Lactuca sativa) (Han et al, 2010), safflower (Carthamus tinctorius) (Li et al, 2010), zinna (Zinnia elegans) (Zhang et al, 2005), and sunflower (Helianthus annuus) (Zhang et al, 2005) and even so, only one study has identified Asteraceae miRNAs using EST analysis (Han et al, 2010). Even though these studies have been conducted on various members of the Asteraceae, few plant species in this family have been fully sequenced and newly identified plant miRNAs are continuously being deposited in miRbase (GriffithsJones et al, 2008).…”