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Abstract
Although Lycium chinense (goji berry) is an important traditional Chinese medicinal plant, little genome information is available for this plant, particularly at the small-RNA level. Recent findings indicate that the evolutionary role of miRNAs is very important for a better understanding of gene regulation in different plant species. To elucidate small RNAs and their potential target genes in fruit and shoot tissues, high-throughput RNA sequencing technology was used followed by qRT-PCR and RLM 5’-RACE experiments. A total of 60 conserved miRNAs belonging to 31 families and 30 putative novel miRNAs were identified. A total of 62 significantly differentially expressed miRNAs were identified, of which 15 (14 known and 1 novel) were shoot-specific, and 12 (7 known and 5 novel) were fruit-specific. Additionally, 28 differentially expressed miRNAs were recorded as up-regulated in fruit tissues. The predicted potential targets were involved in a wide range of metabolic and regulatory pathways. GO (Gene Ontology) enrichment analysis and the KEGG (Kyoto Encyclopedia of Genes and Genomes) database revealed that “metabolic pathways” is the most significant pathway with respect to the rich factor and gene numbers. Moreover, five miRNAs were related to fruit maturation, lycopene biosynthesis and signaling pathways, which might be important for the further study of fruit molecular biology. This study is the first, to detect known and novel miRNAs, and their potential targets, of L. chinense. The data and findings that are presented here might be a good source for the functional genomic study of medicinal plants and for understanding the links among diversified biological pathways.
Highlights
Lycium chinense (Mill.), popularly known as Chinese boxthorn or goji berry and originating from China, is widely distributed in the temperate and subtropical regions of Japan, Korea and southeastern parts of Asia and is even found in European countries [1]
The same observation was previously reported on Arabidopsis thaliana [36], Citrus sinensis [40], Medicago truncatula [41] etc
1.36% of the sRNA reads were repeat-associated in the shoot and 1.61% in the fruit libraries. These repeat-associated reads were remarkably more frequent than any other class of sRNA in the two sRNA libraries (Table 2). These results suggested that the short-interfering RNAs (siRNAs) that are related to repeat and transposons might have a dominating affiliation both in the shoot and fruit tissues of L. chinense
Summary
Lycium chinense (Mill.), popularly known as Chinese boxthorn or goji berry and originating from China, is widely distributed in the temperate and subtropical regions of Japan, Korea and southeastern parts of Asia and is even found in European countries [1]. The dry fruits of Lycium species possess a wide range of clinical importance, such as anti-inflammatory effects [4], anti-aging qualities [5], anticancer and immunomodulating activities [6, 7], and blood glucose- and lipid level-reducing capabilities [8]. This species has many fascinating aspects, there is limited genome and molecular information. The gene regulation and functions of miRNAs need to be elucidated in this species
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