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Small RNAs sequencing in sweet sorghum under cadmium stress

ABSTRACT: Four small RNA libraries from two contrasting sweet sorghum genotypes were sequenced. In this study, One hundred and ninety-five conserved miRNAs belonging to 56 families and 25 putative novel miRNAs from 28 precursors were identified, among which 38 conserved and 24 novel miRNAs were differentially expressed under Cd stress and/or between H18 and L69. Two groups of them: miR169p/q-nov_23 and miR408 were further focused through the coexpression analysis and might be involved in Cd transport, cytoskeleton activity and cell wall construction by regulating their targets. This study presents new insights into the regulatory roles of miRNAs in Cd accumulation and tolerance in sweet sorghum and will help to develop high-Cd accumulation or high Cd-resistant germplasm of sweet sorghum through molecular breeding and/or genetic engineering approaches.

ORGANISM(S): Sorghum bicolor

PROVIDER: GSE145617 | GEO | 2023/10/12

REPOSITORIES: GEO

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Project description:Small RNAs (sRNAs) are emerging as important regulators of biological processes in plants. To characterize the small RNA species and expression changes in ‘Anliu’ sweet orange (wild type, WT) and its red-flesh mutant (MT) with lycopene accumulation, we used high-throughput pyrosequencing to identify and quantitatively profile sRNAs. We identified 112 known miRNAs belonging to 64 families from the sweet orange. Comparative analysis revealed that 63 of the 112 known miRNAs exhibited significant expression differences between WT and MT. We also identified 12 novel miRNAs and 9 miRNA candidates from sweet orange; the 12 novel miRNAs are in line with the biogenesis characteristics including the stem-loop structure of the pre-miRNAs and existence of the miRNA*s in the sRNA libraries. Comparative profiling revealed that 10 novel miRNAs and 8 miRNA candidates are differentially expressed between WT and MT. Potential targets of these differentially expressed miRNAs included several important genes that are involved in carotenoid biosynthesis, such as geranylgeranyl pyrophosphate synthase (GGPS) and lycopene β-cyclase (LYCb). Moreover, GO and KEGG annotation revealed that high ranked miRNA-target genes are those implicated in transcription regulation, protein modification and photosynthesis. We proposed that miRNA-target genes are the hot-spots for generating sRNAs. This study provides the first large scale cloning and characterization of citrus miRNAs, which also lays a foundation for unraveling the mechanism of lycopene accumulation in the sweet orange mutant on post-transcription level. Size fractionated small RNAs (16-30 bp) from total RNA extracts was ligated to 5' and 3' adapters, and reverse transcribed. After PCR amplification the sample was subjected to Solexa sequencing. The resultant 35nt sequence data were filtered according to base quality value. The remained sequences were used to trim 5' and 3' adaptors. The clean tags were used for further analysis.

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Small RNAs sequencing in sweet sorghum under cadmium stress

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