Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Solexa sequencing of small RNAs in Chinese Amphioxus

ABSTRACT: We applied Solexa sequencing technology to identify Amphioxus microRNA genes. We identified 113 amphioxus microRNA genes, 55 were conserved across species and coded for 45 nonredundant mature miRNAs, whereas 58 were amphioxus-specific and accounted for 53 mature miRNAs. Analyzing the evolutionary history of amphioxus miRNAs, we found amphioxus possessed many miRNAs that are also found in chordates and vertebrates, suggesting these miRNAs may represent cephalochordate lineage innovation. By detailed comparison of the miRNA phylogenetic histories, we further found that amphioxus is more vertebrate-like than tunicates. Keywords: Small RNA 18-30 nt small RNAs from 12 adult Chinese Amphioxus were sequenced in one Solexa lane.

ORGANISM(S): Branchiostoma belcheri

SUBMITTER: li qibin

PROVIDER: E-GEOD-16859 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Identification and characterization of novel amphioxus microRNAs by Solexa sequencing.

Chen Xi X Li Qibin Q Wang Jin J Guo Xing X Jiang Xiangrui X Ren Zhiji Z Weng Chunyue C Sun Guoxun G Wang Xiuqiang X Liu Yaping Y Ma Lijia L Chen Jun-Yuan JY Wang Jun J Zen Ke K Zhang Junfeng J Zhang Chen-Yu CY

Genome biology 20090717 7

<h4>Background</h4>microRNAs (miRNAs) are endogenous small non-coding RNAs that regulate gene expression at the post-transcriptional level. While the number of known human and murine miRNAs is continuously increasing, information regarding miRNAs from other species such as amphioxus remains limited.<h4>Results</h4>We combined Solexa sequencing with computational techniques to identify novel miRNAs in the amphioxus species B. belcheri (Gray). This approach allowed us to identify 113 amphioxus miR ...[more]

PMID: 19615057

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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.

Dataset Information

Solexa sequencing of small RNAs in Chinese Amphioxus

Publications

Identification and characterization of novel amphioxus microRNAs by Solexa sequencing.

Similar Datasets

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