Novel and Conserved Micrornas in Dalian Purple Urchin (Strongylocentrotus Nudus) Identified by Next Generation Sequencing

Abstract

MicroRNAs are regulators in regulation of broad range of phenotypes. The purple urchin, Strongylocentrotus nudus, is one of the most important marine economic animals that widely distributed in the cold seas along the coasts of eastern pacific area. To date, only 45 microRNAs have been identified in a related species, Strongylocentrotus purpurtus, and there is no report on S. nudus microRNAs. Herein, solexa sequencing technology was used to high throughput sequencing analysis of microRNAs in small RNA library isolated from five tissues of S. nudus. Totally, 8,966,865 reads were yielded, 131,015 of which were related to 415 unique microRNAs including 345 deuterostoma conserved and 70 urchin specific microRNAs, as well as 5 microRNA* sequences. The miRNA features including length distribution, end variations and genomic locations were characterized. Annotation of targets revealed a broad range of biological processes and signal transduction pathways that regulated by urchin miRNAs, of which signal transduction mechanisms was the subgroup containing the maximum targets. In addition, the expression of 100 miRNAs in female gonad was confirmed using microRNA microarray analysis. This study provides a first large scale cloning and characterization of S.nudus miRNAs and their potential targets, providing the foundation for further characterization for their role in the regulation of diversity of physiological processes.

Identification of Radish (Raphanus sativus L.) miRNAs and Their Target Genes to Explore miRNA-Mediated Regulatory Networks in Lead (Pb) Stress Responses by High-Throughput Sequencing and Degradome Analysis

“…2). Overall, the distribution of sRNA size in this study was consistent with the results reported in other model plant species, such as Arabidopsis (Rajagopalan et al 2006) and rice (Wei et al 2011).…”

“…Then, transcriptome de novo assembly was carried out using the short-read assembling program Trinity (Grabherr et al 2011). A proprietary pipeline script, ACG T101-miR v4.2 (LC Sciences, Houston, TX, USA), was used for sRNA sequencing data analysis (Li et al 2010a;Wei et al 2011). The key functions of this script included removing various unmappable sequencing reads by a series of digital filters and performing mappable unique sequencing to the latest release of miRBase and the reference genome sequences.…”

Discovery of MicroRNAs of the Stable Fly (Diptera: Muscidae) by High-Throughput Sequencing

“…Sequencing data analysis was performed using the proprietary ACGT101-miR v4.2 pipeline script (LC Sciences; Li et al 2010, Meyer et al 2011, Wei et al 2011. After adapter trimming and quality Þltering of 28,574,374 raw reads, 22,543,231 (78.9%) of the reads were mapped to the following databases: Drosophila melanogaster Meigen genomic or transcript sequences (FlyBase assembly r5.44, ftp://ftp.ßybase.net/) and miRBase 18 (GrifÞths-Jones et al 2008, Kozomara and GrifÞths-Jones 2011; ftp://mirbase.org/), including both mature miRNAs (miRs) and premiRs for 28 arthropod species, including representative data from Diptera (dme, dan, der, dgr, dmo, dpe, dps, dse, dsi, dvi, dwi, dya, aae, aga, ame, cqu), Lepidoptera (bmo), Coleoptera (tca), Hemiptera (api), Hymenoptera (ngi, nlo, nvi), and Orthoptera (lmi), as well as noninsect mandibulate (smr, dpu) and chelicerate (isc, rmi) species.…”

The gene vitellogenin affects microRNA regulation in honey bee (Apis mellifera) fat body and brain

“…Previous microRNA profiling studies using microarrays or deep-sequencing have separated a small subset of highly expressed microRNAs from a larger group of microRNAs that are expressed at low levels (Shao et al, 2010;Cristino et al, 2011;Li et al, 2011;Wei et al, 2011). Based on these studies, we assigned a cutoff of 1000 intensity units above which microRNAs would be considered as highly expressed to generate a subset of microRNAs for closer comparison.…”