Identification and developmental profiling of conserved and novel microRNAs in Manduca sexta

Abstract

MicroRNAs (miRNAs) are a group of small RNAs involved in translation inhibition or mRNA degradation. Due to its large size, Manduca sexta has long been used as a model to study insect physiology and biochemistry. While transcriptome studies have greatly enriched our knowledge on M. sexta structural genes, little is known about posttranscriptional regulation by miRNAs in this lepidopteran species. We constructed four small RNA libraries from embryos, 4th instar feeding larvae, pupae, and adults, obtained 21 million reads of 18-31 nucleotides by Illumina sequencing, and found 163 conserved and 13 novel miRNAs. By searching the M. sexta genome assembly, we identified precursors of 82 conserved miRNAs, 76 of which had mapped reads in one or more of these libraries. After normalization, we compared numbers of miRNA and miRNA-star reads in these libraries and observed abundance changes during development. Interestingly, mse-miR-281-star, mse-miR-31-star, mse-miR-965-star, mse-miR-9a-star, msemiR-9b-star, mse-miR-2a-star, mse-miR-92b-star and mse-miR-279c-star are either more abundant or maintained at similar levels compared to respective mature miRNA strand. Expression profiling of the first set of miRNAs provided insights to their possible involvement in developmental regulation. This study will aid in the annotation of miRNA genes in the genome.

Identification and profiling of Manduca sexta microRNAs and their possible roles in regulating specific transcripts in fat body, hemocytes, and midgut

“…Sequence analyses were performed as described previously (Zhang et al, 2012). Briefly, small RNAs without perfect match to the 3′-adaptor were disposed.…”

“…Our recent study reported miRNA profiles in M. sexta fat body and hemocytes with or without pathogen stimulation and suggested potential regulatory pairs of miRNAs and immunity-related genes (Zhang et al, 2014). Sequencing the tissue RNAs yielded better coverage of the miRNA repertoire than the whole body samples (Zhang et al, 2012). However, tissue specificity of miRNA expression has not yet been explored in fat body or hemocytes.…”

“…In the tobacco hornworm Manduca sexta , 164 conserved and 16 novel microRNAs have been identified experimentally (Zhang et al, 2012, 2014). To extend the list of microRNAs in this lepidopteran model species and further explore their possible regulatory roles, we constructed and sequenced small RNA libraries of M. sexta fat body, hemocytes and midgut, since transcriptomes of these tissues from the 5 th instar larvae had been studied quite extensively.…”

Global analysis of microRNA species in the gall midgeMayetiola destructor

“…Besides, miR-iab-4-3p is highly expressed in the egg and larval stages but have very low expression in other stages . In M. sexta, 30 miRNA species such as mse-miR-8 and mse-miR-71 were highly expressed in embryo, and 16 miRNA species were found to have dominant expression level in the adult stage including mse-miR-100 and mse-miR-277 (Zhang et al, 2012).…”

Genome‐wide identification, expression profiling, and target gene analysis of microRNAs in the Onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae), vectors of tospoviruses (Bunyaviridae)

“…High‐throughput next‐generation sequencing (NGS) emerged as a powerful tool to identify miRNAs from animals and plants (Calla & Geib, 2015; Guillem, Bastian, Maria‐Dolors, & Xavier, 2016; Nandety, Sharif, Kamita, Ramasamy, & Falk, 2015; Song et al., 2011; Wang et al., 2012; Wu et al., 2013). It has accelerated the pace of miRNA discovery from various animals and plants (Avesson, Reimegard, Wagner, & Söderbom, 2012; Burnside et al., 2008; Ge et al., 2013; Hu et al., 2012; Kang et al., 2012; Koh et al., 2010; Zhang et al., 2012). …”