Small RNA sequencing study of the nematode phylum
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ABSTRACT:
ORGANISM(S): Romanomermis culicivorax Caenorhabditis elegans Paragordius varius Nippostrongylus brasiliensis Hypsibius dujardini Enoplus brevis Odontophora rectangula Globodera pallida Trichinella spiralis Brugia malayi Pristionchus pacificus
PROVIDER: GSE56651 | GEO | 2015/02/01
SECONDARY ACCESSION(S): PRJNA244167
REPOSITORIES: GEO
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Project description:Comparison of small RNA profiles across nematode evolution Sequencing of small RNAs (15-33nt)
2015-02-01 | E-GEOD-56651 | biostudies-arrayexpress
Project description:Small RNA sequencing study of the nematode phylum
| PRJNA244167 | ENA
Project description:Small RNA pathways play diverse regulatory roles in the nematode C. elegans. However, our understanding of small RNA pathways, their conservation, and their roles in other nematodes is limited. Here, we analyzed small RNA pathways in the parasitic nematode Ascaris. Ascaris has ten Argonautes with five worm-specific Argonautes (WAGOs) that are associated with secondary 5’-triphosphate small RNAs (22-24G-RNAs). These Ascaris WAGOs and their small RNAs target repetitive sequences (WAGO-1, WAGO-2, WAGO-3, and NRDE-3) or mature mRNAs (CSR-1, NRDE-3, and WAGO-3) and are similar to the C. elegans mutator, nuclear, and CSR-1 small RNA pathways. Ascaris CSR-1 likely functions to “license” gene expression in the absence of an Ascaris piRNA pathway. Ascaris ALG-4 and its associated 26G-RNAs target and appear to repress specific mRNAs during meiosis in the testes. Notably, Ascaris WAGOs (WAGO-3 and NRDE-3) small RNAs change their targets between repetitive sequences and mRNAs during spermatogenesis or in early embryos illustrating target plasticity of these WAGOs. We provide a unique and comprehensive view of mRNA and small RNA expression throughout nematode spermatogenesis that illustrates the dynamics and flexibility of small RNA pathways. Overall, our study provides key insights into the conservation and divergence of nematode small RNA pathways.
2021-12-15 | GSE189061 | GEO
Project description:Deep Small RNA Sequencing from the Nematode Ascaris Reveals Conservation, Functional Diversification, and Novel Developmental Profiles
| PRJNA136965 | ENA
Project description:All the reports on insect small RNAs come from holometabolous insects. However, small RNAs of hemimetabolous insects have not yet been investigated.Study of hemimetabolous insect small RNAs could provide more insights into evolution and function of small RNAs in hemi- and holometabolous insects. The locust is an important, economically harmful hemimetabolous insect and its phase changes is an interesting phenomenon.Here, we used high-throughput sequencing to characterize and compare the small RNA transcriptomes of gregarious and solitary phases in locusts. We found abundant small RNAs and their different expression profiles in the two phases. Small RNAs were sequenced from gregarious and solitary phases of Locusta migratoria,respectively.
2009-01-16 | E-GEOD-12640 | biostudies-arrayexpress
Project description:All the reports on insect small RNAs come from holometabolous insects. However, small RNAs of hemimetabolous insects have not yet been investigated.Study of hemimetabolous insect small RNAs could provide more insights into evolution and function of small RNAs in hemi- and holometabolous insects. The locust is an important, economically harmful hemimetabolous insect and its phase changes is an interesting phenomenon.Here, we used high-throughput sequencing to characterize and compare the small RNA transcriptomes of gregarious and solitary phases in locusts. We found abundant small RNAs and their different expression profiles in the two phases.
2009-01-16 | GSE12640 | GEO
Project description:We report small RNA sequencing of the entomopathogenic nematode Steinernema carpocapsae. The nematodes were grown in liquid culture in homogenates of pig kidney/fat and infective juveniles were gathered. Then Galleria mellonella insect haemolymph was added to simulate insect infection, control nematodes weren't added haemolymph. Nematodes were collected after two hours after haemolymph addition.
2016-09-05 | GSE85256 | GEO
Project description:Eukaryotic cells express several classes of small RNAs that regulate gene expression and ensure genome maintenance. Endogenous siRNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs) mainly control gene and transposon expression in the germline, while microRNAs (miRNAs) generally function in post-transcriptional gene silencing in both somatic and germline cells. To provide an evolutionary and developmental perspective on small RNA pathways in nematodes, we identified and characterized known and novel small RNA classes through gametogenesis and embryo development in the parasitic nematode Ascaris suum and compared them with known small RNAs of Caenorhabditis elegans. piRNAs, Piwi-clade Argonautes, and other proteins associated with the piRNA pathway have been lost in Ascaris. miRNAs are synthesized immediately following fertilization in utero, prior to pronuclear fusion, and before the first cleavage of the zygote. This is the earliest expression of small RNAs ever described at a developmental stage long thought to be transcriptionally quiescent. A comparison of the two classes of Ascaris endo-siRNAs, 22G-RNAs and 26G-RNAs, to those in C. elegans, suggests great diversification and plasticity in the use of small RNA pathways during spermatogenesis in different nematodes. Our data reveal conserved characteristics of nematode small RNAs as well as features unique to Ascaris that illustrate significant flexibility in the use of small RNAs pathways, some of which are likely an adaptation to AscarisM-bM-^@M-^Y life cycle and parasitism. We constructed and analyzed 51 libraries from discrete regions of gametogenesis and synchronized stages of embryo development in the parasitic nematode Ascaris, using three types of small RNA libraries preparation methods: 1) 28 libraries of 18-34 or 18-40 nt RNAs with a 5M-bM-^@M-^Y monophosphate (5M-bM-^@M-^Y monophosphate libraries), 2) 4 libraries of 18-34 nt RNAs with a 5M-bM-^@M-^Y monophosphate but treated with periodate to enrich for small RNAs with 3M-bM-^@M-^Y end modifications (5M-bM-^@M-^Y monophosphate, 3M-bM-^@M-^Y end modified), and 3) 19 libraries of 18-28 or 18-40 nt RNAs with a 5M-bM-^@M-^Y triphosphate, diphosphate, or monophosphate (5M-bM-^@M-^Y allphosphate). These libraries enabled us to identify different small RNAs, characterize their different 5M-bM-^@M-^Y and 3M-bM-^@M-^Y ends, and their expression profiles through gametogenesis and embryogenesis.
2011-06-16 | E-GEOD-26955 | biostudies-arrayexpress
Project description:We have performed small RNA sequencing in the nematodes Caenorhabditis elegans, C. briggsae, C. remanei and Pristionchus pacificus, which have diverged up to 400 million years ago, to establish the repertoire and evolutionary dynamics of miRNAs in these species. In addition to previously known miRNA genes from C. elegans and C. briggsae we demonstrate expression of many of their homologs in C. remanei and P. pacificus, and identified in total more than 100 novel expressed miRNA genes, the majority of which belong to P. pacificus. More than half of all identified miRNA genes were found to be conserved at the seed level in all four nematode species, whereas only a few miRNAs appear to be species-specific. In our compendium of miRNAs we observed evidence for known mechanisms of miRNA evolution, including antisense transcription and arm switching, as well as miRNA family expansion through gene duplication. In addition, we identified a novel mode of miRNA evolution, termed ‘hairpin shifting’, in which an alternative hairpin is formed with up- or downstream sequences, leading to shifting of the hairpin and creation of novel miRNA* species. Finally, we identified 21U-RNAs in all four nematodes, including P. pacificus, where the upstream 21U-RNA motif is more diverged. However, the genomic distribution of 21U-RNA clusters in P. pacificus appears more scattered throughout the genome as compared to C. elegans. The identification and systematic analysis of small RNA repertoire in four nematode species described here provides a valuable resource for understanding the evolutionary dynamics of miRNA-mediated gene regulation. Small RNAs were cloned from mixed stage animals. Sequencing was performed using the 454 GS FLX platform.
2009-09-07 | E-GEOD-15169 | biostudies-arrayexpress