title: The germline of the malaria mosquito produces abundant miRNAs, endo-siRNAs, piRNAs and 29-nt small RNAs.
abstract: BACKGROUND
  Small RNAs include different classes essential for endogenous gene regulation and cellular defence against genomic parasites. However, a comprehensive analysis of the small RNA pathways in the germline of the mosquito Anopheles gambiae has never been performed despite their potential relevance to reproductive capacity in this malaria vector.
  
  
  RESULTS
  We performed small RNA deep sequencing during larval and adult gonadogenesis and find that they predominantly express four classes of regulatory small RNAs. We identified 45 novel miRNA precursors some of which were sex-biased and gonad-enriched , nearly doubling the number of previously known miRNA loci. We also determine multiple genomic clusters of 24-30 nt Piwi-interacting RNAs (piRNAs) that map to transposable elements (TEs) and 3'UTR of protein coding genes. Unusually, many TEs and the 3'UTR of some endogenous genes produce an abundant peak of 29-nt small RNAs with piRNA-like characteristics. Moreover, both sense and antisense piRNAs from TEs in both Anopheles gambiae and Drosophila melanogaster reveal novel features of piRNA sequence bias. We also discovered endogenous small interfering RNAs (endo-siRNAs) that map to overlapping transcripts and TEs.
  
  
  CONCLUSIONS
  This is the first description of the germline miRNome in a mosquito species and should prove a valuable resource for understanding gene regulation that underlies gametogenesis and reproductive capacity. We also provide the first evidence of a piRNA pathway that is active against transposons in the germline and our findings suggest novel piRNA sequence bias. The contribution of small RNA pathways to germline TE regulation and genome defence in general is an important finding for approaches aimed at manipulating mosquito populations through the use of selfish genetic elements.
authors.affiliation: Division of Oncology, Department of Surgery and Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College, London, UK. l.castellano@imperial.ac.uk.
authors.forename: Leandro
authors.initials: L
authors.lastname: Castellano
authors.affiliation: Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche (ITB-CNR), Segrate, Milan, Italy. ermanno.rizzi@itb.cnr.it.
authors.forename: Ermanno
authors.initials: E
authors.lastname: Rizzi
authors.affiliation: Division of Oncology, Department of Surgery and Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College, London, UK. j.krell@imperial.ac.uk.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Krell
authors.affiliation: Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy. manlio.dicristina@unipg.it.
authors.forename: Manlio
authors.initials: M
authors.lastname: Di Cristina
authors.affiliation: Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW7 2AZ, United Kingdom. r.galizi11@imperial.ac.uk.
authors.forename: Roberto
authors.initials: R
authors.lastname: Galizi
authors.affiliation: Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW7 2AZ, United Kingdom. a.mori10@imperial.ac.uk.
authors.forename: Ayako
authors.initials: A
authors.lastname: Mori
authors.affiliation: Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW7 2AZ, United Kingdom. tam.cy.j@gmail.com.
authors.forename: Janis
authors.initials: J
authors.lastname: Tam
authors.affiliation: Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche (ITB-CNR), Segrate, Milan, Italy. gianluca.debellis@itb.cnr.it.
authors.forename: Gianluca
authors.initials: G
authors.lastname: De Bellis
authors.affiliation: Division of Oncology, Department of Surgery and Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College, London, UK. j.stebbing@imperial.ac.uk.
authors.forename: Justin
authors.initials: J
authors.lastname: Stebbing
authors.affiliation: Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW7 2AZ, United Kingdom. acrs@imperial.ac.uk.|Dipartimento di Medicina Sperimentale Via Gambuli, Centro di Genomica Funzionale, University of Perugia, 06132, Perugia, Italy. acrs@imperial.ac.uk.
authors.forename: Andrea
authors.initials: A
authors.lastname: Crisanti
authors.affiliation: Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW7 2AZ, United Kingdom. t.nolan@imperial.ac.uk.
authors.forename: Tony
authors.initials: T
authors.lastname: Nolan
mesh_terms: D000818:Animals; D009033:Culicidae / Q000235:genetics* / Q000254:growth & development; D018507:Gene Expression Regulation, Developmental; D049750:Genome, Insect; D005854:Germ Cells; D006066:Gonads; D059014:High-Throughput Nucleotide Sequencing; D008288:Malaria / Q000235:genetics* / Q000469:parasitology; D035683:MicroRNAs / Q000096:biosynthesis* / Q000235:genetics; D034741:RNA, Small Interfering / Q000096:biosynthesis* / Q000235:genetics
chemical_list: D035683:MicroRNAs; D034741:RNA, Small Interfering