The piRNA Pathway
PIWI clade proteins of the Argonaute family and their guiding PIWI-interacting RNAs (piRNAs) form the core of an RNA interference-based regulatory machinery that is mostly exclusive to animals (Gebert & Rosenkranz 2015, Ozata et al. 2019). The classical view of this system, known as the piRNA pathway, is that of a 'guardian of the genome' (Malone and Hannon 2009). This is because the initially discovered and prime function of the piRNA pathway is the defense of the genome against transposable elements (or transposons), especially in the germline (Aravin et al. 2006, Grivna et al. 2006, Brennecke et al. 2007). If left unchecked these 'selfish' mobile genetic elements proliferate in the genome and can cause serious harm to genome integrity, e. g. by disrupting protein-coding genes (Kazazian et al. 1988, Miki et al. 1992). This is particularly critical in the germline, where any such genomic changes are passed on to the next generation. However, some genes and long non-coding RNAs have also been shown to be regulated by the piRNA pathway (Rouget et al. 2010, Gou et al. 2014, Watanabe et al. 2015, Gebert et al. 2015). Its targets can be regulated, both, transcriptionally and post-transcriptionally and they are recognized through sequence complementarity to piRNAs, which guide their associated PIWI proteins to the corresponding RNA sequence (Brennecke et al. 2007, Aravin et al. 2008). While in vertebrates, the piRNA pathway is very much restricted to the germline, in invertebrate groups such as arthropods and mollusks, piRNAs are in addition ubiquitously found in somatic tissues (Lewis et al. 2018, Jehn et al. 2018). Moreover, PIWI proteins and piRNAs were even identified in somatic stem cells of quite basal taxa, such as sponges and cnidarians (Funayama et al. 2010, Juliano et al. 2014), suggesting that the piRNA pathway emerged early in the evolution of animals before the emergence of a separated germline.

piRNA Clusters
In almost all animal species, large piRNA-producing loci, the so-called piRNA clusters, give rise to the vast majority of piRNAs and are viewed to be central to the piRNA pathway. These genomic loci are transcribed uni- or bidirectionally into long precursor RNAs (Figure 1), which in turn are processed into 24-30nt mature piRNAs, mostly beginning with a uracil base at their 5' ends, as they are loaded onto PIWI proteins (Czech and Hannon 2016). These PIWI/piRNA complexes, together with other protein components, can then find their targets and elicit transcriptional and post-transcription silencing (Ozata et al. 2019). The latter involves mechanisms that further increase the amount of piRNAs, namely ping pong amplification (Brennecke et al. 2007, Gunawardane et al. 2007) and piRNA phasing (Mohn et al. 2015, Han et al. 2015).

Figure 1. Biogenesis of piRNAs from piRNA Clusters to PIWI/piRNA Complexes and Target Silencing. piRNA clusters are transcribed into large piRNA precursor RNAs, which are processed into pre-piRNAs and loaded onto PIWI proteins. PIWI/piRNA complexes recognize target transcripts and process them within the ping-pong cycle and the phased biogenesis piRNA pathway.

With notable exceptions such as nematodes, typically up to a few hundred piRNA clusters, with sizes ranging between a few thousand base pairs to hundreds of thousands, are dispersed throughout a given genome. Importantly, they tend to occupy different genomic territories in different lineages, such as pericentric heterochromatin in flies (Brennecke et al. 2007), or more euchromatic regions in mammals (Li et al. 2013). However, piRNA clusters are not static and evolve rapidly on a large scale, quickly coming and going, while evolving neutrally on the sequence level (Assis and Kondrashov 2009, Chirn et al. 2015, Gebert et al. 2019). Therefore, the regulatory network that piRNA clusters and their targets form (Figure 2), can enormously vary between species and broader phylogenetic groups.

Figure 2. piRNA Clusters as Genome Regulators. Large piRNA-producing loci (piRNA clusters), up to >100kb, are distributed around the genome and produce piRNAs that regulate targets transcriptionally and/or post-transcriptionally. The figure is a simple schematic of the complex regulatory relations between piRNA clusters and target sequences, which can be transposable elements, protein-coding genes, or even long non-coding RNAs.

References

piRNA Cluster Prediction and sRNA Annotation Pipeline
Step 1: Download of raw sRNAseq reads [.fasta] from NCBI's sequence read archive (SRA)
Step 2: Download of genome sequence [.fa], repeat annotation [.out] and gene set [.gff] from GenBank/RefSeq
Step 3: Adapter prediction and trimming, size cutoff and low-complexity sequence filtering of raw reads with unitas
Step 4: Mapping of processed reads on genome sequence with seqmap
Step 5: sRNA annotation of mapped reads and miRNA removal with unitas giving read composition, positional nucleotide composition, length distribution, ping-pong signature
Step 6: piRNA cluster prediction with proTRAC using miRNA-free mapped reads, genome sequence, repeat annotation and gene set [options: -1Tor10A 0.5, -1Tand10A 0.3, -clsize 5000]

How to use
The piRNA cluster database is divided into three sections, represented by three panels. The top section is the primary entry point, in which you can choose your favorite species from overall 51, either from a cladogram with selectable species symbols or from a table of all available species. The latter also includes systematic information, as well as download links to assemblies, piRNA clusters, and clustered piRNAs. Further, the top panel includes a list of publications linked to the available species, of which datasets are included in the piRNA cluster database.
The "browse clusters" section includes a selectable list of piRNA clusters for a chosen species and a piRNA expression browser for a given piRNA cluster for all available samples. Each sample can be selected/deselected. On top, the browser includes gene and repeat annotation with additional mouse-over information boxes.
The final panel contains the SRA dataset section. This section is temporarily unavailable while the underlying dataset files are being restored.

Please do not hesitate to contact us if you encounter any problems with the piRNA cluster database or if you would like to see a specific dataset, including from species that are not yet part of the database, to be added.
Daniel Gebert: [email protected]

PUBLICATIONS

Authors	Title (click to select SRA datasets)	Journal	Bibliographics	Species	PubMed ID
Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, Cheloufi S, Hodges E, Anger M, Sachidanandam R, Schultz RM, Hannon GJ	Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes.	Nature	2008 453:534-8	Mus musculus	18404147
Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z, Kellis M, Grutzner F, Stark A, Hannon GJ	Conservation of small RNA pathways in platypus.	Genome Res	2008 18:995-1004	Ornithorhynchus anatinus	18463306
Aravin AA, Sachidanandam R, Bourc'his D, Schaefer C, Pezic D, Toth KF, Bestor T, Hannon GJ	A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice.	Mol Cell	2008 31:785-99	Mus musculus	18922463
Reuter M, Chuma S, Tanaka T, Franz T, Stark A, Pillai RS	Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profile.	Nat Struct Mol Biol	2009 16:639-46	Mus musculus	19465913
Robine N, Lau NC, Balla S, Jin Z, Okamura K, Kuramochi-Miyagawa S, Blower MD, Lai EC	A broadly conserved pathway generates 3'UTR-directed primary piRNAs.	Curr Biol	2009 19:2066-76	Mus musculus, Xenopus tropicalis	20022248
Kamminga LM, Luteijn MJ, den Broeder MJ, Redl S, Kaaij LJ, Roovers EF, Ladurner P, Berezikov E, Ketting RF	Hen1 is required for oocyte development and piRNA stability in zebrafish.	EMBO J	2010 29:3688-700	Danio rerio	20859253
Haase AD, Fenoglio S, Muerdter F, Guzzardo PM, Czech B, Pappin DJ, Chen C, Gordon A, Hannon GJ	Probing the initiation and effector phases of the somatic piRNA pathway in Drosophila.	Genes Dev	2010 24:2499-504	Drosophila melanogaster	20966049
Yan Z, Hu HY, Jiang X, Maierhofer V, Neb E, He L, Hu Y, Hu H, Li N, Chen W, Khaitovich P	Widespread expression of piRNA-like molecules in somatic tissues.	Nucleic Acids Res	2011 39:6596-607	Macaca mulatta	21546553
Li M, Liu Y, Wang T, Guan J, Luo Z, Chen H, Wang X, Chen L, Ma J, Mu Z, Jiang AA, Zhu L, Lang Q, Zhou X, Wang J, Zeng W, Li N, Li K, Gao X, Li X	Repertoire of porcine microRNAs in adult ovary and testis by deep sequencing.	Int J Biol Sci	2011 7:1045-55	Sus scrofa	21927574
Kaaij LJ, Hoogstrate SW, Berezikov E, Ketting RF	piRNA dynamics in divergent zebrafish strains reveal long-lasting maternal influence on zygotic piRNA profiles.	RNA	2013 19:345-56	Danio rerio	23335638
Adelman ZN, Anderson MA, Wiley MR, Murreddu MG, Samuel GH, Morazzani EM, Myles KM	Cooler temperatures destabilize RNA interference and increase susceptibility of disease vector mosquitoes to viral infection.	PLoS Negl Trop Dis	2013 7:e2239	Aedes aegypti	23738025
Harding JL, Horswell S, Heliot C, Armisen J, Zimmerman LB, Luscombe NM, Miska EA, Hill CS	Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements.	Genome Res	2014 24:96-106	Xenopus tropicalis	24065776
Platt RN 2nd, Vandewege MW, Kern C, Schmidt CJ, Hoffmann FG, Ray DA	Large numbers of novel miRNAs originate from DNA transposons and are coincident with a large species radiation in bats.	Mol Biol Evol	2014 31:1536-45	Eptesicus fuscus	24692655
Hirano T, Iwasaki YW, Lin ZY, Imamura M, Seki NM, Sasaki E, Saito K, Okano H, Siomi MC, Siomi H	Small RNA profiling and characterization of piRNA clusters in the adult testes of the common marmoset, a model primate.	RNA	2014 20:1223-37	Callithrix jacchus	24914035
Xu F, Wang X, Feng Y, Huang W, Wang W, Li L, Fang X, Que H, Zhang G	Identification of conserved and novel microRNAs in the Pacific oyster Crassostrea gigas by deep sequencing.	PLoS One	2014 9:e104371	Crassostrea gigas	25137038
Rengaraj D, Lee SI, Park TS, Lee HJ, Kim YM, Sohn YA, Jung M, Noh SJ, Jung H, Han JY	Small non-coding RNA profiling and the role of piRNA pathway genes in the protection of chicken primordial germ cells.	BMC Genomics	2014 15:757	Gallus gallus	25185950
Lau K, Lai KP, Bao JY, Zhang N, Tse A, Tong A, Li JW, Lok S, Kong RY, Lui WY, Wong A, Wu RS	Identification and expression profiling of microRNAs in the brain, liver and gonads of marine medaka (Oryzias melastigma) and in response to hypoxia.	PLoS One	2014 9:e110698	Oryzias melastigma	25350659
Peng X, Thierry-Mieg J, Thierry-Mieg D, Nishida A, Pipes L, Bozinoski M, Thomas MJ, Kelly S, Weiss JM, Raveendran M, Muzny D, Gibbs RA, Rogers J, Schroth GP, Katze MG, Mason CE	Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR).	Nucleic Acids Res	2015 43:D737-42	Macaca mulatta	25392405
Kowalczykiewicz D, Swiercz A, Handschuh L, Lesniak K, Figlerowicz M, Wrzesinski J	Characterization of Sus scrofa small non-coding RNAs present in both female and male gonads.	PLoS One	2014 9:e113249	Sus scrofa	25415416
Gao Y, Guo W, Hu Q, Zou M, Tang R, Chi W, Li D	Characterization and differential expression patterns of conserved microRNAs and mRNAs in three genders of the rice field eel (Monopterus albus).	Sex Dev	2014 8:387-98	Monopterus albus	25427634
Lee M, Choi Y, Kim K, Jin H, Lim J, Nguyen TA, Yang J, Jeong M, Giraldez AJ, Yang H, Patel DJ, Kim VN	Adenylation of maternally inherited microRNAs by Wispy.	Mol Cell	2014 56:696-707	Drosophila melanogaster, Danio rerio	25454948
Lai KP, Li JW, Wang SY, Chiu JM, Tse A, Lau K, Lok S, Au DW, Tse WK, Wong CK, Chan TF, Kong RY, Wu RS	Tissue-specific transcriptome assemblies of the marine medaka Oryzias melastigma and comparative analysis with the freshwater medaka Oryzias latipes.	BMC Genomics	2015 16:135	Oryzias melastigma	25765076
Rosenkranz D, Rudloff S, Bastuck K, Ketting RF, Zischler H	Tupaia small RNAs provide insights into function and evolution of RNAi-based transposon defense in mammals.	RNA	2015 21:911-22	Tupaia belangeri	25802409
Garcia-Lopez J, Alonso L, Cardenas DB, Artaza-Alvarez H, Hourcade Jde D, Martinez S, Brieno-Enriquez MA, Del Mazo J	Diversity and functional convergence of small noncoding RNAs in male germ cell differentiation and fertilization.	RNA	2015 21:946-62	Mus musculus	25805854
Roovers EF, Rosenkranz D, Mahdipour M, Han CT, He N, Chuva de Sousa Lopes SM, van der Westerlaken LA, Zischler H, Butter F, Roelen BA, Ketting RF	Piwi proteins and piRNAs in mammalian oocytes and early embryos.	Cell Rep	2015 10:2069-82	Bos taurus, Macaca fascicularis, Homo sapiens	25818294
Gebert D, Ketting RF, Zischler H, Rosenkranz D	piRNAs from Pig Testis Provide Evidence for a Conserved Role of the Piwi Pathway in Post-Transcriptional Gene Regulation in Mammals.	PLoS One	2015 10:e0124860	Sus scrofa	25950437
Tse AC, Li JW, Chan TF, Wu RS, Lai KP	Hypoxia induces miR-210, leading to anti-apoptosis in ovarian follicular cells of marine medaka Oryzias melastigma.	Aquat Toxicol	2015 165:189-96	Oryzias melastigma	26074452
Wasik KA, Tam OH, Knott SR, Falciatori I, Hammell M, Vagin VV, Hannon GJ	RNF17 blocks promiscuous activity of PIWI proteins in mouse testes.	Genes Dev	2015 29:1403-15	Mus musculus	26115953
Ishizu H, Iwasaki YW, Hirakata S, Ozaki H, Iwasaki W, Siomi H, Siomi MC	Somatic Primary piRNA Biogenesis Driven by cis-Acting RNA Elements and trans-Acting Yb.	Cell Rep	2015 12:429-40	Drosophila melanogaster	26166564
Wu J, Xiong S, Jing J, Chen X, Wang W, Gui JF, Mei J	Comparative Transcriptome Analysis of Differentially Expressed Genes and Signaling Pathways between XY and YY Testis in Yellow Catfish.	PLoS One	2015 10:e0134626	Tachysurus fulvidraco	26241040
Erwin AA, Galdos MA, Wickersheim ML, Harrison CC, Marr KD, Colicchio JM, Blumenstiel JP	piRNAs Are Associated with Diverse Transgenerational Effects on Gene and Transposon Expression in a Hybrid Dysgenic Syndrome of D. virilis.	PLoS Genet	2015 11:e1005332	Drosophila virilis	26241928
Wang Y, Jiang F, Wang H, Song T, Wei Y, Yang M, Zhang J, Kang L	Evidence for the expression of abundant microRNAs in the locust genome.	Sci Rep	2015 5:13608	Locusta migratoria	26329925
Yang XZ, Chen JY, Liu CJ, Peng J, Wee YR, Han X, Wang C, Zhong X, Shen QS, Liu H, Cao H, Chen XW, Tan BC, Li CY	Selectively Constrained RNA Editing Regulation Crosstalks with piRNA Biogenesis in Primates.	Mol Biol Evol	2015 32:3143-57	Macaca mulatta	26341297
Ignacio C, Hicks SD, Burke P, Lewis L, Szombathyne-Meszaros Z, Middleton FA	Alterations in serum microRNA in humans with alcohol use disorders impact cell proliferation and cell death pathways and predict structural and functional changes in brain.	BMC Neurosci	2015 16:55	Rattus norvegicus	26341662
Jia KT, Zhang J, Jia P, Zeng L, Jin Y, Yuan Y, Chen J, Hong Y, Yi M	Identification of MicroRNAs in Zebrafish Spermatozoa.	Zebrafish	2015 12:387-97	Danio rerio	26418264
Calla B, Geib SM	MicroRNAs in the oriental fruit fly, Bactrocera dorsalis: extending Drosophilid miRNA conservation to the Tephritidae.	BMC Genomics	2015 16:740	Bactrocera dorsalis	26438165
Williams Z, Morozov P, Mihailovic A, Lin C, Puvvula PK, Juranek S, Rosenwaks Z, Tuschl T	Discovery and Characterization of piRNAs in the Human Fetal Ovary.	Cell Rep	2015 13:854-863	Homo sapiens	26489470
Ahmed A, Ward NJ, Moxon S, Lopez-Gomollon S, Viaut C, Tomlinson ML, Patrushev I, Gilchrist MJ, Dalmay T, Dotlic D, Munsterberg AE, Wheeler GN	A Database of microRNA Expression Patterns in Xenopus laevis.	PLoS One	2015 10:e0138313	Xenopus laevis	26506012
Ninova M, Ronshaugen M, Griffiths-Jones S	MicroRNA evolution, expression, and function during short germband development in Tribolium castaneum.	Genome Res	2016 26:85-96	Tribolium castaneum	26518483
Quah S, Breuker CJ, Holland PW	A Diversity of Conserved and Novel Ovarian MicroRNAs in the Speckled Wood (Pararge aegeria).	PLoS One	2015 10:e0142243	Pararge aegeria	26556800
Vaz C, Wee CW, Lee GP, Ingham PW, Tanavde V, Mathavan S	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish.	BMC Genomics	2015 16:950	Danio rerio	26574018
Chirn GW, Rahman R, Sytnikova YA, Matts JA, Zeng M, Gerlach D, Yu M, Berger B, Naramura M, Kile BT, Lau NC	Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals.	PLoS Genet	2015 11:e1005652	Drosophila melanogaster, Drosophila erecta, Drosophila yakuba, Drosophila virilis, Rattus norvegicus, Oryctolagus cuniculus	26588211
George P, Jensen S, Pogorelcnik R, Lee J, Xing Y, Brasset E, Vaury C, Sharakhov IV	Increased production of piRNAs from euchromatic clusters and genes in Anopheles gambiae compared with Drosophila melanogaster.	Epigenetics Chromatin	2015 8:50	Anopheles gambiae	26617674
Pires CV, Freitas FC, Cristino AS, Dearden PK, Simoes ZL	Transcriptome Analysis of Honeybee (Apis Mellifera) Haploid and Diploid Embryos Reveals Early Zygotic Transcription during Cleavage.	PLoS One	2016 11:e0146447	Apis mellifera	26751956
Vandewege MW, Platt RN 2nd, Ray DA, Hoffmann FG	Transposable Element Targeting by piRNAs in Laurasiatherians with Distinct Transposable Element Histories.	Genome Biol Evol	2016 8:1327-37	Canis lupus familiaris, Eptesicus fuscus, Equus caballus	27060702
Ren L, Li W, Tao M, Qin Q, Luo J, Chai J, Tang C, Xiao J, Tang X, Lin G, Zhang C, Duan W, Hong Y, Liu S	Homoeologue expression insights into the basis of growth heterosis at the intersection of ploidy and hybridity in Cyprinidae.	Sci Rep	2016 6:27040	Carassius auratus	27265401
Koenig EM, Fisher C, Bernard H, Wolenski FS, Gerrein J, Carsillo M, Gallacher M, Tse A, Peters R, Smith A, Meehan A, Tirrell S, Kirby P	The beagle dog MicroRNA tissue atlas: identifying translatable biomarkers of organ toxicity.	BMC Genomics	2016 17:649	Canis lupus familiaris	27535741
Toombs JA, Sytnikova YA, Chirn GW, Ang I, Lau NC, Blower MD	Xenopus Piwi proteins interact with a broad proportion of the oocyte transcriptome.	RNA	2017 23:504-520	Xenopus tropicalis, Xenopus laevis	28031481
Wu S, Ren X, Li Y, Guo W, Lei X, Yao J, Yang X	Effect of dietary Astragalus Polysaccharide supplements on testicular miRNA expression profiles and enzymatic changes of breeder cocks.	Sci Rep	2017 7:38864	Gallus gallus	28054553
Rice ES, Kohno S, John JS, Pham S, Howard J, Lareau LF, O'Connell BL, Hickey G, Armstrong J, Deran A, Fiddes I, Platt RN 2nd, Gresham C, McCarthy F, Kern C, Haan D, Phan T, Schmidt C, Sanford JR, Ray DA, Paten B, Guillette LJ Jr, Green RE	Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling.	Genome Res	2017 27:686-696	Alligator mississippiensis	28137821
Locati MD, Pagano JFB, Girard G, Ensink WA, van Olst M, van Leeuwen S, Nehrdich U, Spaink HP, Rauwerda H, Jonker MJ, Dekker RJ, Breit TM	Expression of distinct maternal and somatic 5.8S, 18S, and 28S rRNA types during zebrafish development.	RNA	2017 23:1188-1199	Danio rerio	28500251
Zhang B, Mao YS, Diermeier SD, Novikova IV, Nawrocki EP, Jones TA, Lazar Z, Tung CS, Luo W, Eddy SR, Sanbonmatsu KY, Spector DL	Identification and Characterization of a Class of MALAT1-like Genomic Loci.	Cell Rep	2017 19:1723-1738	Anolis carolinensis	28538188
Chen X, Ma C, Chen C, Lu Q, Shi W, Liu Z, Wang H, Guo H	Integration of lncRNA-miRNA-mRNA reveals novel insights into oviposition regulation in honey bees.	PeerJ	2017 5:e3881	Apis mellifera	29018616
Warnefors M, Mossinger K, Halbert J, Studer T, VandeBerg JL, Lindgren I, Fallahshahroudi A, Jensen P, Kaessmann H	Sex-biased microRNA expression in mammals and birds reveals underlying regulatory mechanisms and a role in dosage compensation.	Genome Res	2017 27:1961-1973	Monodelphis domestica, Mus musculus	29079676
Whitfield ZJ, Dolan PT, Kunitomi M, Tassetto M, Seetin MG, Oh S, Heiner C, Paxinos E, Andino R	The Diversity, Structure, and Function of Heritable Adaptive Immunity Sequences in the Aedes aegypti Genome.	Curr Biol	2017 27:3511-3519.e7	Aedes aegypti	29129531
Lewis SH, Quarles KA, Yang Y, Tanguy M, Frezal L, Smith SA, Sharma PP, Cordaux R, Gilbert C, Giraud I, Collins DH, Zamore PD, Miska EA, Sarkies P, Jiggins FM	Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements.	Nat Ecol Evol	2018 2:174-181	Limulus polyphemus, Parasteatoda tepidariorum, Locusta migratoria, Oncopeltus fasciatus, Acyrthosiphon pisum, Bombus terrestris, Apis mellifera, Nicrophorus vespilloides, Tribolium castaneum, Plutella xylostella, Trichoplusia ni, Musca domestica, Centruroides sculpturatus, Drosophila virilis, Aedes aegypti	29203920
Mohammed J, Flynt AS, Panzarino AM, Mondal MMH, DeCruz M, Siepel A, Lai EC	Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus.	Genome Res	2018 28:52-65	Drosophila erecta, Drosophila sechellia, Drosophila virilis, Drosophila yakuba	29233922
Gainetdinov IV, Skvortsova YV, Kondratieva SA, Klimov A, Tryakin AA, Azhikina TL	Assessment of piRNA biogenesis and function in testicular germ cell tumors and their precursor germ cell neoplasia in situ.	BMC Cancer	2018 18:20	Homo sapiens	29301509
Fu Y, Yang Y, Zhang H, Farley G, Wang J, Quarles KA, Weng Z, Zamore PD	The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology.	Elife	2018 7:	Trichoplusia ni	29376823
Guo X, Ma Z, Du B, Li T, Li W, Xu L, He J, Kang L	Dop1 enhances conspecific olfactory attraction by inhibiting miR-9a maturation in locusts.	Nat Commun	2018 9:1193	Locusta migratoria	29567955
Jiang L, Wang Q, Yu J, Gowda V, Johnson G, Yang J, Kan X, Yang X	miRNAome expression profiles in the gonads of adult Melopsittacus undulatus.	PeerJ	2018 6:e4615	Melopsittacus undulatus	29666766
Funikov SY, Kulikova DA, Krasnov GS, Rezvykh AP, Chuvakova LN, Shostak NG, Zelentsova ES, Blumenstiel JP, Evgen'ev MB	Spontaneous gain of susceptibility suggests a novel mechanism of resistance to hybrid dysgenesis in Drosophila virilis.	PLoS Genet	2018 14:e1007400	Drosophila virilis	29813067
Chang KW, Tseng YT, Chen YC, Yu CY, Liao HF, Chen YC, Tu YE, Wu SC, Liu IH, Pinskaya M, Morillon A, Pain B, Lin SP	Stage-dependent piRNAs in chicken implicated roles in modulating male germ cell development.	BMC Genomics	2018 19:425	Gallus gallus	29859049
Zhou L, Lim MYT, Kaur P, Saj A, Bortolamiol-Becet D, Gopal V, Tolwinski N, Tucker-Kellogg G, Okamura K	Importance of miRNA stability and alternative primary miRNA isoforms in gene regulation during Drosophila development.	Elife	2018 7:e38389	Drosophila melanogaster	30024380
Zhao C, Fan S, Qiu L	Identification of MicroRNAs and Their Target Genes Associated with Ovarian Development in Black Tiger Shrimp (Penaeus monodon) Using High-Throughput Sequencing.	Sci Rep	2018 8:11602	Penaeus monodon	30072718
Gay S, Bugeon J, Bouchareb A, Henry L, Delahaye C, Legeai F, Montfort J, Le Cam A, Siegel A, Bobe J, Thermes V	MiR-202 controls female fecundity by regulating medaka oogenesis.	PLoS Genet	2018 14:e1007593	Oryzias latipes	30199527
Liu Y, Sun Y, Li Y, Bai H, Xu S, Xu H, Ni A, Yang N, Chen J	Identification and differential expression of microRNAs in the testis of chicken with high and low sperm motility.	Theriogenology	2018 122:94-101	Gallus gallus	30243140
Jehn J, Gebert D, Pipilescu F, Stern S, Kiefer JST, Hewel C, Rosenkranz D	PIWI genes and piRNAs are ubiquitously expressed in mollusks and show patterns of lineage-specific adaptation.	Commun Biol	2018 1:137	Lymnaea stagnalis, Crassostrea gigas	30272016
Espiritu EB, Crunk AE, Bais A, Hochbaum D, Cervino AS, Phua YL, Butterworth MB, Goto T, Ho J, Hukriede NA, Cirio MC	The Lhx1-Ldb1 complex interacts with Furry to regulate microRNA expression during pronephric kidney development.	Sci Rep	2018 8:16029	Xenopus laevis	30375416
Penso-Dolfin L, Moxon S, Haerty W, Di Palma F	The evolutionary dynamics of microRNAs in domestic mammals.	Sci Rep	2018 8:17050	Oryctolagus cuniculus, Canis lupus familiaris, Equus caballus	30451897
Desvignes T, Batzel P, Sydes J, Eames BF, Postlethwait JH	miRNA analysis with Prost! reveals evolutionary conservation of organ-enriched expression and post-transcriptional modifications in three-spined stickleback and zebrafish.	Sci Rep	2019 9:3913	Gasterosteus aculeatus	30850632
Gebert D, Zischler H, Rosenkranz D	Primate piRNA Cluster Evolution Suggests Limited Relevance of Pseudogenes in piRNA-Mediated Gene Regulation.	Genome Biol Evol	2019 11:1088-1104	Microcebus murinus	30888404
Li B, He X, Zhao Y, Bai D, Bou G, Zhang X, Su S, Dao L, Liu R, Wang Y, Manglai D	Identification of piRNAs and piRNA clusters in the testes of the Mongolian horse.	Sci Rep	2019 9:5022	Equus caballus	30903011
Kong QR, Zhang JM, Zhang XL, Zong M, Zheng KL, Liu L, Meng FX, Zhang TT, Weng XG, Mu YS, Liu ZH	Endo-siRNAs repress expression of SINE1B during in†vitro maturation of porcine oocyte.	Theriogenology	2019 135:19-24	Sus scrofa	31189122
Zhao Y, Lu GA, Yang H, Lin P, Liufu Z, Tang T, Xu J	Run or die in the evolution of new microRNAs - Testing the Red Queen hypothesis on de novo new genes.	Mol Biol Evol	2019 135:19-24	Drosophila erecta	33306129
Wu S, Guo W, Li X, Liu Y, Li Y, Lei X, Yao J, Yang X	Paternal chronic folate supplementation induced the transgenerational inheritance of acquired developmental and metabolic changes in chickens.	Proc Biol Sci	2019 286:20191653	Gallus gallus	31506054
Linsen SE, de Wit E, de Bruijn E, Cuppen E	Small RNA expression and strain specificity in the rat.	BMC Genomics	2010 11:249	Rattus norvegicus	20403161
Tindell SJ, Rouchka EC, Arkov AL	Glial granules contain germline proteins in the Drosophila brain, which regulate brain transcriptome.	Commun Biol	2020 3:699	Drosophila melanogaster	33219296
Han BW, Wang W, Li C, Weng Z, Zamore PD	piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production.	Science	2015 348:817-821	Drosophila melanogaster	25977554
Venkei ZG, Choi CP, Feng S, Chen C, Jacobsen SE, Kim JK, Yamashita YM	A kinesin Klp10A mediates cell cycle-dependent shuttling of Piwi between nucleus and nuage.	PLoS Genet	2020 16:e1008648	Drosophila melanogaster	32168327
Sun YH, Zhu J, Xie LH, Li Z, Meduri R, Zhu X, Song C, Chen C, Ricci EP, Weng Z, Li XZ	Ribosomes guide pachytene piRNA formation on long intergenic piRNA precursors.	Nat Cell Biol	2020 22:200-212	Mus musculus	32015435
Gan H, Lin X, Zhang Z, Zhang W, Liao S, Wang L, Han C	piRNA profiling during specific stages of mouse spermatogenesis.	RNA	2011 17:1191-1203	Mus musculus	21602304
Li XZ, Roy CK, Dong X, Bolcun-Filas E, Wang J, Han BW, Xu J, Moore MJ, Schimenti JC, Weng Z, Zamore PD	An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes.	Mol Cell	2013 50:67-81	Mus musculus	23523368

BROWSE CLUSTERS     ID   

ID (click to select)	Species	Location	Start	End	Size	Max. rpm
Apis-0001	Acyrthosiphon pisum	Scaffold188	180002	222641	42640	7766
Apis-0002	Acyrthosiphon pisum	Scaffold28	145228	181870	36643	15565
Apis-0003	Acyrthosiphon pisum	Scaffold91	461000	495760	34761	4274
Apis-0004	Acyrthosiphon pisum	Scaffold627	12209	45875	33667	6424
Apis-0005	Acyrthosiphon pisum	Scaffold82	147338	179019	31682	4574
Apis-0006	Acyrthosiphon pisum	Scaffold36	1019062	1044661	25600	11773
Apis-0007	Acyrthosiphon pisum	Scaffold887	13	24244	24232	35400
Apis-0008	Acyrthosiphon pisum	Scaffold81	2822	26553	23732	6242
Apis-0009	Acyrthosiphon pisum	Scaffold25	140040	162632	22593	1904
Apis-0010	Acyrthosiphon pisum	Scaffold137	375324	396874	21551	53705
Apis-0011	Acyrthosiphon pisum	Scaffold57	641045	662032	20988	1586
Apis-0012	Acyrthosiphon pisum	Scaffold265	282598	302996	20399	2088
Apis-0013	Acyrthosiphon pisum	Scaffold43	558065	578111	20047	3113
Apis-0014	Acyrthosiphon pisum	Scaffold137	460060	478911	18852	24219
Apis-0015	Acyrthosiphon pisum	Scaffold1016	9019	26903	17885	1943
Apis-0016	Acyrthosiphon pisum	Scaffold30	146031	163017	16987	2363
Apis-0017	Acyrthosiphon pisum	Scaffold50	1206414	1223367	16954	2777
Apis-0018	Acyrthosiphon pisum	Scaffold30	104099	121021	16923	2344
Apis-0019	Acyrthosiphon pisum	Scaffold224	338578	355431	16854	6967
Apis-0020	Acyrthosiphon pisum	Scaffold1324	4952	21617	16666	2182
Apis-0021	Acyrthosiphon pisum	Scaffold95	70054	85252	15199	1602
Apis-0022	Acyrthosiphon pisum	Scaffold10	1630003	1645008	15006	2563
Apis-0023	Acyrthosiphon pisum	Scaffold8	410007	425007	15001	1594
Apis-0024	Acyrthosiphon pisum	Scaffold82	53027	67051	14025	1812
Apis-0025	Acyrthosiphon pisum	Scaffold43	527082	540999	13918	2022
Apis-0026	Acyrthosiphon pisum	Scaffold412	583567	597009	13443	10245
Apis-0027	Acyrthosiphon pisum	Scaffold180	134999	147999	13001	3732
Apis-0028	Acyrthosiphon pisum	Scaffold3	1625005	1637983	12979	1487
Apis-0029	Acyrthosiphon pisum	Scaffold51	176000	188025	12026	1437
Apis-0030	Acyrthosiphon pisum	Scaffold112	11004	23006	12003	2203
Apis-0031	Acyrthosiphon pisum	Scaffold46	376001	388000	12000	1452
Apis-0032	Acyrthosiphon pisum	Scaffold5	883033	895001	11969	1520
Apis-0033	Acyrthosiphon pisum	Scaffold202	113024	124884	11861	2162
Apis-0034	Acyrthosiphon pisum	Scaffold83	60005	71796	11792	2480
Apis-0035	Acyrthosiphon pisum	Scaffold1567	1238	12720	11483	4012
Apis-0036	Acyrthosiphon pisum	Scaffold5	600519	611938	11420	6836
Apis-0037	Acyrthosiphon pisum	Scaffold223	21000	32018	11019	1424
Apis-0038	Acyrthosiphon pisum	Scaffold2211	35	10992	10958	1637
Apis-0039	Acyrthosiphon pisum	Scaffold615	102224	112764	10541	11853
Apis-0040	Acyrthosiphon pisum	Scaffold2354	139	10668	10530	1957
Apis-0041	Acyrthosiphon pisum	Scaffold83	312000	322026	10027	1350
Apis-0042	Acyrthosiphon pisum	Scaffold245	136999	147010	10012	1456
Apis-0043	Acyrthosiphon pisum	Scaffold112	190027	200020	9994	1663
Apis-0044	Acyrthosiphon pisum	Scaffold14	1015017	1024997	9981	1449
Apis-0045	Acyrthosiphon pisum	Scaffold158	597000	606876	9877	1476
Apis-0046	Acyrthosiphon pisum	Scaffold14	1035120	1044995	9876	1338
Apis-0047	Acyrthosiphon pisum	Scaffold28	984197	993963	9767	2632
Apis-0048	Acyrthosiphon pisum	Scaffold1803	1063	10158	9096	915
Apis-0049	Acyrthosiphon pisum	Scaffold509	142643	151724	9082	1517
Apis-0050	Acyrthosiphon pisum	Scaffold9	876004	885026	9023	1253
Apis-0051	Acyrthosiphon pisum	Scaffold33	661005	670020	9016	1204
Apis-0052	Acyrthosiphon pisum	Scaffold20	921039	930025	8987	1765
Apis-0053	Acyrthosiphon pisum	Scaffold131	570122	579025	8904	947
Apis-0054	Acyrthosiphon pisum	Scaffold30	1184126	1193020	8895	1325
Apis-0055	Acyrthosiphon pisum	Scaffold33	118999	127868	8870	1062
Apis-0056	Acyrthosiphon pisum	Scaffold4	2172382	2180946	8565	1098
Apis-0057	Acyrthosiphon pisum	Scaffold137	302064	310599	8536	1407
Apis-0058	Acyrthosiphon pisum	Scaffold46	509198	517715	8518	1188
Apis-0059	Acyrthosiphon pisum	Scaffold30	650492	658979	8488	1172
Apis-0060	Acyrthosiphon pisum	Scaffold3182	5001	13460	8460	1844
Apis-0061	Acyrthosiphon pisum	Scaffold1370	7151	15185	8035	311
Apis-0062	Acyrthosiphon pisum	Scaffold1765	1030	9027	7998	900
Apis-0063	Acyrthosiphon pisum	Scaffold237	141008	148988	7981	913
Apis-0064	Acyrthosiphon pisum	Scaffold112	262026	269994	7969	1001
Apis-0065	Acyrthosiphon pisum	Scaffold40	815000	822916	7917	984
Apis-0066	Acyrthosiphon pisum	Scaffold191	105000	112865	7866	895
Apis-0067	Acyrthosiphon pisum	Scaffold395	54110	61900	7791	949
Apis-0068	Acyrthosiphon pisum	Scaffold849	225	7991	7767	957
Apis-0069	Acyrthosiphon pisum	Scaffold21	135285	143008	7724	1005
Apis-0070	Acyrthosiphon pisum	Scaffold140	3000	10632	7633	890
Apis-0071	Acyrthosiphon pisum	Scaffold3	1536035	1543587	7553	917
Apis-0072	Acyrthosiphon pisum	Scaffold2	1688007	1695448	7442	790
Apis-0073	Acyrthosiphon pisum	Scaffold39	541442	548838	7397	1133
Apis-0074	Acyrthosiphon pisum	Scaffold478	12761	19929	7169	3622
Apis-0075	Acyrthosiphon pisum	Scaffold113	140922	148023	7102	2793
Apis-0076	Acyrthosiphon pisum	Scaffold1205	27000	34101	7102	841
Apis-0077	Acyrthosiphon pisum	Scaffold237	160000	167019	7020	839
Apis-0078	Acyrthosiphon pisum	Scaffold33	427015	434016	7002	833
Apis-0079	Acyrthosiphon pisum	Scaffold31	1046093	1053006	6914	867
Apis-0080	Acyrthosiphon pisum	Scaffold37	1311060	1317971	6912	1245
Apis-0081	Acyrthosiphon pisum	Scaffold1106	22052	28941	6890	825
Apis-0082	Acyrthosiphon pisum	Scaffold245	102946	109831	6886	780
Apis-0083	Acyrthosiphon pisum	Scaffold126	432508	439352	6845	859
Apis-0084	Acyrthosiphon pisum	Scaffold302	2214	9006	6793	736
Apis-0085	Acyrthosiphon pisum	Scaffold452	108934	115703	6770	1253
Apis-0086	Acyrthosiphon pisum	Scaffold9	730302	737018	6717	943
Apis-0087	Acyrthosiphon pisum	Scaffold4	1968000	1974683	6684	820
Apis-0088	Acyrthosiphon pisum	Scaffold115	722297	728964	6668	771
Apis-0089	Acyrthosiphon pisum	Scaffold55	59562	66210	6649	1146
Apis-0090	Acyrthosiphon pisum	Scaffold26	54041	60678	6638	820
Apis-0091	Acyrthosiphon pisum	Scaffold45	392005	398614	6610	706
Apis-0092	Acyrthosiphon pisum	Scaffold8574	1029	7638	6610	1046
Apis-0093	Acyrthosiphon pisum	Scaffold8	290006	296612	6607	978
Apis-0094	Acyrthosiphon pisum	Scaffold11	1001184	1007756	6573	1240
Apis-0095	Acyrthosiphon pisum	Scaffold82	684659	691169	6511	1009
Apis-0096	Acyrthosiphon pisum	Scaffold131	541590	547995	6406	819
Apis-0097	Acyrthosiphon pisum	Scaffold18	2481323	2487694	6372	380
Apis-0098	Acyrthosiphon pisum	Scaffold2242	9298	15562	6265	821
Apis-0099	Acyrthosiphon pisum	Scaffold8	565623	571878	6256	414
Apis-0100	Acyrthosiphon pisum	Scaffold802	19697	25909	6213	923
Apis-0101	Acyrthosiphon pisum	Scaffold6	668931	675020	6090	782
Apis-0102	Acyrthosiphon pisum	Scaffold26	674001	680026	6026	716
Apis-0103	Acyrthosiphon pisum	Scaffold112	233003	239024	6022	784
Apis-0104	Acyrthosiphon pisum	Scaffold746	69000	75020	6021	677
Apis-0105	Acyrthosiphon pisum	Scaffold2	1954002	1960018	6017	793
Apis-0106	Acyrthosiphon pisum	Scaffold157	224009	230021	6013	708
Apis-0107	Acyrthosiphon pisum	Scaffold24	148049	153992	5944	690
Apis-0108	Acyrthosiphon pisum	Scaffold14	897005	902934	5930	665
Apis-0109	Acyrthosiphon pisum	Scaffold1052	40009	45919	5911	704
Apis-0110	Acyrthosiphon pisum	Scaffold20	995399	1001301	5903	830
Apis-0111	Acyrthosiphon pisum	Scaffold30	729001	734876	5876	799
Apis-0112	Acyrthosiphon pisum	Scaffold37	1536017	1541764	5748	617
Apis-0113	Acyrthosiphon pisum	Scaffold83	489331	495017	5687	657
Apis-0114	Acyrthosiphon pisum	Scaffold102	800194	805809	5616	7014
Apis-0115	Acyrthosiphon pisum	Scaffold110	415049	420650	5602	1499
Apis-0116	Acyrthosiphon pisum	Scaffold25	464855	470239	5385	858
Apis-0117	Acyrthosiphon pisum	Scaffold20	132309	137663	5355	794
Apis-0118	Acyrthosiphon pisum	Scaffold206	221677	226992	5316	790
Apis-0119	Acyrthosiphon pisum	Scaffold253	167154	172365	5212	946
Apis-0120	Acyrthosiphon pisum	Scaffold11	93999	99025	5027	721
Apis-0121	Acyrthosiphon pisum	Scaffold4	1949999	1955024	5026	620
Apis-0122	Acyrthosiphon pisum	Scaffold43	177002	182026	5025	598
Apis-0123	Acyrthosiphon pisum	Scaffold8	543001	548025	5025	609
Apis-0124	Acyrthosiphon pisum	Scaffold169	285000	290018	5019	616
Apis-0125	Acyrthosiphon pisum	Scaffold307	157006	162024	5019	38406
Apis-0126	Acyrthosiphon pisum	Scaffold47	518013	523028	5016	638
Apis-0127	Acyrthosiphon pisum	Scaffold297	143001	148012	5012	682

SRA DATASET SECTION

Temporarily unavailable Detailed SRA dataset reports and downloads are currently offline. We are working on restoring this feature. The species overview and piRNA cluster browser remain available.