Identification and characterization of conserved and novel miRNAs in different development stages of Atrijuglans hetaohei Yang (Lepidoptera: Gelechioidea)

다국어 초록 (Multilingual Abstract)

Atrijuglans hetaohei Yang (Lepidoptera: Gelechioidea) is a kind of walnut pest, which mainly damage Juglans regia(Juglandales: Juglandaceae) and is widely distributed in China. The information of microRNAs, e.g., the conservedand novel miRNAs of this species is still unknown. In the present study, the miRNAs in larval and adultstages of A. hetaohei were identified by high throughput sequencing with reference to the genome database of theBombyx mori. A total of 132 conserved miRNAs belonging to 64 families and seven novel miRNAs were obtained,among which 118 miRNAs were identified in both libraries, 4 and 17 miRNAs were only detected to adultspecificand larval-specific libraries, respectively. The most abundant miRNAs in A. hetaohei were miR-1a-3p, let-7, miR-2766 and miR-184. Comparative analysis revealed that 4 novel miRNAs and 47 conserved miRNAs weredifferentially expressed (P < 0.05) between two libraries. Abundance changes of miRNAs were observed fromlarva to adult: 19 miRNAs were up-regulated and 21 miRNAs were down-regulated. The metamorphosis andapoptosis associated miRNAs including miR-1a-3p, miR-133, let-7, miR-2766, miR-184 and miR-34 were discussedfor their predicted functions in insect development. The different expressions of these miRNAs wererelevant to dorso-ventral axis formation, phototransduction, insect hormone biosynthesis, circadian rhythm andmitogen-activated protein kinase (MAPK) signaling pathway. qRT-PCR analysis of ten miRNAs showed similarexpression patterns as high throughput analysis, most miRNAs were highly expressed in adult stage, while miR-8-3p, miR-305-3p and miR-2766 were highly expressed in larvae. The results preliminarily revealed the characterizationof conserved and novel miRNAs in different development stages of A. hetaohei. The different expressionsand associated functions of these miRNAs will provide a basis for understanding post-transcriptionallevel during A. hetaohei development and growth.

참고문헌 (Reference)

1 Bushati, N., "microRNA functions" 23 : 175-205, 2007

2 Friedlander, M.R., "miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades" 40 : 37-52, 2011

3 Kozomara, A., "miRBase: annotating high confidence microRNAs using deep sequencing data" 42 : D68-D73, 2014

4 Kugler, J.-M., "miR-989 is required for border cell migration in the Drosophila ovary" 8 : e67075-, 2013

5 Martin, B.L., "Wnt signaling and the evolution of embryonic posterior development" 19 : R215-R219, 2009

6 Uhlirova, M., "Use of Sindbis virus-mediated RNA interference to demonstrate a conserved role of broad-complex in insect metamorphosis" 100 : 15607-15612, 2003

7 Yu, X., "The silkworm (Bombyx mori) microRNAs and their expressions in multiple developmental stages" 3 : e2997-, 2008

8 Yoon, W.H., "The role of microRNAs in development" 1 : 1-11, 2009

9 Wang, Q., "The mitochondrial genome of Atrijuglans hetaohei Yang (Lepidoptera: Gelechioidea) and related phylogenetic analyses" 581 : 66-74, 2016

10 Kato, M., "The mir-34 microRNA is required for the DNA damage response in vivo in C. elegans and in vitro in human breast cancer cells" 28 : 2419-2424, 2009

11 Niwa, R., "The evolution of animal microRNA function" 17 : 145-150, 2007

12 Lu, J., "The birth and death of microRNA genes in Drosophila" 40 : 351-355, 2008

13 Sempere, L.F., "Temporal regulation of microRNA expression in Drosophila melanogaster mediated by hormonal signals and broad-complex gene activity" 259 : 9-18, 2003

14 Song, J., "Studies on the bionomics and integrated control of Atrijuglans hetaohei Yang" 1 : 006-, 1990

15 Li, R., "SOAP2: an improved ultrafast tool for short read alignment" 25 : 1966-1967, 1996

16 Burge, S., "Rfam 11.0: 10 years of RNA families" 41 : D226-D232, 2013

17 Lucas, K.J., "Regulation of physiological processes by microRNAs in insects" 11 : 1-7, 2015

18 Kolliopoulou, A., "Recent progress in RNAi research in Lepidoptera: intracellular machinery, antiviral immune response and prospects for insect pest control" 6 : 28-34, 2014

19 Nie, Z., "RIP-seq of BmAgo2-associated small RNAs reveal various types of small noncoding RNAs in the silkworm, Bombyx mori" 14 : 1-, 2013

20 Ge, W., "Overlapping functions of microRNAs in control of apoptosis during Drosophila embryogenesis" 19 : 839-846, 2012

21 Tian, M., "Outbreaking regularity of Atrijuglans hetauhei and its comprehensive control techniques" 2 : 127-129, 2010

22 Kainz, F., "Notch/Delta signalling is not required for segment generation in the basally branching insect Gryllus bimaculatus" 138 : 5015-5026, 2011

23 Gridley, T., "Notch signaling and inherited disease syndromes" 12 : R9-R13, 2003

24 Li, W., "Molecular cloning and immunofluorescence localization of sex pheromone binding protein 2 from Atrijuglans hetaohei (Lepidoptera: Heliodinidae)" 58 : 1054-1062, 2015

25 Bartel, D.P., "MicroRNAs: genomics, biogenesis, mechanism, and function" 116 : 281-297, 2004

26 Liu, S., "MicroRNAs show diverse and dynamic expression patterns in multiple tissues of Bombyx mori" 11 : 1-, 2010

27 Sokol, N.S., "Mesodermally expressed Drosophila microRNA-1 is regulated by Twist and is required in muscles during larval growth" 19 : 2343-2354, 2005

28 Li, P., "Localized expression pattern of miR-184 in Drosophila" 38 : 355-358, 2011

29 Kanehisa, M., "KEGG for linking genomes to life and the environment" 36 : D480-D484, 2008

30 Sheng, Z., "Juvenile hormone acid methyl transferase is a key regulatory enzyme for juvenile hormone synthesis in the Eri silkworm, Samia cynthica ricini" 69 : 143-154, 2008

31 Ellango, R., "Isolation of new micro RNAs from the diamondback moth (Lepidoptera: Yponomeutidae) genome by a computational method" 97 : 877-885, 2014

32 Ge, X., "Identification of microRNAs in Helicoverpa armigera and Spodoptera litura based on deep sequencing and homology analysis" 9 : 1-15, 2013

33 Hafner, M., "Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing" 44 : 3-12, 2008

34 Li, S.-C., "Identification of homologous microRNAs in 56 animal genomes" 96 : 1-9, 2010

35 Zhang, X., "Identification of conserved and novel microRNAs in Manduca sexta and their possible roles in the expression regulation of immunity-related genes" 47 : 12-22, 2014

36 Stark, A., "Identification of Drosophila microRNA targets" 1 : e60-, 2003

37 Zhang, X., "Identification and developmental profiling of conserved and novel microRNAs in Manduca sexta" 42 : 381-395, 2012

38 Yi, S., "Identification and characterization of microRNAs involved in growth of blunt snout bream (Megalobrama amblycephala) by Solexa sequencing" 14 : 754-, 2013

39 Jiao, Y., "Identification and characterization of microRNAs in pearl oyster Pinctada martensii by Solexa deep sequencing" 16 : 54-62, 2014

40 He, P., "Identification and characteristics of microRNAs from Bombyx mori" 9 : 248-, 2008

41 Chawla, G., "Hormonal activation of let-7-C microRNAs via EcR is required for adult Drosophila melanogaster morphology and function" 139 : 1788-1797, 2012

42 Chen, M., "Genome-wide expression profiling of microRNAs in poplar upon infection with the foliar rust fungus Melampsora larici-populina" 16 : 696-, 2015

43 Benson, D.A., "GenBank" 43 : D30-, 2015

44 Kontogiannatos, D., "Functional characterization of a juvenile hormone esterase related gene in the moth Sesamia nonagrioides through RNA interference" 8 : e73834-, 2013

45 Courteau, L.A., "Differential expression of microRNA species in a freeze tolerant insect, Eurosta solidaginis" 65 : 210-214, 2012

46 Mukherjee, K., "Development and immunity-related microRNAs of the lepidopteran model host Galleria mellonella" 15 : 705-, 2014

47 Schulte, J.H., "Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma" 2010

48 Jagadeeswaran, G., "Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development" 11 : 1-, 2010

49 Huang, Y., "Computational identification and characteristics of novel microRNAs from the silkworm (Bombyx mori L.)" 37 : 3171-3176, 2010

50 Hao, X., "Component analysis of the sex pheromone gland secretion for Atrijuglans hetaohei Yang" 4 : 409-411, 2007

51 Hui, J., "Biological characteristics of Atrijuglans hetaohei and integrated control measures" 2 : 014-, 2010

52 Salminen, A., "Apoptosis and aging: increased resistance to apoptosis enhances the aging process" 68 : 1021-1031, 2011

53 Hentze, J.L., "Accessory gland as a site for prothoracicotropic hormone controlled ecdysone synthesis in adult male insects" 8 : e55131-, 2013

54 Quah, S., "A diversity of conserved and novel ovarian microRNAs in the Speckled Wood (Pararge aegeria)" 10 : e0142243-, 2015