Integrative analysis of transcriptomic profile reveals potential roles of miRNAs in regulating development of <italic style="font-style: italic">Marsupenaeus</italic> <italic style="font-style: italic">japonicas</italic>

Jing WANG; Longjun PU; Xiaojuan ZHANG; Cuicui LIANG; Dandan DONG; Jiantao GUAN; Huarong GUO

doi:10.1007/s00343-023-2403-3

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Integrative analysis of transcriptomic profile reveals potential roles of miRNAs in regulating development of Marsupenaeus japonicas

Biology | Updated：2024-10-15

- Integrative analysis of transcriptomic profile reveals potential roles of miRNAs in regulating development of Marsupenaeus japonicas
- Integrative analysis of transcriptomic profile reveals potential roles of miRNAs in regulating development of Marsupenaeus japonicas
- 海洋湖沼学报(英文) 2024年42卷第1期页码：201-215
- Affiliations：
  
  1.Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
  2.Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
  3.Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Author bio：
  
  huarongguo@ouc.edu.cn
- Funds：
  
  the National Natural Science Foundation of China(32273116);the Natural Science Foundation of Shandong Province (China)(ZR2020MC189);the National Key R&D Program of China(2018YFD0901301)
- DOI：10.1007/s00343-023-2403-3
  中图分类号：
- 收稿：2022-12-30，
  
  录用：2023-02-13，
  
  网络首发：2023-03-07，
  
  纸质出版：2024-01-03
- Accepted：
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Integrative analysis of transcriptomic profile reveals potential roles of miRNAs in regulating development of Marsupenaeus japonicas[J]. 海洋湖沼学报(英文), 2024,42(1):201-215.

WANG Jing,PU Longjun,ZHANG Xiaojuan,et al.Research PaperIntegrative analysis of transcriptomic profile reveals potential roles of miRNAs in regulating development of ,Marsupenaeus,japonicas[J].Journal of Oceanology and Limnology,2024,42(01):201-215.
Integrative analysis of transcriptomic profile reveals potential roles of miRNAs in regulating development of Marsupenaeus japonicas[J]. 海洋湖沼学报(英文), 2024,42(1):201-215. DOI： 10.1007/s00343-023-2403-3.

WANG Jing,PU Longjun,ZHANG Xiaojuan,et al.Research PaperIntegrative analysis of transcriptomic profile reveals potential roles of miRNAs in regulating development of ,Marsupenaeus,japonicas[J].Journal of Oceanology and Limnology,2024,42(01):201-215. DOI： 10.1007/s00343-023-2403-3.

摘要

Abstract

Regulation of microRNAs (miRNAs) on various biological processes has been a surprising and exciting field. Identification of miRNAs is the first step to comprehensively understand their functions. However

attempts on global identification and functional verification of miRNAs are very limited in penaeid shrimp

Marsupenaeus

japonicus

an economically important aquatic species. By performing an integrated analysis of transcriptomic profile from gastrula embryos of

japonicus

21 conserved miRNAs in

japonicas

(mja-miRNAs)

belonging to 19 miRNA families

were identified and characterized. Of the 21 mja-miRNAs

15 miRNAs were successfully verified to be predominantly expressed in gastrula stage

where they displayed dynamic e

xpression patterns compared with those in naupliuin stage. Based on perfect or near-perfect match to target region

120 target genes were predicted at transcriptome-wide level. Noteworthy

gene ontology (GO) classification and metabolic pathway annotation revealed eight targets that were actively involved in developmental processes. Of the predicted miRNA-mRNA pairs

six targets were then randomly selected and experimentally validated by dual luciferase reporter assay

where three pairs were proved with potential targeting activity. Overall

to search for conserved miRNAs potentially involved in early development of

japonicus

we combined in silico and experimental methods

which can be applied in other organisms as well. Our data implied important roles of miRNAs in the early embryonic development and also suggested the presence of complex miRNA-mRNA functional networks in

japonicus

关键词

Keywords

references

Abramov R , Fu G D , Zhang Y et al . 2013 . Expression and regulation of miR-17a and miR-430b in zebrafish ovarian follicles . General and Comparative Endocrinology , 188 : 309 - 315 , https://doi.org/10.1016/j.ygcen.2013.02.012 https://doi.org/10.1016/j.ygcen.2013.02.012 .

Adai A , Johnson C , Mlotshwa S et al . 2005 . Computational prediction of miRNAs in Arabidopsis thaliana . Genome Research , 15 ( 1 ): 78 - 91 , https://doi.org/10.1101/gr.2908205 https://doi.org/10.1101/gr.2908205 .

Ambros V . 2004 . The functions of animal microRNAs . Nature , 431 ( 7006 ): 350 - 355 , https://doi.org/10.1038/nature02871 https://doi.org/10.1038/nature02871 .

Ashburner M , Ball C A , Blake J A et al . 2000 . Gene Ontology: tool for the unification of biology . Nature Genetics , 25 ( 1 ): 25 - 29 , https://doi.org/10.1038/75556 https://doi.org/10.1038/75556 .

Barozai M Y K . 2012 . Identification and characterization of the microRNAs and their targets in Salmo salar . Gene , 499 ( 1 ): 163 - 168 , https://doi.org/10.1016/j.gene.2012.03.006 https://doi.org/10.1016/j.gene.2012.03.006 .

Bartel D P . 2004 . MicroRNAs: genomics, biogenesis, mechanism, and function . Cell , 116 ( 2 ): 281 - 297 , https://doi.org/10.1016/s0092-8674(04)00045-5 https://doi.org/10.1016/s0092-8674(04)00045-5 .

Bernstein E , Caudy A A , Hammond S M et al . 2001 . Role for a bidentate ribonuclease in the initiation step of RNA interference . Nature , 409 ( 6818 ): 363 - 366 , https://doi.org/10.1038/35053110 https://doi.org/10.1038/35053110 .

Bizuayehu T T , Babiak J , Norberg B et al . 2012 . Sex-biased miRNA expression in Atlantic halibut ( Hippoglossus hippoglossus ) brain and gonads . Sexual Development , 6 ( 5 ): 257 - 266 , https://doi.org/10.1159/000341378 https://doi.org/10.1159/000341378 .

Brzuzan P , Woźny M , Wolińska L et al . 2010 . MicroRNA expression in liver of whitefish ( Coregonus lavaretus ) exposed to microcystin-LR . Environmental Biotechnology , 6 ( 2 ): 53 - 60 .

Carthew R W , Sontheimer E J . 2009 . Origins and mechanisms of miRNAs and siRNAs . Cell , 136 ( 4 ): 642 - 655 , https://doi.org/10.1016/j.cell.2009.01.035 https://doi.org/10.1016/j.cell.2009.01.035 .

Chen G F , Zhang C Y , Jiang F J et al . 2014 . Bioinformatics analysis of hemocyte miRNAs of scallop Chlamys farreri against acute viral necrobiotic virus (AVNV) . Fish & Shellfish Immunology , 37 ( 1 ): 75 - 86 , https://doi.org/10.1016/j.fsi.2014.01.002 https://doi.org/10.1016/j.fsi.2014.01.002 .

Chi W , Tong C B , Gan X N et al . 2011 . Characterization and comparative profiling of miRNA transcriptomes in bighead carp and silver carp . PLoS One , 6 ( 8 ): e23549 , https://doi.org/10.1371/journal.pone.0023549 https://doi.org/10.1371/journal.pone.0023549 .

Conesa A , Götz S , García-Gómez J M et al . 2005 . Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research . Bioinformatics , 21 ( 18 ): 3674 - 3676 , https://doi.org/10.1093/bioinformaticx/bti610 https://doi.org/10.1093/bioinformaticx/bti610 .

Crooks G E , Hon G , Chandonia J M et al . 2004 . WebLogo: a sequence logo generator . Genome Research , 14 ( 6 ): 1188 - 1190 , https://doi.org/10.1101/gr.849004 https://doi.org/10.1101/gr.849004 .

Denli A M , Tops B B J , Plasterk R H A et al . 2004 . Processing of primary microRNAs by the microprocessor complex . Nature , 432 ( 7014 ): 231 - 235 , https://doi.org/10.1038/nature03049 https://doi.org/10.1038/nature03049 .

Flynt A S , Thatcher E J , Burkewitz K et al . 2009 . miR-8 microRNAs regulate the response to osmotic stress in zebrafish embryos . Journal of Cell Biology , 185 ( 1 ): 115 - 127 , https://doi.org/10.1083/jcb.200807026 https://doi.org/10.1083/jcb.200807026 .

Giraldez A J , Cinalli R M , Glasner M E et al . 2005 . MicroRNAs regulate brain morphogenesis in zebrafish . Science , 308 ( 5723 ): 833 - 838 , https://doi.org/10.1126/science.1109020 https://doi.org/10.1126/science.1109020 .

Götz S , García-Gómez J M , Terol J et al . 2008 . High-throughput functional annotation and data mining with the Blast2GO suite . Nucleic Acids Research , 36 ( 10 ): 3420 - 3435 , https://doi.org/10.1093/nar/gkn176 https://doi.org/10.1093/nar/gkn176 .

Grabherr M G , Haas B J , Yassour M et al . 2011 . Full-length transcriptome assembly from RNA-Seq data without a reference genome . Nature Biotechnology , 29 ( 7 ): 644 - 652 , https://doi.org/10.1038/nbt.1883 https://doi.org/10.1038/nbt.1883 .

Guo H , Lu Z C , Zhu X W et al . 2018 . Differential expression of microRNAs in hemocytes from white shrimp Litopenaeus vannamei under copper stress . Fish & Shellfish Immunology , 74 : 152 - 161 , https://doi.org/10.1016/j.fsi.2017.12.053 https://doi.org/10.1016/j.fsi.2017.12.053 .

Haas B J , Papanicolaou A , Yassour M et al . 2013 . De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis . Nature Protocols , 8 ( 8 ): 1494 - 1512 , https://doi.org/10.1038/nprot.2013.084 https://doi.org/10.1038/nprot.2013.084 .

Han Q , Li P T , Lu X B et al . 2013 . Improved primary cell culture and subculture of lymphoid organs of the greasyback shrimp Metapenaeus ensis . Aquaculture , 410 - 411 : 101 - 113 , https://doi.org/10.1016/j.aquaculture.2013.06.024 https://doi.org/10.1016/j.aquaculture.2013.06.024 .

He L , Wang Y L , Li Q et al . 2015 . Profiling microRNAs in the testis during sexual maturation stages in Eriocheir sinensis . Animal Reproduction Science , 162 : 52 - 61 , https://doi.org/10.1016/j.anireprosci.2015.09.008 https://doi.org/10.1016/j.anireprosci.2015.09.008 .

He Y Y , Li Z X , Zhang H E et al . 2019 . Genome-wide identification of Chinese shrimp ( Fenneropenaeus chinensis ) microRNA responsive to low pH stress by deep sequencing . Cell Stress and Chaperones , 24 ( 4 ): 689 - 695 , https://doi.org/10.1007/s12192-019-00989-x https://doi.org/10.1007/s12192-019-00989-x .

He Z H , Zhong Y Q , Hou D Q et al . 2022 . Integrated analysis of mRNA-seq and miRNA-seq reveals the molecular mechanism of the intestinal immune response in Marsupenaeus japonicus under decapod iridescent virus 1 infection . Frontiers in Immunology , 12 : 807093 , https://doi.org/10.3389/fimmu.2021.807093 https://doi.org/10.3389/fimmu.2021.807093 .

Hofacker I L . 2003 . Vienna RNA secondary structure server . Nucleic Acids Research , 31 ( 13 ): 3429 - 3431 , https://doi.org/10.1093/nar/gkg599 https://doi.org/10.1093/nar/gkg599 .

Huang T Z , Xu D D , Zhang X B . 2012 . Characterization of host microRNAs that respond to DNA virus infection in a crustacean . BMC Genomics , 13 : 159 , https://doi.org/10.1186/1471-2164-13-159 https://doi.org/10.1186/1471-2164-13-159 .

John B , Enright A J , Aravin A et al . 2004 . Human microRNA targets . PLoS Biology , 2 ( 11 ): e363 , https://doi.org/10.1371/journal.pbio.0020363 https://doi.org/10.1371/journal.pbio.0020363 .

Kanehisa M , Goto S . 2000 . KEGG: kyoto encyclopedia of genes and genomes . Nucleic Acids Research , 28 ( 1 ): 27 - 30 , https://doi.org/10.1093/nar/28.1.27 https://doi.org/10.1093/nar/28.1.27 .

Kanoksinwuttipong N , Jaree P , Somboonwiwat K . 2022 . Shrimp pmo-miR-750 regulates the expression of sarcoplasmic calcium-binding protein facilitating virus infection in Penaeus monodon . Fish & Shellfish Immunology , 129 : 74 - 84 , https://doi.org/10.1016/j.fsi.2022.08.046 https://doi.org/10.1016/j.fsi.2022.08.046 .

Kapsimali M , Kloosterman W P , de Bruijn E et al . 2007 . MicroRNAs show a wide diversity of expression profiles in the developing and mature central nervous system . Genome Biology , 8 ( 8 ): R173 , https://doi.org/10.1186/gb-2007-8-8-r173 https://doi.org/10.1186/gb-2007-8-8-r173 .

Kenny N J , Namigai E K O , Marlétaz F et al . 2015 . Draft genome assemblies and predicted microRNA complements of the intertidal lophotrochozoans Patella vulgata (Mollusca, Patellogastropoda) and Spirobranchus ( Pomatoceros ) lamarcki (Annelida, Serpulida) . Marine Genomics , 24 : 139 - 146 , https://doi.org/10.1016/j.margen.2015.07.004 https://doi.org/10.1016/j.margen.2015.07.004 .

Kloosterman W P , Steiner F A , Berezikov E et al . 2006 . Cloning and expression of new microRNAs from zebrafish . Nucleic Acids Research , 34 ( 9 ): 2558 - 2569 , https://doi.org/10.1093/nar/gkl278 https://doi.org/10.1093/nar/gkl278 .

Lai E C , Tomancak P , Williams R W et al . 2003 . Computational identification of Drosophila microRNA genes . Genome Biology , 4 ( 7 ): R42 , https://doi.org/10.1186/gb-2003-4-7-r42 https://doi.org/10.1186/gb-2003-4-7-r42 .

Laity J H , Lee B M , Wright P E . 2001 . Zinc finger proteins: new insights into structural and functional diversity . Current Opinion in Structural Biology , 11 ( 1 ): 39 - 46 , https://doi.org/10.1016/s0959-440x(00)00167-6 https://doi.org/10.1016/s0959-440x(00)00167-6 .

Li P T , Wang Y H , Wang Y J et al . 2017a . Whole transcriptome sequencing and analysis of gastrula embryos of Marsupenaeus japonicus (Bate, 1888) . Madridge Journal of Aquaculture Research & Development , 1 ( 1 ): 1 - 7 , https://doi.org/10.18689/mjard-1000101 https://doi.org/10.18689/mjard-1000101 .

Li S K , Zhu S , Li C B et al . 2013 . Characterization of microRNAs in mud crab Scylla paramamosain under Vibrio parahaemolyticus infection . PLoS One , 8 ( 8 ): e73392 , https://doi.org/10.1371/journal.pone.0073392 https://doi.org/10.1371/journal.pone.0073392 .

Li X P , Meng X H , Luo K et al . 2017b . The identification of microRNAs involved in the response of Chinese shrimp Fenneropenaeus chinens is to white spot syndrome virus infection . Fish & Shellfish Immunology , 68 : 220 - 231 , https://doi.org/10.1016/j.fsi.2017.05.060 https://doi.org/10.1016/j.fsi.2017.05.060 .

Li Y D , Zhou F L , Huang J H et al . 2020 . Transcriptome and miRNA profiles of black tiger shrimp, Penaeus monodon , under different salinity conditions . Frontiers in Marine Science , 7 : 579381 , https://doi.org/10.3389/fmars.2020.579381 https://doi.org/10.3389/fmars.2020.579381 .

Li Z X , Wang J Y , He Y Y et al . 2019 . Comprehensive identification and profiling of Chinese shrimp ( Fenneropenaeus chinensis ) microRNAs in response to high pH stress using Hiseq2000 sequencing . Aquaculture Research , 50 ( 11 ): 3154 - 3162 , https://doi.org/10.1111/are.14269 https://doi.org/10.1111/are.14269 .

Lizé M , Klimke A , Dobbelstein M . 2011 . MicroRNA-449 in cell fate determination . Cell Cycle , 10 ( 17 ): 2874 - 2882 , https://doi.org/10.4161/cc.10.17.17181 https://doi.org/10.4161/cc.10.17.17181 .

Lund E , Güttinger S , Calado A et al . 2004 . Nuclear export of microRNA precursors . Science , 303 ( 5654 ): 95 - 98 , https://doi.org/10.1126/science.1090599 https://doi.org/10.1126/science.1090599 .

Lv J J , Liu P , Gao B Q et al . 2016 . The identification and characteristics of salinity-related microRNAs in gills of Portunus trituberculatus . Cell Stress and Chaperones , 21 ( 1 ): 63 - 74 , https://doi.org/10.1007/s12192-015-0641-9 https://doi.org/10.1007/s12192-015-0641-9 .

Martín-Gómez L , Villalba A , Kerkhoven R H et al . 2014 . Role of microRNAs in the immunity process of the flat oyster Ostrea edulis against bonamiosis . Infection, Genetics and Evolution , 27 : 40 - 50 , https://doi.org/10.1016/j.meegid.2014.06.026 https://doi.org/10.1016/j.meegid.2014.06.026 .

Millard R S , Bickley L K , Bateman K S et al . 2021 . Global mRNA and miRNA analysis reveal key processes in the initial response to infection with WSSV in the pacific whiteleg shrimp . Viruses , 13 ( 6 ): 1140 , https://doi.org/10.3390/v13061140 https://doi.org/10.3390/v13061140 .

Miller J , McLachlan A D , Klug A . 1985 . Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes . The EMBO Journal , 4 ( 6 ): 1609 - 1614 , https://doi.org/10.1002/j.1460-2075.1985.tb03825.x https://doi.org/10.1002/j.1460-2075.1985.tb03825.x .

Mortazavi A , Williams B A , McCue K et al . 2008 . Mapping and quantifying mammalian transcriptomes by RNA-Seq . Nature Methods , 5 ( 7 ): 621 - 628 , https://doi.org/10.1038/nmeth.1226 https://doi.org/10.1038/nmeth.1226 .

Ordas A , Kanwal Z , Lindenberg V et al . 2013 . MicroRNA-146 function in the innate immune transcriptome response of zebrafish embryos to Salmonella typhimurium infection . BMC Genomics , 14 ( 1 ): 696 , https://doi.org/10.1186/1471-2164-14-696 https://doi.org/10.1186/1471-2164-14-696 .

Ou J T , Liu Q , Bian Y X et al . 2022a . Integrated analysis of mRNA and microRNA transcriptome related to immunity and autophagy in shrimp hemocytes infected with Spiroplasma eriocheiris . Fish & Shellfish Immunology , 130 : 436 - 452 , https://doi.org/10.1016/j.fsi.2022.09.035 https://doi.org/10.1016/j.fsi.2022.09.035 .

Ou J T , Chen H , Luan X Q et al . 2022b . Leveraging lncRNA-miRNA-mRNA network to reveal anti- Spiroplasma eriocheiris infection mechanisms in Macrobrachium nipponense . Aquaculture , 557 : 738286 , https://doi.‍org/10.1016/j.aquaculture.2022.738286 https://doi.‍org/10.1016/j.aquaculture.2022.738286 .

Pu L J , Wang J , Wang Y et al . 2018 . Computational identification and characterization of microRNAs and their targets in Penaeus monodon . Journal of Oceanology and Limnology , 36 ( 3 ): 853 - 869 , https://doi.org/10.1007/s00343-018-6348-x https://doi.org/10.1007/s00343-018-6348-x .

Ramachandra R K , Salem M , Gahr S et al . 2008 . Cloning and characterization of microRNAs from rainbow trout ( Oncorhynchus mykiss ): their expression during early embryonic development . BMC Developmental Biology , 8 ( 1 ): 41 , https://doi.org/10.1186/1471-213X-8-41 https://doi.org/10.1186/1471-213X-8-41 .

Ramachandran R , Fausett B V , Goldman D . 2010 . Ascl1a regulates Müller glia dedifferentiation and retinal regeneration through a Lin-28-dependent, let-7 microRNA signalling pathway . Nature Cell Biology , 12 ( 11 ): 1101 - 1107 , https://doi.org/10.1038/ncb2115 https://doi.org/10.1038/ncb2115 .

Ruan L W , Bian X F , Ji Y C et al . 2011 . Isolation and identification of novel microRNAs from Marsupenaeus japonicus . Fish & Shellfish Immunology , 31 ( 2 ): 334 - 340 , https://doi.org/10.1016/j.fsi.2011.05.023 https://doi.org/10.1016/j.fsi.2011.05.023 .

Sha Z X , Gong G Y , Wang S L et al . 2014 . Identification and characterization of Cynoglossus semilaevis microRNA response to Vibrio anguillarum infection through high-throughput sequencing . Developmental & Comparative Immunology , 44 ( 1 ): 59 - 69 , https://doi.org/10.1016/j.dci.2013.11.014 https://doi.org/10.1016/j.dci.2013.11.014 .

Ünlü E S , Gordon D M , Telli M . 2015 . Small RNA sequencing based identification of miRNAs in Daphnia magna . PLoS One , 10 ( 9 ): e0137617 , https://doi.‍org/10.1371/journal.pone.0137617 https://doi.‍org/10.1371/journal.pone.0137617 . https://do 10.1371/journal.pone.0137617 http://dx.doi.org/10.1371/journal.pone.0137617

Wan L C , Zhang H Y , Lu S F et al . 2012 . Transcriptome-wide identification and characterization of miRNAs from Pinus densata . BMC Genomics , 13 ( 1 ): 132 , https://doi.org/10.1186/1471-2164-13-132 https://doi.org/10.1186/1471-2164-13-132 .

Wang J Y , Yang X D , Xu H B et al . 2012a . Identification and characterization of microRNAs and their target genes in Brassica oleracea . Gene , 505 ( 2 ): 300 - 308 , https://doi.org/10.1016/j.gene.2012.06.002 https://doi.org/10.1016/j.gene.2012.06.002 .

Wang M , Wang Q L , Wang B M . 2012b . Identification and characterization of microRNAs in Asiatic cotton ( Gossypium arboretum L .). PLoS One , 7 ( 4 ): e33696 , https://doi.org/10.1371/journal.pone.0033696 https://doi.org/10.1371/journal.pone.0033696 .

Wang W , Zhong P , Yi J Q et al . 2019 . Potential role for microRNA in facilitating physiological adaptation to hypoxia in the Pacific whiteleg shrimp Litopenaeus vannamei . Fish & Shellfish Immunology , 84 : 361 - 369 , https://doi.org/10.1016/j.fsi.2018.09.079 https://doi.org/10.1016/j.fsi.2018.09.079 .

Wang Z L , Feng Y Y , Li J Y et al . 2020 . Integrative microRNA and mRNA analysis reveals regulation of ER stress in the Pacific white shrimp Litopenaeus vannamei under acute cold stress . Comparative Biochemistry and Physiology Part D: Genomics and Proteomics , 33 : 100645 , https://doi.org/10.1016/j.cbd.2019.100645 https://doi.org/10.1016/j.cbd.2019.100645 .

Wienholds E , Kloosterman W P , Miska E et al . 2005a . MicroRNA expression in zebrafish embryonic development . Science , 309 ( 5732 ): 310 - 311 , https://doi.org/10.1126/science.1114519 https://doi.org/10.1126/science.1114519 .

Wienholds E , Plasterk R H A . 2005b . MicroRNA function in animal development . FEBS Letters , 579 ( 26 ): 5911 - 5922 , https://doi.org/10.1016/j.febslet.2005.07.070 https://doi.org/10.1016/j.febslet.2005.07.070 .

Xiao J , Zhong H , Zhou Y et al . 2014 . Identification and characterization of microRNAs in ovary and testis of Nile tilapia ( Oreochromis niloticus ) by using solexa sequencing technology . PLoS One , 9 ( 1 ): e86821 , https://doi.org/10.1371/journal.pone.0086821 https://doi.org/10.1371/journal.pone.0086821 .

Xie C X , Xu S L , Yang L L et al . 2011 . mRNA/microRNA profile at the metamorphic stage of olive flounder ( Paralichthys olivaceus ) . Comparative and Functional Genomics , 2011 : 256038 , https://doi.org/10.1155/2011/256038 https://doi.org/10.1155/2011/256038 .

Xu Z Q , Qin Q , Ge J C et al . 2012 . Bioinformatic identification and validation of conservative microRNAs in Ictalurus punctatus . Molecular Biology Reports , 39 ( 12 ): 10395 - 10405 , https://doi.org/10.1007/s11033-012-1918-z https://doi.org/10.1007/s11033-012-1918-z .

Yan B , Zhao L H , Guo J T et al . 2012 . miR-429 regulation of osmotic stress transcription factor 1 (OSTF1) in tilapia during osmotic stress . Biochemical and Biophysical Research Communications , 426 ( 3 ): 294 - 298 , https://doi.org/10.1016/j.bbrc.2012.08.029 https://doi.org/10.1016/j.bbrc.2012.08.029 .

Yin Z J , Li C H , Han X L et al . 2008 . Identification of conserved microRNAs and their target genes in tomato ( Lycopersicon esculentum ) . Gene , 414 ( 1-2 ): 60 - 66 , https://doi.org/10.1016/j.gene.2008.02.007 https://doi.org/10.1016/j.gene.2008.02.007 .

Yu X , Wang H , Lu Y Z et al . 2012 . Identification of conserved and novel microRNAs that are responsive to heat stress in Brassica rapa . Journal of Experimental Botany , 63 ( 2 ): 1025 - 1038 , https://doi.‍org/10.1093/jxb/err337 https://doi.‍org/10.1093/jxb/err337 . https://do 10.1093/jxb/err337 http://dx.doi.org/10.1093/jxb/err337

Zeng Y , Cullen B R . 2005 . Efficient processing of primary microRNA hairpins by DROSHA requires flanking nonstructured RNA sequences . Journal of Biological Chemistry , 280 ( 30 ): 27595 - 27603 , https://doi.org/10.1074/jbc.M504714200 https://doi.org/10.1074/jbc.M504714200 .

Zhang B H , Pan X P , Anderson T A . 2006a . Identification of 188 conserved maize microRNAs and their targets . FEBS Letters , 580 ( 15 ): 3753 - 3762 , https://doi.org/10.1016/j.febslet.2006.05.063 https://doi.org/10.1016/j.febslet.2006.05.063 .

Zhang B H , Pan X P , Cox S B et al . 2006b . Evidence that miRNAs are different from other RNAs . Cellular and Molecular Life Sciences , 63 ( 2 ): 246 - 254 , https://doi.org/10.1007/s00018-005-5467-7 https://doi.org/10.1007/s00018-005-5467-7 .

Zhang P J , Li C H , Shao Y N et al . 2014 . Identification and characterization of miR-92a and its targets modulating Vibrio splendidus challenged Apostichopus japonicus . Fish & Shellfish Immunology , 38 ( 2 ): 383 - 388 , https://doi.org/10.1016/j.fsi.2014.04.007 https://doi.org/10.1016/j.fsi.2014.04.007 .

Zhang Z , Schwartz S , Wagner L et al . 2000 . A greedy algorithm for aligning DNA sequences . Journal of Computational Biology , 7 ( 1-2 ): 203 - 214 , https://doi.org/10.1089/10665270050081478 https://doi.org/10.1089/10665270050081478 .

Zheng J B , Cao J W , Mao Y et al . 2018 . Identification of microRNAs with heat stress responsive and immune properties in Marsupenaeus japonicus based on next-generation sequencing and bioinformatics analysis: essential regulators in the heat stress-host interactions . Fish & Shellfish Immunology , 81 : 390 - 398 , https://doi.org/10.1016/j.fsi.2018.05.030 https://doi.org/10.1016/j.fsi.2018.05.030 .

Zhou Z , Wang L L , Song L S et al . 2014 . The identification and characteristics of immune-related microRNAs in haemocytes of oyster Crassostrea gigas . PLoS One , 9 ( 2 ): e88397 , https://doi.org/10.1371/journal.pone.0088397 https://doi.org/10.1371/journal.pone.0088397 .

Zhu F , Wang Z , Sun B Z . 2016 . Differential expression of microRNAs in shrimp Marsupenaeus japonicus in response to Vibrio alginolyticus infection . Developmental & Comparative Immunology , 55 : 76 - 79 , https://doi.org/10.1016/j.dci.2015.10.012 https://doi.org/10.1016/j.dci.2015.10.012 .

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DOI：10.1007/s00343-023-2403-3

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