References
Abdel-Ghany SE, Hamilton M, Jacobi JL, et al. (2016) A survey of the sorghum transcriptome using single-molecule long reads. Nature Communications 7 .
Anders S HW (2012) Differential expression of RNA-Seq data at the gene level – the DESeq package.Heidelberg, Germany: European Molecular Biology Laboratory (EMBL) , 1-24.
Arendt D, Tosches MA, Marlow H (2016) From nerve net to nerve ring, nerve cord and brain - evolution of the nervous system. Nature Reviews Neuroscience 17 , 61-72.
Bairoch A, Bougueleret L, Altairac S, Amendolia V, Zhang J (2010) The Universal Protein Resource (UniProt) 2009. Nucleic acids research 37 , D169-D174.
Ballar P, Zhong Y, Nagahama M, et al. (2007) Identification of SVIP as an endogenous inhibitor of endoplasmic reticulum-associated degradation. Journal of Biological Chemistry 282 , 33908-33914.
Beier S, Thiel T, Munch T, Scholz U, Mascher M (2017) MISA-web: a web server for microsatellite prediction.Bioinformatics 33 , 2583-2585.
Bobkova NV, Poltavtseva RA, Leonov SV, Sukhikh GT (2020) Neuroregeneration: Regulation in Neurodegenerative Diseases and Aging. Biochemistry-Moscow 85 , 108-130.
Chen XF, Yang GL, Kong J, et al. (2012) Effect of artificial culture and selective breeding on the genetic diversity of Macrobrachium rosenbergii. Acta Hydrobiologica Sinica 36 , 866-873.
Chen Y, Zhou J (2017) LncRNAs: macromolecules with big roles in neurobiology and neurological diseases.Metabolic Brain Disease 32 , 281-291.
FAO (2022) The State of World Fisheries and Aquaculture 2022, Towards Blue Transformation FAO, Rome.
Feng X, Guan N, Xu ES, Miao Y, Li CG (2021) Transcription Factors Leading to High Expression of Neuropeptide L1CAM in Brain Metastases from Lung Adenocarcinoma and Clinical Prognostic Analysis. Disease Markers 2021 .
Forouhan M, Lim WF, Zanetti-Domingues LC, et al. (2022) AR cooperates with SMAD4 to maintain skeletal muscle homeostasis. Acta Neuropathologica 143 , 713-731.
Fu LM, Niu BF, Zhu ZW, Wu ST, Li WZ (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28 , 3150-3152.
Ghafouri-Fard S, Najafi S, Hussen BM, et al. (2022) DLX6-AS1: A Long Non-coding RNA With Oncogenic Features. Frontiers in Cell and Developmental Biology10 .
Hu H, Miao YR, Jia LH, et al.(2019) AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors. Nucleic acids research 47 , D33-D38.
Hu X, Chen W, Li J, et al.(2018) ZFLNC: a comprehensive and well-annotated database for zebrafish lncRNA. Database-the Journal of Biological Databases and Curation .
Jayasankar V, Tomy S, Wilder MN (2020) Insights on Molecular Mechanisms of Ovarian Development in Decapod Crustacea: Focus on Vitellogenesis-Stimulating Factors and Pathways. Frontiers in Endocrinology 11 .
Kanehisa M, Goto S, Kawashima S, Nakaya A, S,, S. K. (2000) KEGG: kyoto encyclopaedia of genes and genomes. Nucleic acids research volume 28 , 27-30.
Kang YJ, Yang DC, Kong L, et al. (2017) CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features. Nucleic acids research45 , W12-W16.
Kelley D, Rinn J (2012) Transposable elements reveal a stem cell-specific class of long noncoding RNAs.Genome Biology 13 .
Khan S (2022) Endoplasmic Reticulum in Metaplasticity: From Information Processing to Synaptic Proteostasis.Molecular Neurobiology 59 , 5630-5655.
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nature Methods 9 , 357-U354.
Levy T, Rosen O, Manor R, et al. (2019) Production of WW males lacking the masculine Z chromosome and mining the Macrobrachium rosenbergii genome for sex-chromosomes.Scientific reports 9 .
Li AM, Zhang JY, Zhou ZY (2014) PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme. BMC Bioinformatics 15 .
Liao JY (2001) The Morphology and Structure of the Brain of the Prawn,Macrobrachium rosenbergii (Crustacea:Decapoda). Acta Scientiarum Naturalium Universitatis Sunyatseni 40 , 85-88.
Liao JY, Zhang YF, Sun JX, Lin YA (2001) Partial isolation and bioassay of gonad-stimulating hormone from the brain of Macrobrachium rosenbergii. JOURNAL OF FISHERIES OF CHINA 25 , 5-10.
Liu D, Yang JQ, Tang WQ, et al. (2020) SINE Retrotransposon variation drives Ecotypic disparity in natural populations of Coilia nasus. Mobile Dna 11 .
Liu X, Ma KY, Liu ZQ, et al.(2019) Transcriptome analysis of the brain of the Chinese mitten crab, Eriocheir sinensis, for neuropeptide abundance profiles during ovarian development. Animal Reproduction Science 201 , 63-70.
Ma KY, Yu SH, Du YX, et al.(2019) Construction of a Genomic Bacterial Artificial Chromosome (BAC) Library for the Prawn Macrobrachium rosenbergii and Initial Analysis of ZW Chromosome-Derived BAC Inserts. Marine Biotechnology21 , 206-216.
Ministry of Agriculture and Rural Affairs, National Fisheries Technology Extension Center, China Society of Fisheries (2020) China Fishery Statistical Yearbook China Agriculture Press, Beijing.
Mistry J, Chuguransky S, Williams L, et al. (2021) Pfam: The protein families database in 2021.Nucleic acids research 49 , D412-D419.
Mohamed KS, Diwan AD (1991) Neuroendocrine regulation of ovarian maturation in the Indian white prawn Penaeus indicus H. Milne Edwards. Aquaculture 98 , 381-393.
Morro B, Broughton R, Balseiro P, et al. (2021) Endoplasmic reticulum stress as a key mechanism in stunted growth of seawater rainbow trout (Oncorhynchus mykiss).BMC genomics 22 .
Necsulea A, Soumillon M, Warnefors M, et al. (2014) The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature 505 , 635-+.
Nufer O, Kappeler F, Guldbrandsen S, Hauri HP (2003) ER export of ERGIC-53 is controlled by cooperation of targeting determinants in all three of its domains. Journal of Cell Science 116 , 4429-4440.
Qian TM, Qiao PP, Lu YN, Wang HK (2022) Transcription factor SS18L1 regulates the proliferation, migration and differentiation of Schwann cells in peripheral nerve injury. Frontiers in Veterinary Science 9 .
Roach NP, Sadowski N, Alessi AF, et al. (2020) The full-length transcriptome of C. elegans using direct RNA sequencing. Genome research 30 , 299-312.
Roberts A, Pachter L (2013) Streaming fragment assignment for real-time analysis of sequencing experiments.Nature Methods 10 , 71-U99.
Rowlerson A, Radaelli G, Mascarello F, Veggetti A (1997) Regeneration of skeletal muscle in two teleost fish: Sparus aurata and Brachydanio rerio. Cell and Tissue Research 289 , 311-322.
Santos CA, Andrade SCS, Teixeira AK, et al. (2021) Transcriptome differential expression analysis reveals the activated genes in Litopenaeus vannamei shrimp families of superior growth performance. Aquaculture 531 .
Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.Bioinformatics 31 , 3210-3212.
Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27 , 431-432.
Sun L, Luo HT, Bu DC, et al.(2013) Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic acids research 41 .
Tan K, Jiang HG, Jiang D, Wang W (2020) Sex reversal and the androgenic gland (AG) in Macrobrachium rosenbergii : A review. Aquaculture and Fisheries 5 , 283-288.
van de Weijer ML, Bassik MC, Luteijn RD, et al. (2014) A high-coverage shRNA screen identifies TMEM129 as an E3 ligase involved in ER-associated protein degradation.Nature Communications 5 .
Vedula P, Kashina A (2018) The makings of the ’actin code’: regulation of actin’s biological function at the amino acid and nucleotide level. Journal of Cell Science131 .
Wang ZK, Luan S, Meng XH, et al. (2019) Comparative transcriptomic characterization of the eyestalk in Pacific white shrimp (Litopenaeus vannamei) during ovarian maturation. General and Comparative Endocrinology 274 , 60-72.
Wyganowska-Swiatkowska M, Urbaniak P, Nohawica MM, Kotwicka M, Jankun J (2015) Enamel matrix proteins exhibit growth factor activity: A review of evidence at the cellular and molecular levels. Experimental and Therapeutic Medicine9 , 2025-2033.
Xia J, Liu D, Zhou WZ, et al.(2022) Comparative transcriptome analysis of brain and gonad reveals reproduction-related miRNAs in the giant prawn, Macrobrachium rosenbergii. Frontiers in Genetics 13 .
Xian HP, Zhuo ZL, Sun YJ, Liang B, Zhao XT (2018) Circulating long non-coding RNAs HULC and ZNFX1-AS1 are potential biomarkers in patients with gastric cancer. Oncology Letters 16 , 4689-4698.
Yan BL, Xue B, Zhao L, Gao H (2016) Progress on the research of the growth-related genes in crustaceans.Transactions of Oceanology and Limnology 4 , 97-104.
Yang G, Lu ZJ, Qin ZD, et al.(2020) Insight into the Regulatory Relationships between the Insulin-Like Androgenic Gland Hormone Gene and the Insulin-Like Androgenic Gland Hormone-binding Protein Gene in Giant Freshwater Prawns (Macrobrachium rosenbergii). International journal of molecular sciences 21 .
Yuan WL, Jiang SW, Sun D, et al. (2019) Transcriptome profiling analysis of sex-based differentially expressed mRNAs and lncRNAs in the brains of mature zebrafish (Danio rerio). BMC genomics 20 .
Yutaka K, Noriko Y, Yuichi K, Takeshi O (2022) Effect of co-overexpression of the cargo receptor ERGIC-53/MCFD2 on antibody production and intracellular IgG secretion in recombinant Chinese hamster ovary cells. Journal of bioscience and bioengineering 22 , 190-196.
Zhang XJ, Yuan JB, Sun YM, et al. (2019) Penaeid shrimp genome provides insights into benthic adaptation and frequent molting. Nature Communications10 .