Full-Length Transcriptomes and Sex-Based Differentially Expressed Genes in the Brain and Ganglia of Giant River Prawn Macrobrachium rosenbergii

Dong Liu; Zhenzhen Hong; Lang Gui; Li Zhao; Yude Wang; Shengming Sun; Mingyou Li

doi:10.3390/biom13030460

Full-Length Transcriptomes and Sex-Based Differentially Expressed Genes in the Brain and Ganglia of Giant River Prawn Macrobrachium rosenbergii

Biomolecules. 2023 Mar 2;13(3):460. doi: 10.3390/biom13030460.

Authors

Dong Liu^{1

2

3}, Zhenzhen Hong^{1

2

3}, Lang Gui², Li Zhao^{1

2}, Yude Wang⁴, Shengming Sun², Mingyou Li^{1

2}

Affiliations

¹ Key Laboratory of Integrated Rice-Fish Farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China.
² Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China.
³ Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China.
⁴ State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, China.

Abstract

Macrobrachium rosenbergii is an important aquaculture prawn that exhibits sexual dimorphism in growth, with males growing much faster than females. However, the mechanisms controlling these complex traits are not well understood. The nervous system plays an important role in regulating life functions. In the present work, we applied PacBio RNA-seq to obtain and characterize the full-length transcriptomes of the brains and thoracic ganglia of female and male prawns, and we performed comparative transcriptome analysis of female and male prawns. A total of 159.1-Gb of subreads were obtained with an average length of 2175 bp and 93.2% completeness. A total of 84,627 high-quality unigenes were generated and annotated with functional databases. A total of 6367 transcript factors and 6287 LncRNAs were predicted. In total, 5287 and 6211 significantly differentially expressed genes (DEGs) were found in the brain and thoracic ganglion, respectively, and confirmed by qRT-PCR. Of the 435 genes associated with protein processing pathways in the endoplasmic reticula, 42 DEGs were detected, and 21/26 DEGs with upregulated expression in the male brain/thoracic ganglion. The DEGs in this pathway are regulated by multiple LncRNAs in polypeptide folding and misfolded protein degradation in the different organs and sexes of the prawn. Our results provide novel theories and insights for studying the nervous system, sexual control, and growth dimorphism.

Keywords: LncRNA; RNA-seq; gene; prawn; signal pathway.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Brain
Female
Ganglia
Male
Palaemonidae* / genetics
Penaeidae*
RNA, Long Noncoding* / genetics
RNA, Long Noncoding* / metabolism
Transcriptome / genetics

Substances

RNA, Long Noncoding

Grants and funding

This research was funded by the Science and Technology Innovation Action Plan of the Science and Technology Commission of Shanghai Municipality (21015801200) and the State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China (2020KF002).