Comparative Transcriptome Analysis of Gonads for the Identification of Sex-Related Genes in Giant Freshwater Prawns (Macrobrachium Rosenbergii) Using RNA Sequencing

Jiang, Jianping; Yuan, Xiang; Qingqing, Qiu; Huang, Guanghua; Jiang, Qinyang; Fu, Penghui; Zhang, Yu; Jia, Yinhai; Yang, Xiurong; Jiang, Hesheng

doi:10.3390/genes10121035

Cited by 25 publications

(14 citation statements)

References 74 publications

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“…Nucleotide excision repair, DNA replication and homologous recombination were the three most enriched KEGG pathways from the gonads, illustrating that the gonads affect the growth and development of GFP principally through regulating gene expression. However, the most enriched KEGG pathways identified in this study differ from those reported by earlier studies (Jiang, Yuan, et al., 2019; Jiang, Min, et al., 2019). We thus believe that growth‐related signalling pathways are not limited to what we have herein discovered; there are still many aspects that remain unexplored and therefore unknown.…”

Section: Discussioncontrasting

confidence: 99%

“…Jiang, Yuan, et al. (2019) identified 23 putative sex‐related genes in GFPs and reported valuable data pertaining to molecular mechanisms underlying gonadal development and sex determination. They also investigated the functions of some genes, providing insights into the regulation mechanism of ovarian maturation.…”

Section: Discussionmentioning

confidence: 99%

“…As a pivotal tool to study biological/physiological mechanisms, transcriptome analyses can facilitate the identification of differentially expressed genes (DEGs) according to the different growth characteristics of GFPs, help screen key genes involved in pertinent growth pathways and help comprehensively elucidate the growth regulation mechanisms of GFPs. In GFPs, de novo transcriptome sequencing analysis has been previously used, for example, for comparison of DEGs between small‐ and big‐sized individuals (Nguyen Thanh, Zhao, & Liu, 2014), identification of genes and markers associated with reproduction (Jung et al., 2016), detection of genes involved in ovarian maturation (Jiang, Yuan, et al., 2019) and identification of genes potentially affecting social dominance hierarchy in adult males (Aziz et al., 2017).…”

Section: Introductionmentioning

confidence: 99%

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Identification of differentially expressed genes and signalling pathways to elucidate molecular mechanisms underlying growth differences among the male morphotypes of Macrobrachium rosenbergii

Tang

Xia²,

Cai³

et al. 2020

Aquac Res

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The giant freshwater prawn (GFP) Macrobrachium rosenbergii is an economically important aquaculture species in China. In culture, it is common for males to show unique morphotypes, which exhibit distinct heterogenous individual growth. Little information is currently available on the molecular mechanisms underlying growth differences among male morphotypes of GFPs. Thus, we herein aimed to identify key genes and signalling pathways to elucidate molecular mechanisms underlying growth differences among the male morphotypes of GFPs. We performed transcriptome analyses using RNA‐Seq to compare the following male morphotypes of GFPs: orange claw males, old blue claw males and small males. In total, 97.44 Gb clean data were obtained, and 1,857,760 unigenes were annotated by alignment with public protein databases. Moreover, we found 2,072 and 22,431 differentially expressed genes (DEGs) from the eyestalk and gonads respectively. Gene ontology analyses revealed that ‘system process’ and ‘multicellular organismal process’ were the most enriched in the eyestalk and gonad tissue samples respectively. Furthermore, Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that pathways associated with gene regulation may play a key role in GFP growth. To summarize, this study provides a valuable repository of novel transcripts for various male morphotypes of GFPs and gives further insights into the molecular mechanisms underlying growth differences in GFPs, which should promote the breeding of commercially cultivated GFPs.

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Section: Discussioncontrasting

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Identification of differentially expressed genes and signalling pathways to elucidate molecular mechanisms underlying growth differences among the male morphotypes of Macrobrachium rosenbergii

Tang

Xia²,

Cai³

et al. 2020

Aquac Res

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“…It is spliced in the absence of the female Tra/Tra-2 complex, carried out by non-sex-specific splicing machinery ( 21 , 37 , 38 ). Nevertheless, Fru showed sexual dimorphism in ovaries and testis, which displayed upregulated expression in ovaries of M. rosenbergii in the comparative transcriptomic database of gonads ( 42 ).…”

Section: Discussionmentioning

confidence: 99%

Full Functional Sex Reversal Achieved Through Silencing of MroDmrt11E Gene in Macrobrachium rosenbergii: Production of All-Male Monosex Freshwater Prawn

Chen

Wang

et al. 2022

Front. Endocrinol.

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The freshwater prawn Macrobrachium rosenbergii is one kind of important economic aquaculture species and displays remarkable sexual dimorphism. The molecular mechanism of sexual differentiation in M. rosenbergii has been primarily unraveled through the research efforts of the androgenic gland and its related genes. However, the understanding of conserved genes involved in the molecular mechanism underpinning sex determination and sexual differentiation of M. rosenbergii is still fragmentary. MroDmrt11E is a member of the doublesex and mab-3-related transcription factor (Dmrt) gene family and is prominently expressed in the testis. In the present study, in vivo knockdown of MroDmrt11E at the postlarva stage in male prawn induced a complete and functional sex reversal and achieved the production of an all-male monosex population. Furthermore, a great deal of new information of upregulated and downregulated transcriptions involved in sexual differentiation of MroDmrt11E knockdown was enriched by comparative transcriptomic analysis. The effects of RNAi-mediated gene knockdown of MroDmrt11E on the differentially expressed and sex-related candidate genes, such as transformer, fruitless, feminization, insulin-like androgenic gland gene, Dmrt gene family, were primarily focused on, and their possible molecular regulatory relationships in sexual differentiation were analyzed. Meanwhile, the response of primary Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathways was investigated to expound the potential roles of MroDmrt11E in male sexual differentiation, which provided a deeper understanding of the molecular regulatory network underlying sexual differentiation of M. rosenbergii. The finding provided a novel sexual manipulation technique through silencing of Dmrt gene family for achieving a complete and functional sex reversal and offered a new insight regarding the mechanism of the Dmrt gene family in the sexual differentiation of crustaceans.

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“…RNA sequencing (RNA-seq) has become a powerful approach for generating a vast majority of sequence data and cDNA sequences, which might provide new and comprehensive information for genetic research [5]. For decades, a substantial number of RNA-seq studies have been conducted to understand gene expression and molecular mechanisms, moreover, RNAseq is particularly widely used for nonmodel species that lack a reference genome [6][7][8][9], it provides insights into mRNA splicing and gene expression and has been used to screen candidate genes; however, the gene structure and full-length sequence are limited [10,11]. In addition, the extent of alternative splicing (AS) and transcriptome diversity remain largely unknown due to its short read length [12].…”

Section: Introductionmentioning

confidence: 99%

SMRT sequencing of the full-length transcriptome of Gekko gecko

et al. 2022

Self Cite

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Tokay Gecko (Gekko gecko) is a rare and endangered medicinal animal in China. Its dry body has been used as an anti-asthmatic agent for two thousand years. To date, the genome and transcriptome of this species remain poorly understood. Here, we adopted single molecule real-time (SMRT) sequencing to obtain full-length transcriptome data and characterized the transcriptome structure. We identified 882,273 circular consensus (CCS) reads, including 746,317 full-length nonchimeric (FLNC) reads. The transcript cluster analysis revealed 212,964 consensus sequences, including 203,994 high-quality isoforms. In total, 111,372 of 117,888 transcripts were successfully annotated against eight databases (Nr, eggNOG, Swiss-Prot, GO, COG, KOG, Pfam and KEGG). Furthermore, 23,877 alternative splicing events, 169,128 simple sequence repeats (SSRs), 10,437 lncRNAs and 7,932 transcription factors were predicted across all transcripts. To our knowledge, this report is the first to document the G. gecko transcriptome using SMRT sequencing. The full-length transcript data might accelerate transcriptome research and lay the foundation for further research on G. gecko.

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Comparative Transcriptome Analysis of Gonads for the Identification of Sex-Related Genes in Giant Freshwater Prawns (Macrobrachium Rosenbergii) Using RNA Sequencing

Cited by 25 publications

References 74 publications

Identification of differentially expressed genes and signalling pathways to elucidate molecular mechanisms underlying growth differences among the male morphotypes of Macrobrachium rosenbergii

Identification of differentially expressed genes and signalling pathways to elucidate molecular mechanisms underlying growth differences among the male morphotypes of Macrobrachium rosenbergii

Full Functional Sex Reversal Achieved Through Silencing of MroDmrt11E Gene in Macrobrachium rosenbergii: Production of All-Male Monosex Freshwater Prawn

SMRT sequencing of the full-length transcriptome of Gekko gecko

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