Identification of Candidate Genes of Male Sexual Development From Androgenic Gland in Macrobrachium Nipponense Through Performing Long-reads and Next Generation Transcriptome Sequencing After Eyestalk Ablation

Abstract The eyestalk of crustacean species contained many neurosecretory structures, affected the process of reproduction, molting, metabolism of glucose and other function in crustaceans. In this study, we aimed to selected important metabolic pathways and candidate genes involved in the male sexual development through performing the long-reads and next generation transcriptome sequencing of androgenic gland after the ablation of eyestalk from Macrobrachium nipponense. qPCR analysis revealed that the mRNA expression of Mn-IAG was significantly increased after ablation both of the single-side (SS) and double-side (DS) eyestalk, compared with that of control group (CG). The long-reads transcriptome generated 49,480 non-redundant transcripts. A total of 1,319, 2,092 and 4,351 differentially expressed genes (DEGs) were identified between CG vs SS, SS vs DS and CG vs DS, respectively, indicating the ablation of double-side eyestalk has more important regulatory roles than that of single-side ablation on male sexual development, which was consistent with that of qPCR analysis. Cell cycle, Cellular senescence, Oxidative phosphorylation, Glycolysis/Gluconeogenesis and Steroid hormone biosynthesis were the main enriched metabolic pathways in all of these three comparisons, and the important genes from these metabolic pathways were also selected. The qPCR verifications of 10 GEDs were as the same as that of RNA-seq. The qPCR and RNAi analysis of Hydroxysteroid dehydrogenase like 1 (HSDL1) revealed that HSDL1 has the positive regulatory effected on testis development. This study provided valuable evidences on male sexual development in M. nipponense, promoting the studies on male sexual development in other crustacean as well.

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Identification of candidate genes from androgenic gland in Macrobrachium nipponense regulated by eyestalk ablation

Scientific Reports ◽

10.1038/s41598-021-99022-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Shubo Jin ◽

Yin Fu ◽

Yuning Hu ◽

Hongtuo Fu ◽

Sufei Jiang ◽

...

Keyword(s):

Candidate Genes ◽

Sexual Development ◽

Metabolic Pathways ◽

Control Group ◽

Androgenic Gland ◽

Macrobrachium Nipponense ◽

Eyestalk Ablation ◽

Qpcr Analysis ◽

Single Side ◽

Long Read

AbstractThe eyestalk of crustaceans, such as Macrobrachium nipponense, contains many neurosecretory hormones affecting the process of reproduction, molting, metabolism of glucose, and other functions. In this study, important metabolic pathways and candidate genes involved in male sexual development were selected from M. nipponense. The methodology involved performing long-read and next generation transcriptome sequencing of genes from the androgenic gland after eyestalk ablation. qPCR analysis revealed that the mRNA expression of Mn-IAG was significantly increased after ablation of both the single-side (SS) and double-side (DS) eyestalk, compared with the control group (CG). The long-read transcriptome generated 49,840 non-redundant transcripts. A total of 1319, 2092 and 4351 differentially expressed genes (DEGs) were identified between CG versus SS, SS versus DS and CG versus DS, respectively. These data indicated that ablation of the double-sided eyestalk played stronger regulatory roles than the single-side ablation on male sexual development in M. nipponense. This was consistent with the qPCR analysis. Cell Cycle, Cellular Senescence, Oxidative Phosphorylation, Glycolysis/Gluconeogenesis and Steroid Hormone Biosynthesis were the primary enriched metabolic pathways in all three comparisons, and the important genes from these metabolic pathways were also selected. qPCR permitted secondary confirmation of ten DEGs identified through RNA-seq. RNAi-mediated silencing analyses of Hydroxysteroid dehydrogenase like 1 (HSDL1) revealed that HSDL1 has a positive regulatory effect on testes development. This study provides valuable insight into male sexual development in M. nipponense, including metabolic pathways and genes, paving the way for advanced studies on male sexual development in this species and in other crustaceans.

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Transcriptome Profiling Analysis of the Testis After Eyestalk Ablation for Selection of the Candidate Genes Involved in the Male Sexual Development in Macrobrachium nipponense

Frontiers in Genetics ◽

10.3389/fgene.2021.675928 ◽

2021 ◽

Vol 12 ◽

Author(s):

Shubo Jin ◽

Yin Fu ◽

Yuning Hu ◽

Hongtuo Fu ◽

Sufei Jiang ◽

...

Keyword(s):

Candidate Genes ◽

Sexual Development ◽

Metabolic Pathways ◽

Transcriptome Profiling ◽

Negative Effects ◽

Macrobrachium Nipponense ◽

Eyestalk Ablation ◽

Testis Development ◽

Single Side ◽

Profiling Analysis

The eyestalk of crustacean species secretes many hormones, affecting the process of reproduction, molting, metabolism of glucose, and other functions in crustaceans. In this study, important metabolic pathways and candidate genes involved in the male sexual development were identified through performing the transcriptome profiling analysis of the testis after the ablation of eyestalk from Macrobrachium nipponense. The histological observations revealed that the testis development became vigorous after eyestalk ablation, indicating that the hormones secreted by the eyestalk have negative effects on the testis development in M. nipponense. Transcriptome profiling analysis revealed that 1,039, 1,226, and 3,682 differentially expressed genes (DEGs) were identified between normal prawns (CG) vs single-side eyestalk ablation prawns (SS), SS vs double-side eyestalk ablation prawns (DS), and CG vs DS, respectively, indicating that the ablation of double-side eyestalk has more significant regulatory roles on male sexual development than that of single-side ablation, which was consistent with the histological observations. Lysosome, Apoptosis, Glycolysis/Gluconeogenesis, and Insulin signaling pathway were the main enriched metabolic pathways in all of these three comparisons, and the important genes from these metabolic pathways were also selected. The qPCR verifications of 10 DEGs from these metabolic pathways were the same as those of RNA-seq. The qPCR, in situ hybridization, and RNA interference analysis of Mn-NFkBα revealed that NFkBα has a positive regulatory effect on testis development. This study provided new insights on male sexual development in M. nipponense, promoting the studies on male sexual development in other crustaceans as well.

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Potential Functions of Gem-Associated Protein 2-Like Isoform X1 in the Oriental River Prawn Macrobrachium nipponense: Cloning, qPCR, In Situ Hybridization, and RNAi Analysis

International Journal of Molecular Sciences ◽

10.3390/ijms20163995 ◽

2019 ◽

Vol 20 (16) ◽

pp. 3995 ◽

Cited By ~ 2

Author(s):

Shubo Jin ◽

Yuning Hu ◽

Hongtuo Fu ◽

Sufei Jiang ◽

Yiwei Xiong ◽

...

Keyword(s):

In Situ Hybridization ◽

Sexual Development ◽

Developmental Stages ◽

Quantitative Polymerase Chain Reaction ◽

Negative Effects ◽

Macrobrachium Nipponense ◽

Reading Frame ◽

Gonad Differentiation ◽

Qpcr Analysis

Gem-associated protein 2-like isoform X1 (GEM) was previously predicted to be involved in the sexual development of male Macrobrachium nipponense. In this study, we analyze the GEM functions in depth using quantitative polymerase chain reaction (qPCR), in situ hybridization, and RNA interference (RNAi). The full-length Mn-GEM cDNA sequence was 1018 base pairs (bp) long with an open reading frame of 777 bp encoding 258 amino acids. qPCR analysis of Mn-GEM in different tissues and developmental stages showed that Mn-GEM was highly expressed in the gonad and from post-larval developmental stage day 5 (PL5) to PL15, which indicated that GEM has potential roles in gonad differentiation and development in M. nipponense. In situ hybridization and qPCR analysis of various stages of the reproductive cycle of the testis and ovary indicated that GEM may promote spermatid development and gametogenesis in M. nipponense. After injecting with double-stranded RNA (dsRNA) of Mn-GEM, mRNA expression of Mn-insulin-like androgenic gland hormone (Mn-IAG) and the content of testosterone increased with the decrease of Mn-GEM expression, indicating that GEM has negative effects on the male sexual differentiation and development in M. nipponense. Results of this study highlight the functions of GEM in M. nipponense, which can be applied to future studies of male sexual development in M. nipponense and other crustacean species.

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Investigation of novel functions of three genes in oriental river prawn,Macrobrachium nipponense: Molecular Cloning, Expression, andIn situHybridization Analysis

10.1101/441147 ◽

2018 ◽

Author(s):

Shubo Jin ◽

Hongtuo Fu ◽

Yuning Hu ◽

Shengming Sun ◽

Sufei Jiang ◽

...

Keyword(s):

Amino Acids ◽

Sexual Development ◽

Cdna Sequence ◽

The Novel ◽

Androgenic Gland ◽

Macrobrachium Nipponense ◽

Testis Development ◽

Gland Cells ◽

Oriental River Prawn

AbstractThree genes were predicted to be potentially involved in the male sexual development inM.nipponense, including the Gem-associated protein 2-like isoform X1 (GEM), Ferritin peptide, and DNA polymerase zeta catalytic subunit (Rev3). In this study, we aimed to investigate their novel functions in depth. The full-length cDNA sequence of Mn-GEM was 1,018 bp, encoding 258 amino acids. The partial Mn-Rev3 cDNA sequence was 6,832 bp, encoding 1,203 amino acids. Tissue distribution indicated that all of these three genes have higher expression level in testis and androgenic gland, implying their novel functions in male sexual development. In situ hybridization analysis further confirmed the novel roles of these three genes. Rev3 promote the testis development during the whole reproductive cycle, while GEM and ferritin only promote the activation of testis development. Besides, these three genes play essential roles in funicular structure development surrounding the androgenic gland cells, which promote and support the formation of androgenic gland cells. The expression in hepatopancreas cells also suggested their role in immune system inM. nipponense.This study advances our understanding of male sexual development inM. nipponense, as well as providing the basis for further studies of male sexual differentiation and development in crustaceans.

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Search for new candidate genes in RET mutation-negative families with hereditary medullary thyroid carcinoma using next generation sequencing

Endocrine Abstracts ◽

10.1530/endoabs.37.oc6.5 ◽

2015 ◽

Author(s):

Eliska Vaclavikova ◽

Sarka Dvorakova ◽

Vlasta Sykorova ◽

Josef Vcelak ◽

Tereza Halkova ◽

...

Keyword(s):

Next Generation Sequencing ◽

Thyroid Carcinoma ◽

Candidate Genes ◽

Medullary Thyroid Carcinoma ◽

Next Generation ◽

Medullary Thyroid ◽

Ret Mutation ◽

Hereditary Medullary Thyroid Carcinoma ◽

Generation Sequencing

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The mutation screening in candidate genes related to thyroid dysgenesis by targeted next‐generation sequencing panel in the Chinese congenital hypothyroidism

Clinical Endocrinology ◽

10.1111/cen.14577 ◽

2021 ◽

Author(s):

Rui‐Jia Zhang ◽

Guang‐lin Yang ◽

Feng Cheng ◽

Feng Sun ◽

Ya Fang ◽

...

Keyword(s):

Next Generation Sequencing ◽

Candidate Genes ◽

Congenital Hypothyroidism ◽

Mutation Screening ◽

Next Generation ◽

Thyroid Dysgenesis ◽

Targeted Next Generation Sequencing ◽

Generation Sequencing

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Transcriptomic and Metabolic Profiling of High-Temperature Treated Storage Roots Reveals the Mechanism of Saccharification in Sweetpotato (Ipomoea batatas (L.) Lam.)

International Journal of Molecular Sciences ◽

10.3390/ijms22136641 ◽

2021 ◽

Vol 22 (13) ◽

pp. 6641

Author(s):

Chen Li ◽

Meng Kou ◽

Mohamed Hamed Arisha ◽

Wei Tang ◽

Meng Ma ◽

...

Keyword(s):

High Temperature ◽

Metabolic Pathways ◽

Transcriptome Sequencing ◽

Ipomoea Batatas ◽

Sequencing Analysis ◽

Storage Roots ◽

Metabolic Analysis ◽

Cooking Process

The saccharification of sweetpotato storage roots is a common phenomenon in the cooking process, which determines the edible quality of table use sweetpotato. In the present study, two high saccharified sweetpotato cultivars (Y25, Z13) and one low saccharified cultivar (X27) in two growth periods (S1, S2) were selected as materials to reveal the molecular mechanism of sweetpotato saccharification treated at high temperature by transcriptome sequencing and non-targeted metabolome determination. The results showed that the comprehensive taste score, sweetness, maltose content and starch change of X27 after steaming were significantly lower than those of Y25 and Z13. Through transcriptome sequencing analysis, 1918 and 1520 differentially expressed genes were obtained in the two periods of S1 and S2, respectively. Some saccharification-related transcription factors including MYB families, WRKY families, bHLH families and inhibitors were screened. Metabolic analysis showed that 162 differentially abundant metabolites related to carbohydrate metabolism were significantly enriched in starch and sucrose capitalization pathways. The correlation analysis between transcriptome and metabolome confirmed that the starch and sucrose metabolic pathways were significantly co-annotated, indicating that it is a vitally important metabolic pathway in the process of sweetpotato saccharification. The data obtained in this study can provide valuable resources for follow-up research on sweetpotato saccharification and will provide new insights and theoretical basis for table use sweetpotato breeding in the future.

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