Muscle transcriptome resource for growth, lipid metabolism and immune system in Hilsa shad, Tenualosa ilisha

Integrated transcriptome catalog of Tenualosa ilisha as a resource for gene discovery and expression profiling

The silver pride of Bangladesh, migratory shad, Tenualosa ilisha (Hilsa), makes the highest contribution to the total fish production of Bangladesh. Despite its noteworthy contribution, a well-annotated transcriptome data is not available. Here we report a transcriptomic catalog of Hilsa, constructed by assembling RNA-Seq reads from different tissues of the fish including brain, gill, kidney, liver, and muscle. Hilsa fish were collected from different aquatic habitats (fresh, brackish, and sea water) and the sequencing was performed in the next generation sequencing (NGS) platform. De novo assembly of the sequences obtained from 46 cDNA libraries revealed 462,085 transcript isoforms that were subsequently annotated using the Universal Protein Resource Knowledgebase (UniPortKB) as a reference. Starting from the sampling to final annotation, all the steps along with the workflow are reported here. This study will provide a significant resource for ongoing and future research on Hilsa for transcriptome based expression profiling and identification of candidate genes.

Proteomics-based molecular and functional characteristic profiling of muscle tissue in Triploid crucian carp

Triploid crucian carp (TCC) is a kind of artificially bred fish with huge economic value to China. It has several excellent characteristics, such as fast growth, strong disease resistance and delicious taste. However, as a regionally specific fish, the underlying molecular mechanisms of these characteristics are largely unknown. In this study, we performed quantitative proteomics on the muscle tissues of TCC and its parents, allotetraploid (♂), red crucian carp (♀) and common carp. Combined with multiple bioinformatic analysis, we found that the taste of TCC can be mainly attributed to umami amino acid-enriched proteins such as PURBA, PVALBI and ATP5F1B, and that its rapid growth can be mainly ascribed to the high expression and regulation of metabolism-related proteins such as NDUFS1, ENO1A and CS. These play significant roles in substrate and energy metabolism, as well as in bias transformation. Subsequently, we identified several proteins, including MDH1AA, GOT1 and DLAT, that may serve as potential regulators of innate immunity by regulating the biosynthesis and transformation of significant antibiotics and antimicrobial peptides. In conclusion, this study can serve as a significant reference for similar investigations and shed light on the molecular and biological functions of individual proteins in TCC muscle tissue.

Identification of Genes Related to Squab Muscle Growth and Lipid Metabolism from Transcriptome Profiles of Breast Muscle and Liver in Domestic Pigeon (Columba livia)

Simple Summary

Domestic pigeon is an important small poultry species raised for high-quality meat production. However, the relevant gene associated with meat growth and lipid metabolism during the period from dehulling to marketing are not known. Therefore, we aim to identify genes related to squab muscle growth and lip metabolism from transcriptome profiles of breast muscle and liver in domestic pigeon. In this study, we totally found that 4465 differentially expressed genes (DEGs) identified in the breast muscle and liver libraries, which include 2585 genes that were up-regulated and 2122 genes that were down-regulated. Most genes are involved in cell proliferation and differentiation, lipid metabolism and energy metabolism according to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs. We also detected 16 DEGs to verify data from RNA-Seq and qPCR, which were consistent in quantitatively estimating the transcription levels of the tested transcripts by qPCR analysis. The results of this study will lay the foundation for understanding the mechanisms of muscle growth and lipid metabolism in domestic pigeons.

Abstract

The improvements in muscle growth rate and meat quality are the major breeding aims in pigeon industry. Liver and muscle are recognized as important sites for fatty acid metabolism; understanding the role of specific transcripts in the breast muscle and liver might lead to the elucidation of interrelated biological processes. In this study, RNA-Sequencing (RNA-Seq) was applied to compare the transcriptomes of breast muscle and liver tissues among pigeons at five developmental periods (0, 1, 2, 3, 4 weeks post-hatching) to identify candidate genes related to muscle growth and lipid metabolism. There were 3142 differentially expressed genes (DEGs) identified in the breast muscle libraries; 1794 genes were up-regulated while 1531 genes were down-regulated. A total of 1323 DEGs were acquired from the liver libraries, with 791 up-regulated genes and 591 down-regulated genes. By pathway enrichment analysis, a set of significantly enriched pathways were identified for the DEGs, which are potentially involved in cell proliferation and differentiation, lipid metabolism and energy metabolism in pigeon breast muscle and liver. Our results are consistent with previous partial reports from domestic animals and poultry and provide some unidentified genes involved in muscle growth and lipid metabolism. The reliability of the sequencing data was verified through qPCR analysis of 16 genes from eight comparison groups (two genes per group). The findings from this study could contribute to future investigations of muscle growth and lipid metabolism mechanisms and establish molecular approaches to improve muscle growth rate and meat quality in domestic pigeon breeding.

Comparative Transcriptomic Analysis of the Pituitary Gland between Cattle Breeds Differing in Growth: Yunling Cattle and Leiqiong Cattle

The hypothalamic-pituitary-thyroid (HPT) axis hormones regulate the growth and development of ruminants, and the pituitary gland plays a decisive role in this process. In order to identify pivotal genes in the pituitary gland that could affect the growth of cattle by regulating the secretion of hormones, we detected the content of six HPT hormones related to growth in the plasma of two cattle breeds (Yunling and Leiqiong cattle, both also known as the zebu cattle) with great differences in growth and compared the transcriptome data of their pituitary glands. Our study found that the contents of GH, IGF, TSH, thyroxine, triiodothyronine, and insulin were significantly different between the two breeds, which was the main cause of the difference in growth; 175 genes were identified as differentially expressed genes (DEGs). Functional association analyses revealed that DEGs were mainly involved in the process of transcription and signal transduction. Combining the enrichment analysis and protein interaction analysis, eight DEGs were predicted to control the growth of cattle by affecting the expression of growth-related hormones in the pituitary gland. In summary, our results suggested that SLC38A1, SLC38A3, DGKH, GNB4, GNAQ, ESR1, NPY, and GAL are candidates in the pituitary gland for regulating the growth of Yunling and Leiqiong cattle by regulating the secretion of growth-related hormones. This study may help researchers further understand the growth mechanisms and improve the artificial selection of zebu cattle.

A comparative metabolomics study on anadromous clupeid Tenualosa ilisha for better understanding the influence of habitat on nutritional composition

INTRODUCTION

Fish inhabiting different aquatic habitats adapts to the environment by metabolomic readjustments. Understanding the combined activities of all the metabolic pathways (metabolome) helps in better understanding the complex interactions between gene and environment.

OBJECTIVES

The anadromous migratory Tenualosa ilisha is a high value food fish comprising the dominant fishery of the rivers Padma and Hooghly. The present study aimed at understanding the influence of the two habitats on the nutritional composition of hilsa.

METHODS

Metabolite profiling was carried out by GC/MS. De novo assembly of hilsa liver transcriptome was generated under Illumina HiSeq platform and multivariate analysis was employed for correlation and comparison.

RESULTS

GC/MS fingerprinting showed C16:0, C18:1, C20:5 and C22:6 to be the predominant fatty acids present in hilsa liver, which were also found to be significantly higher in Hooghly hilsa. Comparative transcriptome analysis revealed that the differentially expressed genes were mainly associated with 'lipid metabolism' and 'amino acid metabolism' pathways. Multivariate analysis between the metabolites amino acid, fatty acid and corresponding gene expression showed that few genes of amino acid metabolism (EZH1, ALAS2 and ALDH4A1) positively correlated with individual amino acids (lysine, glycine and glutamate) in Hooghly hilsa. Similarly, the key genes for LC-PUFA biosynthesis (ELOVL5, FADS2, CPT1) showed positive correlation with individual LC-PUFAs (C18:3, C20:4, C20:5, C22:6), indicating higher LC-PUFA biosynthesis potential in Hooghly hilsa.

CONCLUSION

Comparative metabolomic study in hilsa from the two different habitats showed that the habitats influence the nutritional composition as evidenced by high abundance of amino acids lysine, leucine and arginine and LC-PUFAs C18:3, C20:4, C20:5, C22:6 in Hooghly hilsa.