RNA-seq as a powerful tool for penaeid shrimp genetic progress

Santos, Camilla A.; Blanck, Danielly Veloso; Freitas, Patrícia D.

doi:10.3389/fgene.2014.00298

Cited by 33 publications

(28 citation statements)

References 41 publications

(115 reference statements)

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“…RNA-seq analysis has been demonstrated to be a powerful method to examine the effects of salinity or temperature on gene expression levels in several invertebrates (Huang et al , 2017; Lv et al , 2013; Meng et al , 2013; Santos et al , 2014; Sellars et al , 2015; Zhao et al , 2012). It has been reported that swimming crab Portunus trituberculatus reared for ten days at different salinity changed the expression levels of osmoregulation-related genes such as those encoding ion transporters and amino acid metabolism-related proteins in their gills (Lv et al , 2013).…”

Section: Introductionmentioning

confidence: 99%

Changes in free amino acid concentrations and associated gene expression profiles in the abdominal muscle of kuruma shrimpMarsupenaeus japonicusreared at different salinity

Koyama

Mizusawa

Hoashi

et al. 2017

Preprint

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3Shrimps inhabiting around the coastal area can survive in a wide range of salinity. 49 However, the molecular mechanisms involved in their adaptation to different 50 environmental salinity have remained largely unknown. In the present study, we reared 51 kuruma shrimp Marsupenaeus japonicus at 1.7 %, 3.4 % and 4.0 % salinity. After rearing 52 for 6, 12, 24 and 72 h, we determined free amino acid concentrations in their abdominal 53 muscle, and performed RNA-seq analysis on this muscle. The concentrations of free 54 amino acids were clearly altered depending on salinity after rearing for 24 h. Glutamine 55 and alanine concentrations were markedly increased following the increase of salinity. In 56 association with such changes, many genes related to amino acid metabolism changed 57 their expression levels. Notably, the increased glutamine content at high salinity appeared 58 to be relevant to the increase of the expression level of the gene encoding 59 glutamate-ammonia ligase which functions in the glutamine metabolism. Furthermore, 60 the alanine content increased at high salinity was likely to be associated with the decrease 61 in the expression levels of the alanine-glyoxylate transaminase gene. Thus, the changes in 62 the concentration of free amino acids for osmoregulation in kuruma shrimp are 63 considered to be regulated by the changes in the expression levels of genes related to 64 amino acid metabolism. 65 66 67 68 69 70 71 109 2015; Zhao et al., 2012). It has been reported that swimming crab Portunus 110 trituberculatus reared for ten days at different salinity changed the expression levels of 111 osmoregulation-related genes such as those encoding ion transporters and amino acid 112 metabolism-related proteins in their gills (Lv et al., 2013). 113 As mentioned above, many genes including ion and amino acid transporters seem to 114 participate in adaptation of crustaceans to the salinity change. However, the molecular 115 mechanisms involved have still remained unclear, since the regulatory mechanisms 116 underlying the changes of free amino acid concentrations are not well understood. 117 In the present study, we targeted kuruma shrimp as experimental animals, which are 118 widely cultured and commercially available, important species. We reared the shrimp 119 samples at different salinity and determined free amino acid concentrations in their 120 6 abdominal muscle. In addition, we performed RNA-seq analysis on the same samples by 121 using a next generation sequencer. 122 123 Materials and methods 124 Animals 125About 40 adult specimens of kuruma shrimp were obtained from Miyazaki Prefecture, 126 Japan, and cultured in 3.4 % salinity tank (60 l) of Kitasato University at 25 ºC for 3 days. 127 Then, they were divided into 3 groups using 60 l tanks each at 1.7 %, 3.4 % and 4.0 % 128

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Section: Introductionmentioning

confidence: 99%

Changes in free amino acid concentrations and associated gene expression profiles in the abdominal muscle of kuruma shrimpMarsupenaeus japonicusreared at different salinity

Koyama

Mizusawa

Hoashi

et al. 2017

Preprint

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“…The transcriptome is the set of ribonucleic acids in the cell , including messenger ribonucleic acid (mRNA), transfer ribonucleic acid (tRNA), ribosomal ribonucleic acid (rRNA), small nuclear ribonucleicacid (snRNA), noncoding ribonucleic acids (ncRNA), and others. These RNAs are differently expressed according to the tissue, the physiological condition, or the stage of development [ 46 ].…”

Section: Rna Sequencing (Rnaseq)mentioning

confidence: 99%

“…It requires lots of resources compared to other techniques. The Data set is large and complex, the large amount of generated data makes the interpretation diffi cult, and usu ally a bioinformatic adviser is needed [ 46 ].…”

Section: Advantages and Limitations Of Rnaseqmentioning

confidence: 99%

Introduction to the Gene Expression Analysis

Segundo-Val

Sanz-Lozano

2016

Methods in Molecular Biology

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In 1941, Beadle and Tatum published experiments that would explain the basis of the central dogma of molecular biology, whereby the DNA through an intermediate molecule, called RNA, results proteins that perform the functions in cells. Currently, biomedical research attempts to explain the mechanisms by which develops a particular disease, for this reason, gene expression studies have proven to be a great resource. Strictly, the term "gene expression" comprises from the gene activation until the mature protein is located in its corresponding compartment to perform its function and contribute to the expression of the phenotype of cell.The expression studies are directed to detect and quantify messenger RNA (mRNA) levels of a specific gene. The development of the RNA-based gene expression studies began with the Northern Blot by Alwine et al. in 1977. In 1969, Gall and Pardue and John et al. independently developed the in situ hybridization, but this technique was not employed to detect mRNA until 1986 by Coghlan. Today, many of the techniques for quantification of RNA are deprecated because other new techniques provide more information. Currently the most widely used techniques are qPCR, expression microarrays, and RNAseq for the transcriptome analysis. In this chapter, these techniques will be reviewed.

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“…2009). These traits can be related to reproduction, sex determination, growth and immunity (Santos et al, 2014). These traits can be related to reproduction, sex determination, growth and immunity (Santos et al, 2014).…”

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confidence: 99%

A review on genome mapping of penaeid shrimps of commercial importance

Harke

Panche

2018

Aquac Res

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Genome mapping of any organism has become vital and most essential to control the gene related functions and also for the production of new traits of the desired properties. Gene mapping has become a very powerful tool in agriculture sector as well as for terrestrial livestock and going to revolutionize both these sectors from the point of view of enhancing production. However, for aquatic organisms, the information pertaining to gene mapping research is limited and only in recent past few attempts have been made in this direction. The rationale behind genome map-

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RNA-seq as a powerful tool for penaeid shrimp genetic progress

Cited by 33 publications

References 41 publications

Changes in free amino acid concentrations and associated gene expression profiles in the abdominal muscle of kuruma shrimpMarsupenaeus japonicusreared at different salinity

Changes in free amino acid concentrations and associated gene expression profiles in the abdominal muscle of kuruma shrimpMarsupenaeus japonicusreared at different salinity

Introduction to the Gene Expression Analysis

A review on genome mapping of penaeid shrimps of commercial importance

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