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Palliyath GK, Jangam AK, Katneni VK, Kaikkolante N, Panjan Nathamuni S, Jayaraman R, Jagabattula S, Moturi M, Shekhar MS. Meta-analysis to Unravel Core Transcriptomic Responses in Penaeus vannamei Exposed to Biotic and Abiotic Stresses. Biochem Genet 2024:10.1007/s10528-024-10772-y. [PMID: 38570440 DOI: 10.1007/s10528-024-10772-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 03/03/2024] [Indexed: 04/05/2024]
Abstract
Shrimp farming, a dominant economic activity in coastal areas, is affected by different abiotic and biotic stress factors. These stressors, under poor management conditions, could affect growth and health of farmed animals. Understanding the common gene expressions in response to stress, regardless of the specific stress factor, holds significant importance in the field of functional genomics. Scope of this study is to identify the core transcriptomic responses in the shrimp species Penaeus vannamei exposed to various abiotic and biotic stress conditions and to decipher their functional importance. To achieve our objective, we gathered and analyzed multiple RNA-seq datasets related to twelve abiotic and nine biotic stress conditions. Through the in silico meta-analysis, we predicted 961 differentially expressed genes (meta-DEGs) for abiotic stress conditions and 517 meta-DEGs for biotic stress conditions, respectively. These meta-DEGs represent genes that are commonly expressed across different stress factors and are indicative of the organism's general response to stress. The annotation of nineteen core up-regulated meta-DEGs revealed their diverse functions in detoxification, cell adhesion, metal ion binding, and oxidative phosphorylation. These genes play a crucial role in stress response and immune defense. For abiotic stress, significant pathways associated with the stress response include tryptophan metabolism, starch and sucrose metabolism, fatty acid degradation, carbohydrate digestion and absorption, phenylalanine metabolism, drug metabolism-other enzymes, arachidonic acid metabolism, and fatty acid elongation. Similarly, for biotic stress, metabolism of xenobiotics by cytochrome P450, pentose and glucuronate interconversions, steroid hormone biosynthesis, and drug metabolism-cytochrome P450 were found to be significant pathway associations. In addition, the study also predicted 17 stress regulatory motifs present in the identified meta-DEGs. These motifs have significance in identifying the stress responses of the organism. The metabolic pathways and regulatory motifs associated with abiotic and biotic stress factors identified through this study could be a valuable resource for developing stress management approaches in shrimp aquaculture.
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Affiliation(s)
| | | | | | | | | | - Roja Jayaraman
- ICAR-Central Institute of Brackishwater Aquaculture, Chennai, India
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Krishnan K, Katneni VK, Prabhudas SK, Kaikkolante N, Jangam AK, Katneni UK, Hauton C, Peruzza L, Mudagandur SS, Koyadan VK, Poochirian JK, Jena J. MRF: a tool to overcome the barrier of inconsistent genome annotations and perform comparative genomics studies for the largest animal DNA virus. Virol J 2023; 20:72. [PMID: 37072853 PMCID: PMC10111743 DOI: 10.1186/s12985-023-02035-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/09/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND The genome of the largest known animal virus, the white spot syndrome virus (WSSV) responsible for huge economic losses and loss of employment in aquaculture, suffers from inconsistent annotation nomenclature. Novel genome sequence, circular genome and variable genome length led to nomenclature inconsistencies. Since vast knowledge has already accumulated in the past two decades with inconsistent nomenclature, the insights gained on a genome could not be easily extendable to other genomes. Therefore, the present study aims to perform comparative genomics studies in WSSV on uniform nomenclature. METHODS We have combined the standard mummer tool with custom scripts to develop missing regions finder (MRF) that documents the missing genome regions and coding sequences in virus genomes in comparison to a reference genome and in its annotation nomenclature. The procedure was implemented as web tool and in command-line interface. Using MRF, we have documented the missing coding sequences in WSSV and explored their role in virulence through application of phylogenomics, machine learning models and homologous genes. RESULTS We have tabulated and depicted the missing genome regions, missing coding sequences and deletion hotspots in WSSV on a common annotation nomenclature and attempted to link them to virus virulence. It was observed that the ubiquitination, transcription regulation and nucleotide metabolism might be essentially required for WSSV pathogenesis; and the structural proteins, VP19, VP26 and VP28 are essential for virus assembly. Few minor structural proteins in WSSV would act as envelope glycoproteins. We have also demonstrated the advantage of MRF in providing detailed graphic/tabular output in less time and also in handling of low-complexity, repeat-rich and highly similar regions of the genomes using other virus cases. CONCLUSIONS Pathogenic virus research benefits from tools that could directly indicate the missing genomic regions and coding sequences between isolates/strains. In virus research, the analyses performed in this study provides an advancement to find the differences between genomes and to quickly identify the important coding sequences/genomes that require early attention from researchers. To conclude, the approach implemented in MRF complements similarity-based tools in comparative genomics involving large, highly-similar, length-varying and/or inconsistently annotated viral genomes.
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Affiliation(s)
- Karthic Krishnan
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Vinaya Kumar Katneni
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India.
| | - Sudheesh K Prabhudas
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Nimisha Kaikkolante
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Ashok Kumar Jangam
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Upendra Kumar Katneni
- The Center for Blood Oxygen Transport and Hemostasis, Department of Pediatrics, University of Maryland School of Medicine, Maryland, USA
| | - Chris Hauton
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton Waterfront Campus, Southampton, UK
| | - Luca Peruzza
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padua, Italy
| | - Shashi Shekhar Mudagandur
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Vijayan K Koyadan
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Jithendran Karingalakkandy Poochirian
- Aquatic Animal Health and Environment Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
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Bhati A, Varghese A, Rajan G, Sridhar V, Mohan Y, Pradeep S, Babu S, Kaikkolante N, Sarma M, Arun S, Sekar AP, Iype T, Santhosh S, Ramchand CN. An effective method for saliva stabilization and magnetic nanoparticles based DNA extraction for genomic applications. Anal Biochem 2021; 624:114182. [PMID: 33781755 DOI: 10.1016/j.ab.2021.114182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 11/26/2022]
Abstract
Introduction of magnetisable solid phase extraction procedures have provided various advantages over spin-column based extraction techniques. Although certain methods for magnetic bead based extraction of DNA from human saliva already exist, there is still a need to address the inadequate purity profile and low yield which occur due to the inefficiency of extraction methods. Hence, an improved method for DNA extraction from human saliva using uncoated magnetic nanoparticles (MNPs) intended to resolve the issues mentioned above is described here. The uncoated magnetic nanoparticles used in this study facilitate reversible binding of DNA and due to the absence of surface coating the particle size remains small thereby providing higher surface area to volume ratio for binding DNA. Another objective of this study was to develop a saliva preservation buffer (SPB) to solve the major challenges associated with storage and easy transportation of saliva sample at room temperature. Human saliva samples stored in the saliva preservation buffer were stable up to 160 days at room temperature without any bacterial or fungal growth and the quality of genomic DNA was intact.
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Affiliation(s)
- Aniruddha Bhati
- MagGenome Technologies Pvt. Ltd., First Floor, Plot No. 153, First Main Road, Industrial Estate, Perungudi, Chennai, 600096, India
| | - Anu Varghese
- MagGenome Technologies Pvt. Ltd., First Floor, Plot No. 153, First Main Road, Industrial Estate, Perungudi, Chennai, 600096, India
| | - Gayathri Rajan
- MagGenome Technologies Pvt. Ltd., First Floor, Plot No. 153, First Main Road, Industrial Estate, Perungudi, Chennai, 600096, India
| | - Vandana Sridhar
- MagGenome Technologies Pvt. Ltd., First Floor, Plot No. 153, First Main Road, Industrial Estate, Perungudi, Chennai, 600096, India
| | - Yedhu Mohan
- MagGenome Technologies Pvt. Ltd., First Floor, Plot No. 153, First Main Road, Industrial Estate, Perungudi, Chennai, 600096, India
| | - Swetha Pradeep
- MagGenome Technologies Pvt. Ltd., First Floor, Plot No. 153, First Main Road, Industrial Estate, Perungudi, Chennai, 600096, India
| | - Seethal Babu
- MagGenome Technologies Pvt. Ltd., First Floor, Plot No. 153, First Main Road, Industrial Estate, Perungudi, Chennai, 600096, India
| | - Nimisha Kaikkolante
- MagGenome Technologies Pvt. Ltd., First Floor, Plot No. 153, First Main Road, Industrial Estate, Perungudi, Chennai, 600096, India
| | - Minu Sarma
- MagGenome Technologies Pvt. Ltd., First Floor, Plot No. 153, First Main Road, Industrial Estate, Perungudi, Chennai, 600096, India
| | - Sreepriya Arun
- MagGenome Technologies Pvt. Ltd., First Floor, Plot No. 153, First Main Road, Industrial Estate, Perungudi, Chennai, 600096, India
| | - Arun Prasath Sekar
- MagGenome Technologies Pvt. Ltd., First Floor, Plot No. 153, First Main Road, Industrial Estate, Perungudi, Chennai, 600096, India
| | - Tessy Iype
- MagGenome Technologies Pvt. Ltd., First Floor, Plot No. 153, First Main Road, Industrial Estate, Perungudi, Chennai, 600096, India.
| | - Sam Santhosh
- MagGenome Technologies Pvt. Ltd., First Floor, Plot No. 153, First Main Road, Industrial Estate, Perungudi, Chennai, 600096, India
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Katneni VK, Shekhar MS, Jangam AK, Paran BC, Selvaraj A, Krishnan K, Kaikkolante N, Prabhudas SK, Gopalapillai G, Koyadan VK. Phylogenetic relations and mitogenome-wide similarity metrics reveal monophyly of Penaeus sensu lato. Ecol Evol 2021; 11:2040-2049. [PMID: 33717440 PMCID: PMC7920775 DOI: 10.1002/ece3.7148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 11/24/2020] [Accepted: 12/10/2020] [Indexed: 11/24/2022] Open
Abstract
Splitting of the genus Penaeus sensu lato into six new genera based on morphological features alone has been controversial in penaeid shrimp taxonomy. Several studies focused on building phylogenetic relations among the genera of Penaeus sensu lato. However, they lack in utilizing full mitochondrial DNA genome of shrimp representing all the six controversial genera. For the first time, the present study targeted the testing of all the six genera of Penaeus sensu lato for phylogenetic relations utilizing complete mitochondrial genome sequence. In addition, the study reports for the first time about the complete mitochondrial DNA genome sequence of Fenneropenaeus indicus, an important candidate species in aquaculture and fisheries, and utilized it for phylogenomics. The maximum likelihood and Bayesian approaches were deployed to generate and comprehend the phylogenetic relationship among the shrimp in the suborder, Dendrobranchiata. The phylogenetic relations established with limited taxon sampling considered in the study pointed to the monophyly of Penaeus sensu lato and suggested collapsing of the new genera to a single genus. Further, trends in mitogenome-wide estimates of average amino acid identity in the order Decapoda and the genus Penaeus sensu lato supported restoration of the old genus, Penaeus, rather promoting the creation of new genera.
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Affiliation(s)
- Vinaya Kumar Katneni
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Mudagandur S. Shekhar
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Ashok Kumar Jangam
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | | | - Ashok Selvaraj
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Karthic Krishnan
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Nimisha Kaikkolante
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Sudheesh K. Prabhudas
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
| | - Gopikrishna Gopalapillai
- Nutrition Genetics and Biotechnology DivisionICAR‐Central Institute of Brackishwater AquacultureChennaiIndia
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