Prem Kumar Meher | Central Institute of Freshwater Aqaculture (original) (raw)

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Papers by Prem Kumar Meher

Research paper thumbnail of Additional file 1 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Additional file 2 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Additional file 7 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Additional file 4 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Additional file 8 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Additional file 5 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Additional file 3 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Additional file 10 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Additional file 6 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Additional file 12 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Additional file 9 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Evaluation of the carcass and commercial characteristics of carps

The role of carcass evaluation techniques in aquaculture research programs, especially in genetic... more The role of carcass evaluation techniques in aquaculture research programs, especially in genetics, breeding, production management, feeding and nutrition, cannot be overemphasized. Knowledge of production efficiencies and growth potentials in relation to desired carcass attributes has provided an impetus to improvements in genetic selection techniques and management of aquatic food animals. Accurate, standard and uniform methods of carcass evaluation are critically important. A standard format developed for collection of data on carps is presented in this paper.

Research paper thumbnail of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

BMC Genomics

Background Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of Sou... more Background Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., post-spawning resting and initiation of gonadal activity appropriate for revealing the associated candidate genes. It can be deciphered by RNA sequencing of tissues involved in BPGL (Brain-Pituitary-Gonad-Liver) axis controlling seasonality. How far such BCGs of this fish are evolutionarily conserved across different phyla is unknown. Such study can be of further use to enhance fish productivity as seasonality restricts seed production beyond monsoon season. Result A total of ~ 150 Gb of transcriptomic data of four tissues viz., BPGL were generated using Illumina TruSeq. De-novo assembled BPGL tissues reveal...

Research paper thumbnail of Incidence and Molecular Analysis of V. cholerae among Some Primitive Tribes in Odisha, India

International Journal of Current Microbiology and Applied Sciences

Research paper thumbnail of Protein fingerprinting profiles in different strains of Aeromonas hydrophila isolated from diseased freshwater fish

World Journal of Microbiology and Biotechnology, May 31, 2005

Aeromonas hydrophila (Ah) strains isolated from diseased fish in India were studied for protein p... more Aeromonas hydrophila (Ah) strains isolated from diseased fish in India were studied for protein profiling using the SDS-PAGE protein fingerprinting profile pattern of whole cells of 12 local strains of A. hydrophila and one reference strain (MTCC 646). Variability among the strains was observed. The average similarity between the 12 strains of A. hydrophila ranged from 0.272 to 0.916. Proteins with molecular mass of 55.6 and 14.67 kDa in Ah1, Ah2 and Ah3, 28.5 and 27.9 kDa in Ah4, Ah5 and Ah6, 21.4 and 19.5 kDa in Ah7, Ah8, Ah9 and 72.9, 91.5 and 71.3 kDa in Ah10, Ah11 and Ah12 were common. The protein polypeptide bands from 19.5 to 86.2 kDa were common in both local strains and reference strain of A. hydrophila. The protein fingerprinting study showed that there is genetic similarity between strains of A. hydrophila and reference strain (MTCC 646). These protein markers may be useful for further strain differentiation in epidemiological study.

Research paper thumbnail of RESEARCH ARTICLE Construction, De-Novo Assembly and Analysis of Transcriptome for Identification of Reproduction-Related Genes and Pathways from Rohu, Labeo rohita

Rohu is a leading candidate species for freshwater aquaculture in South-East Asia. Unlike common ... more Rohu is a leading candidate species for freshwater aquaculture in South-East Asia. Unlike common carp the monsoon breeding habit of rohu restricts its seed production beyond sea-son indicating strong genetic control over spawning. Genetic information is limited in this regard. The problem is exacerbated by the lack of genomic-resources. We identified 182 reproduction-related genes previously by Sanger-sequencing which were less to address the issue of seasonal spawning behaviour of this important carp. Therefore, the present work was taken up to generate transcriptome profile by mRNAseq. 16GB, 72bp paired end (PE) data was generated from the pooled-RNA of twelve-tissues from pre-spawning rohu using IlluminaGA-II-platform. There were 64.97 million high-quality reads producing 62,283 contigs and 88,612 numbers of transcripts using velvet and oases programs, respectively. Gene ontology annotation identified 940 reproduction-related genes consisting of 184 mainly asso-ciated with reprod...

Research paper thumbnail of Activin receptor TypeIIB in rohu (Labeo rohita): Molecular characterization, tissue distribution and Immunohistochemical localization during different stages of gonadal maturation

Activin receptor type IIB (ActRIIB) is a transmembrane serine/threonine kinase receptor which pla... more Activin receptor type IIB (ActRIIB) is a transmembrane serine/threonine kinase receptor which plays a pivotal role in regulating reproduction in vertebrates including teleost. Earlier studies have documented its importance in governing gonadal maturation in higher vertebrates. However, reports on regulation of fish reproductive system by ActRIIB gene are still limited. Here, we report identification and characterization of ActRIIB cDNA of Labeo rohita, a commercially important fish species of the Indian subcontinent. The full-length gene encoding rohu ActRIIB was cloned and found to be of 1674 bp in length. Functional similarities were evident form evolutionary analysis across vertebrates. Real-time PCR to measure the expression of ActRIIB transcript in rohu revealed significant mRNA levels in gonads followed by non-reproductive tissues, including brain, pituitary and muscle. With respect to different gonadal maturation stages, predominant expression of ActRIIB mRNA was observed dur...

Research paper thumbnail of The draft genome of Labeo catla

BMC Research Notes

Objective: Labeo catla (catla), one of the three Indian major carps, is native to the Indo-Ganget... more Objective: Labeo catla (catla), one of the three Indian major carps, is native to the Indo-Gangetic riverine system of India as well as the rivers of Pakistan, Bangladesh, Nepal and Myanmar. Its higher growth rate and compatibility with other major carps, specific surface feeding habit, and consumer preference have increased its popularity in carp polyculture systems among the fish farmers in Indian subcontinent. Recent advancement in sequencing technology coupled with massive parallel sequencing platforms has facilitated accelerated genetic improvement in aquaculture species through integration of genomics tools. A draft genome and allied resources are lacking in catla. Therefore, in the present study, we have performed de-novo assembly of Labeo catla for the first time. Data description: A male farm reared catla was used for extracting high molecular weight genomic DNA followed by sequencing in Oxford Nanopore and Illumina platforms. Approximately, 80× coverage of sequence data was assembled adopting the hybrid assembly strategy. The assembled genome size of catla was 1.01 Gb containing 5345 scaffolds with N50 value 0.7 Mb and more than 92% BUSCO completeness. Gene annotation resulted in 25,812 predicted genes.

Research paper thumbnail of Revealing Alteration in the Hepatic Glucose Metabolism of Genetically Improved Carp, Jayanti Rohu Labeo rohita Fed a High Carbohydrate Diet Using Transcriptome Sequencing

International Journal of Molecular Sciences

Although feed cost is the greatest concern in aquaculture, the inclusion of carbohydrates in the ... more Although feed cost is the greatest concern in aquaculture, the inclusion of carbohydrates in the fish diet, and their assimilation, are still not well understood in aquaculture species. We identified molecular events that occur due to the inclusion of high carbohydrate levels in the diets of genetically improved ‘Jayanti rohu’ Labeo rohita. To reveal transcriptional changes in the liver of rohu, a feeding experiment was conducted with three doses of gelatinized starch (20% (control), 40%, and 60%). Transcriptome sequencing revealed totals of 15,232 (4464 up- and 4343 down-regulated) and 15,360 (4478 up- and 4171 down-regulated) differentially expressed genes. Up-regulated transcripts associated with glucose metabolisms, such as hexokinase, PHK, glycogen synthase and PGK, were found in fish fed diets with high starch levels. Interestingly, a de novo lipogenesis mechanism was found to be enriched in the livers of treated fish due to up-regulated transcripts such as FAS, ACCα, and PPAR...

Research paper thumbnail of De novo Assembly and Genome-Wide SNP Discovery in Rohu Carp, Labeo rohita

Research paper thumbnail of Additional file 1 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Additional file 2 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Additional file 7 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Additional file 4 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Additional file 8 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Additional file 5 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Additional file 3 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Additional file 10 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Additional file 6 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Additional file 12 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Additional file 9 of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

Research paper thumbnail of Evaluation of the carcass and commercial characteristics of carps

The role of carcass evaluation techniques in aquaculture research programs, especially in genetic... more The role of carcass evaluation techniques in aquaculture research programs, especially in genetics, breeding, production management, feeding and nutrition, cannot be overemphasized. Knowledge of production efficiencies and growth potentials in relation to desired carcass attributes has provided an impetus to improvements in genetic selection techniques and management of aquatic food animals. Accurate, standard and uniform methods of carcass evaluation are critically important. A standard format developed for collection of data on carps is presented in this paper.

Research paper thumbnail of Revelation of candidate genes and molecular mechanism of reproductive seasonality in female rohu (Labeo rohita Ham.) by RNA sequencing

BMC Genomics

Background Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of Sou... more Background Carp fish, rohu (Labeo rohita Ham.) is important freshwater aquaculture species of South-East Asia having seasonal reproductive rhythm. There is no holistic study at transcriptome level revealing key candidate genes involved in such circannual rhythm regulated by biological clock genes (BCGs). Seasonality manifestation has two contrasting phases of reproduction, i.e., post-spawning resting and initiation of gonadal activity appropriate for revealing the associated candidate genes. It can be deciphered by RNA sequencing of tissues involved in BPGL (Brain-Pituitary-Gonad-Liver) axis controlling seasonality. How far such BCGs of this fish are evolutionarily conserved across different phyla is unknown. Such study can be of further use to enhance fish productivity as seasonality restricts seed production beyond monsoon season. Result A total of ~ 150 Gb of transcriptomic data of four tissues viz., BPGL were generated using Illumina TruSeq. De-novo assembled BPGL tissues reveal...

Research paper thumbnail of Incidence and Molecular Analysis of V. cholerae among Some Primitive Tribes in Odisha, India

International Journal of Current Microbiology and Applied Sciences

Research paper thumbnail of Protein fingerprinting profiles in different strains of Aeromonas hydrophila isolated from diseased freshwater fish

World Journal of Microbiology and Biotechnology, May 31, 2005

Aeromonas hydrophila (Ah) strains isolated from diseased fish in India were studied for protein p... more Aeromonas hydrophila (Ah) strains isolated from diseased fish in India were studied for protein profiling using the SDS-PAGE protein fingerprinting profile pattern of whole cells of 12 local strains of A. hydrophila and one reference strain (MTCC 646). Variability among the strains was observed. The average similarity between the 12 strains of A. hydrophila ranged from 0.272 to 0.916. Proteins with molecular mass of 55.6 and 14.67 kDa in Ah1, Ah2 and Ah3, 28.5 and 27.9 kDa in Ah4, Ah5 and Ah6, 21.4 and 19.5 kDa in Ah7, Ah8, Ah9 and 72.9, 91.5 and 71.3 kDa in Ah10, Ah11 and Ah12 were common. The protein polypeptide bands from 19.5 to 86.2 kDa were common in both local strains and reference strain of A. hydrophila. The protein fingerprinting study showed that there is genetic similarity between strains of A. hydrophila and reference strain (MTCC 646). These protein markers may be useful for further strain differentiation in epidemiological study.

Research paper thumbnail of RESEARCH ARTICLE Construction, De-Novo Assembly and Analysis of Transcriptome for Identification of Reproduction-Related Genes and Pathways from Rohu, Labeo rohita

Rohu is a leading candidate species for freshwater aquaculture in South-East Asia. Unlike common ... more Rohu is a leading candidate species for freshwater aquaculture in South-East Asia. Unlike common carp the monsoon breeding habit of rohu restricts its seed production beyond sea-son indicating strong genetic control over spawning. Genetic information is limited in this regard. The problem is exacerbated by the lack of genomic-resources. We identified 182 reproduction-related genes previously by Sanger-sequencing which were less to address the issue of seasonal spawning behaviour of this important carp. Therefore, the present work was taken up to generate transcriptome profile by mRNAseq. 16GB, 72bp paired end (PE) data was generated from the pooled-RNA of twelve-tissues from pre-spawning rohu using IlluminaGA-II-platform. There were 64.97 million high-quality reads producing 62,283 contigs and 88,612 numbers of transcripts using velvet and oases programs, respectively. Gene ontology annotation identified 940 reproduction-related genes consisting of 184 mainly asso-ciated with reprod...

Research paper thumbnail of Activin receptor TypeIIB in rohu (Labeo rohita): Molecular characterization, tissue distribution and Immunohistochemical localization during different stages of gonadal maturation

Activin receptor type IIB (ActRIIB) is a transmembrane serine/threonine kinase receptor which pla... more Activin receptor type IIB (ActRIIB) is a transmembrane serine/threonine kinase receptor which plays a pivotal role in regulating reproduction in vertebrates including teleost. Earlier studies have documented its importance in governing gonadal maturation in higher vertebrates. However, reports on regulation of fish reproductive system by ActRIIB gene are still limited. Here, we report identification and characterization of ActRIIB cDNA of Labeo rohita, a commercially important fish species of the Indian subcontinent. The full-length gene encoding rohu ActRIIB was cloned and found to be of 1674 bp in length. Functional similarities were evident form evolutionary analysis across vertebrates. Real-time PCR to measure the expression of ActRIIB transcript in rohu revealed significant mRNA levels in gonads followed by non-reproductive tissues, including brain, pituitary and muscle. With respect to different gonadal maturation stages, predominant expression of ActRIIB mRNA was observed dur...

Research paper thumbnail of The draft genome of Labeo catla

BMC Research Notes

Objective: Labeo catla (catla), one of the three Indian major carps, is native to the Indo-Ganget... more Objective: Labeo catla (catla), one of the three Indian major carps, is native to the Indo-Gangetic riverine system of India as well as the rivers of Pakistan, Bangladesh, Nepal and Myanmar. Its higher growth rate and compatibility with other major carps, specific surface feeding habit, and consumer preference have increased its popularity in carp polyculture systems among the fish farmers in Indian subcontinent. Recent advancement in sequencing technology coupled with massive parallel sequencing platforms has facilitated accelerated genetic improvement in aquaculture species through integration of genomics tools. A draft genome and allied resources are lacking in catla. Therefore, in the present study, we have performed de-novo assembly of Labeo catla for the first time. Data description: A male farm reared catla was used for extracting high molecular weight genomic DNA followed by sequencing in Oxford Nanopore and Illumina platforms. Approximately, 80× coverage of sequence data was assembled adopting the hybrid assembly strategy. The assembled genome size of catla was 1.01 Gb containing 5345 scaffolds with N50 value 0.7 Mb and more than 92% BUSCO completeness. Gene annotation resulted in 25,812 predicted genes.

Research paper thumbnail of Revealing Alteration in the Hepatic Glucose Metabolism of Genetically Improved Carp, Jayanti Rohu Labeo rohita Fed a High Carbohydrate Diet Using Transcriptome Sequencing

International Journal of Molecular Sciences

Although feed cost is the greatest concern in aquaculture, the inclusion of carbohydrates in the ... more Although feed cost is the greatest concern in aquaculture, the inclusion of carbohydrates in the fish diet, and their assimilation, are still not well understood in aquaculture species. We identified molecular events that occur due to the inclusion of high carbohydrate levels in the diets of genetically improved ‘Jayanti rohu’ Labeo rohita. To reveal transcriptional changes in the liver of rohu, a feeding experiment was conducted with three doses of gelatinized starch (20% (control), 40%, and 60%). Transcriptome sequencing revealed totals of 15,232 (4464 up- and 4343 down-regulated) and 15,360 (4478 up- and 4171 down-regulated) differentially expressed genes. Up-regulated transcripts associated with glucose metabolisms, such as hexokinase, PHK, glycogen synthase and PGK, were found in fish fed diets with high starch levels. Interestingly, a de novo lipogenesis mechanism was found to be enriched in the livers of treated fish due to up-regulated transcripts such as FAS, ACCα, and PPAR...

Research paper thumbnail of De novo Assembly and Genome-Wide SNP Discovery in Rohu Carp, Labeo rohita