De novo assembly and characterization of tissue-specific transcriptome in the endangered golden mahseer, Tor putitora

Barat, Ashoktaru; Kumar, Rohit; Goel, Chirag; Singh, Atul K.; Sahoo, Prabhati Kumari

doi:10.1016/j.mgene.2015.11.001

Cited by 10 publications

(4 citation statements)

References 20 publications

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“…Consistent with previous research on the tissue-specific transcriptome of golden mahseer [17], the gene annotation analysis in this study revealed a high degree of homology between golden mahseer and zebrafish (80%), followed by common carp (12%) and Nile tilapia (2%). Conversely, low homology of gene annotations was observed with Atlantic salmon (Salmo salar), southern platyfish (Xiphophorus maculatus), and goldfish (Carassius auratus).…”

Section: Discussionsupporting

confidence: 91%

“…In prior transcriptome studies of golden mahseer tissue, more emphasis was placed on immunogene expression, and the genes involved in local adaptation to the environment [17,18], and the understanding of the genetic information relevant to gonad development and reproduction in this species is thus incomplete. To address this knowledge gap, we conducted an RNA-sequencing (RNA-Seq) study on a complementary DNA (cDNA) library generated from the brain tissue of mature male and female golden mahseer.…”

Section: Introductionmentioning

confidence: 99%

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RNA-Seq Reveals Differential Gene Expression Patterns Related to Reproduction in the Golden Mahseer

Shahi

Singh

Mallik

et al. 2023

Fishes

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Golden mahseer (Tor putitora) is a critically endangered fish with significant economic importance. However, its reproductive challenges in a captive environment pose a limitation to the successful domestication and aquaculture potential of this species. To understand the role of various genes in gonad maturation and reproduction in golden mahseer, we conducted an RNA-sequencing (RNA-Seq) study on the brains of mature male and female specimens. Altogether, 20.6 and 21.5 million reads were generated from the brains of the male and female fish, respectively. A total of 26,989 and 55,600 cDNA coding sequences (CDS) were identified from the male and female brains, respectively, among which 26,258 CDS from the male brain and 53,446 CDS from the female brain demonstrated homology to known protein database sequences. A comprehensive analysis revealed a total of 1187 distinct differentially expressed upregulated genes (DEGs), encompassing 953 DEGs anticipated to exhibit upregulation in the female brain and 234 DEGs in the male brain. Furthermore, in the brain of female and male golden mahseer, a significant downregulation was observed in 492 and 744 genes, respectively, resulting in a cumulative count of 1236 downregulated genes. Validation of the RNA-Seq results was performed by quantitative real-time PCR (qPCR) using 24 genes. Sixteen candidate genes with differential expression levels between the male and female fish were then selected and analyzed via qPCR. The results confirmed that amh, foxl3, dax1, kif20, and tkt were upregulated in the male golden mahseer brain, while cyp19a1a, dmrt2a, gdf9, sox9b, wt-1a, and aqp1 were upregulated in the female golden mahseer brain. Our study elucidates the distinct gene expression profiles in male and female golden mahseer brains and thus offers valuable insights for potential reproductive manipulation strategies in this fish species.

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Section: Discussionsupporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

RNA-Seq Reveals Differential Gene Expression Patterns Related to Reproduction in the Golden Mahseer

Shahi

Singh

Mallik

et al. 2023

Fishes

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“…Seasonality in breeding of fish is highly correlated with such immunity [ 115 ] ZGC Gene ZGC gene is involved in oocyte maturation and ovulation in zebrafish [ 116 ] CMYCB MYCB gene is involved in neuroendocrine secretion in brain and physiological regulation in liver, heart, kidney in fish (European sea bass) affecting growth and differentiation [ 117 ] ARHGEF ARHGEF is also known as Rho Guanine Nucleotide Exchange Factor gene family which is present in all eukaryotes including jawless (Lampreys, Agnatha) as well as jaw (cartilaginous and boney) fishes. These are the adaptive cell signaling mediators of environmental signals in mediating seasonality [ 118 ] DNAJC Also known as HSP 40 play major role in immune responses and their overexpression in liver is associated with defense mechanism [ 119 ] LIMA1 and LIMA1A splice variant LIM Domain And Actin Binding 1 (LIMA1) gene is associated with nuclear receptor essential for gonado-genesis [ 120 ] …”

Section: Resultsmentioning

confidence: 99%

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

et al. 2021

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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 revealed 75,554 differentially expressed transcripts, 115,534 SSRs, 65,584 SNPs, 514 pathways, 5379 transcription factors, 187 mature miRNA which regulates candidate genes represented by 1576 differentially expressed transcripts are available in the form of web-genomic resources. Findings were validated by qPCR. This is the first report in carp fish having 32 BCGs, found widely conserved in fish, amphibian, reptile, birds, prototheria, marsupials and placental mammals. This is due to universal mechanism of rhythmicity in response to environment and earth rotation having adaptive and reproductive significance. Conclusion This study elucidates evolutionary conserved mechanism of photo-periodism sensing, neuroendocrine secretion, metabolism and yolk synthesis in liver, gonadal maturation, muscular growth with sensory and auditory perception in this fish. Study reveals fish as a good model for research on biological clock besides its relevance in reproductive efficiency enhancement.

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“…The development of high-throughput sequencing technology has made transcriptome sequencing widely used, greatly improving the efficiency of gene discovery [ 15 , 16 , 17 , 18 ]. The development of sequencing technology has provided scientists with powerful tools for studying plant transcriptomes.…”

Section: Introductionmentioning

confidence: 99%

Full-Length Transcriptome Analysis of Four Different Tissues of Cephalotaxus oliveri

Wang

2021

IJMS

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Cephalotaxus oliveri is a tertiary relict conifer endemic to China, regarded as a national second-level protected plant in China. This species has experienced severe changes in temperature and precipitation in the past millions of years, adapting well to harsh environments. In view of global climate change and its endangered conditions, it is crucial to study how it responds to changes in temperature and precipitation for its conservation work. In this study, single-molecule real-time (SMRT) sequencing and Illumina RNA sequencing were combined to generate the complete transcriptome of C. oliveri. Using the RNA-seq data to correct the SMRT sequencing data, the four tissues obtained 63,831 (root), 58,108 (stem), 33,013 (leaf) and 62,436 (male cone) full-length unigenes, with a N50 length of 2523, 3480, 3181, and 3267 bp, respectively. Additionally, 35,887, 11,306, 36,422, and 25,439 SSRs were detected for the male cone, leaf, root, and stem, respectively. The number of long non-coding RNAs predicted from the root was the largest (11,113), and the other tissues were 3408 (stem), 3193 (leaf), and 3107 (male cone), respectively. Functional annotation and enrichment analysis of tissue-specific expressed genes revealed the special roles in response to environmental stress and adaptability in the different four tissues. We also characterized the gene families and pathways related to abiotic factors. This work provides a comprehensive transcriptome resource for C. oliveri, and this resource will facilitate further studies on the functional genomics and adaptive evolution of C. oliveri.

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De novo assembly and characterization of tissue-specific transcriptome in the endangered golden mahseer, Tor putitora

Cited by 10 publications

References 20 publications

RNA-Seq Reveals Differential Gene Expression Patterns Related to Reproduction in the Golden Mahseer

RNA-Seq Reveals Differential Gene Expression Patterns Related to Reproduction in the Golden Mahseer

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

Full-Length Transcriptome Analysis of Four Different Tissues of Cephalotaxus oliveri

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