Buffalo liver transcriptome analysis suggests immune tolerance as its key adaptive mechanism during early postpartum negative energy balance

Singh, Shivangi; Golla, Naresh; Sharma, Davinder; Singh, Dheer; Onteru, Suneel Kumar

doi:10.1007/s10142-019-00676-1

Cited by 9 publications

(6 citation statements)

References 53 publications

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“…A recent study by Singh et al [50] isolated the RNA transcripts from buffalo liver tissues with an excellent quality of NGS data having score of FastQC quality up to 30. Further, reported 54 million reads having an alignment percentage of > 84% with reference genome [50]. The 178.57 Gb clean transcriptomic data of our study with a minimum Q score of ≥ Q30 revealed a 1/1000 probability of incorrect base calling and the clean reads with GC contents were 28337044 and 52.77%, respectively.…”

Section: Discussionmentioning

confidence: 99%

“…Thus, using Phred quality scores Q with base calling error probabilities P is a crucial step to access the data quality [ 49 ]. A recent study by Singh et al [ 50 ] isolated the RNA transcripts from buffalo liver tissues with an excellent quality of NGS data having score of FastQC quality up to 30. Further, they reported 54 million reads having an alignment percentage of > 84% with reference genome [ 50 ].…”

Section: Discussionmentioning

confidence: 99%

“…A recent study by Singh et al [ 50 ] isolated the RNA transcripts from buffalo liver tissues with an excellent quality of NGS data having score of FastQC quality up to 30. Further, they reported 54 million reads having an alignment percentage of > 84% with reference genome [ 50 ].…”

Section: Discussionmentioning

confidence: 99%

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De Novo Transcriptome Dataset Generation of the Swamp Buffalo Brain and Non-Brain Tissues

Wang

Hassan

Liu

et al. 2022

BioMed Research International

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The sequenced data availability opened new horizons related to buffalo genetic control of economic traits and genomic diversity. The visceral organs (brain, liver, etc.) significantly involved in energy metabolism, docility, or social interactions. We performed swamp buffalo transcriptomic profiling of 24 different tissues (brain and non-brain) to identify novel transcripts and analyzed the differentially expressed genes (DEGs) of brain vs. non-brain tissues with their functional annotation. We obtained 178.57 Gb clean transcriptomic data with GC contents 52.77%, reference genome alignment 95.36%, exonic coverage 88.49%. Totally, 26363 mRNAs transcripts including 5574 novel genes were obtained. Further, 7194 transcripts were detected as DEGs by comparing brain vs. non-brain tissues group, of which 3,999 were upregulated and 3,195 downregulated. These DEGs were functionally associated with cellular metabolic activities, signal transduction, cytoprotection, and structural and binding activities. The related functional pathways included cancer pathway, PI3k-Akt signaling, axon guidance, JAK-STAT signaling, basic cellular metabolism, thermogenesis, and oxidative phosphorylation. Our study provides an in-depth understanding of swamp buffalo transcriptomic data including DEGs potentially involved in basic cellular activities and development that helped to maintain their working capacity and social interaction with humans, and also, helpful to disclose the genetic architecture of different phenotypic traits and their gene expression regulation.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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De Novo Transcriptome Dataset Generation of the Swamp Buffalo Brain and Non-Brain Tissues

Wang

Hassan

Liu

et al. 2022

BioMed Research International

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“…The data were processed by SPSS 20.0 two-tailed Student’s t-test ( Singh et al, 2019 ). All the results are presented as means ± standard deviation.…”

Section: Matericals and Methodsmentioning

confidence: 99%

MiRNA-Seq reveals key MicroRNAs involved in fat metabolism of sheep liver

Fei

Jin²,

Yuan³

et al. 2023

Front. Genet.

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There is a genetic difference between Hu sheep (short/fat-tailed sheep) and Tibetan sheep (short/thin-tailed sheep) in tail type, because of fat metabolism. Previous studies have mainly focused directly on sheep tail fat, which is not the main organ of fat metabolism. The function of miRNAs in sheep liver fat metabolism has not been thoroughly elucidated. In this study, miRNA-Seq was used to identify miRNAs in the liver tissue of three Hu sheep (short/fat-tailed sheep) and three Tibetan sheep (short/thin-tailed sheep) to characterize the differences in fat metabolism of sheep. In our study, Hu sheep was in a control group, we identified 11 differentially expressed miRNAs (DE miRNAs), including six up-regulated miRNAs and five down-regulated miRNAs. Miranda and RNAhybrid were used to predict the target genes of DE miRNAs, obtaining 3,404 target genes. A total of 115 and 67 GO terms as well as 54 and 5 KEGG pathways were significantly (padj < 0.05) enriched for predicted 3,109 target genes of up-regulated and 295 target genes of down-regulated miRNAs, respectively. oar-miR-432 was one of the most up-regulated miRNAs between Hu sheep and Tibetan sheep. And SIRT1 is one of the potential target genes of oar-miR-432. Furthermore, functional validation using the dual-luciferase reporter assay indicated that the up-regulated miRNA; oar-miR-432 potentially targeted sirtuin 1 (SIRT1) expression. Then, the oar-miR-432 mimic transfected into preadipocytes resulted in inhibited expression of SIRT1. This is the first time reported that the expression of SIRT1 gene was regulated by oar-miR-432 in fat metabolism of sheep liver. These results could provide a meaningful theoretical basis for studying the fat metabolism of sheep.

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“…The liver transcriptome data from our previous study (Singh et al 2019) were analysed in the present study to identify interspecies and intragenus SNPs. The liver transcriptome data were obtained by performing RNA-seq on the liver biopsy samples (NDRI Institutional Animal Ethics Committee approval no.…”

Section: Buffalo Liver Transcriptome Datamentioning

confidence: 99%

Inter-species SNPs from buffalo liver transcriptome indicate diversity in immune pathways between buffalo and cattle

Venkata,

Singh,

Vedamurthy

et al. 2024

Preprint

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Graphical abstract Abstract: The duration of negative energy balance (NEB), a physiological adaptation in females during early postpartum, and its coping mechanisms vary among animals, breeds and species because of genetic differences. However, genetic variations that may influence the NEB differences between cattle and buffaloes were not reported. Therefore, the present study aims to identify such genetic differences between cattle and buffaloes by identifying inter-species single nucleotide polymorphisms (SNPs) by mapping the available liver RNA-seq data earlier obtained from three early postpartum buffaloes and three heifers to the cattle genome (UMD 3.1) using the SNP eff tool. The liver transcriptome data were chosen, as it is the major metabolic organ in balancing metabolic milieu to meet different physiological demands during early postpartum. Using the identified interspecies SNPs, intragenus SNPs (Buffalo) were derived from six different Murrah buffaloes and mapped them to the Bubalus bubalis (ASM312139v1) genome. Further, functional annotation and biological pathway analyses were performed for those genes harbouring the putative SNPs. We identified a total of 1,40,056 interspecies and 188 intragenus SNPs. Functional annotation and pathway analyses revealed that most of the putative interspecies SNPs between the cattle (Bos taurus UMD 3.1) and buffalo (Bubalis bubalus) were in the protein metabolism genes (>1900) predominantly involved in the immune system (>1800 genes). Similarly, most of the putative intragenus SNPs among buffaloes were in the genes of lipid metabolic pathways. In conclusion, our study suggests that cattle and buffaloes might differ in protein metabolism genes involved in immunity at the deoxyribonucleic acid (DNA) level.

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Buffalo liver transcriptome analysis suggests immune tolerance as its key adaptive mechanism during early postpartum negative energy balance

Cited by 9 publications

References 53 publications

De Novo Transcriptome Dataset Generation of the Swamp Buffalo Brain and Non-Brain Tissues

De Novo Transcriptome Dataset Generation of the Swamp Buffalo Brain and Non-Brain Tissues

MiRNA-Seq reveals key MicroRNAs involved in fat metabolism of sheep liver

Inter-species SNPs from buffalo liver transcriptome indicate diversity in immune pathways between buffalo and cattle

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