Fungal Screening on Olive Oil for Extracellular Triacylglycerol Lipases: Selection of a Trichoderma harzianum Strain and Genome Wide Search for the Genes

Abstract Background: Cotton is one of the most important commercial crops as the source of natural fiber, oil and fodder. To protect it from harmful pest populations number of newer transgenic lines have been developed. For quick expression checks in successful agriculture qPCR (quantitative polymerase chain reaction) have become extremely popular. The selection of appropriate reference genes plays a critical role in the outcome of such experiments as the method quantifies expression of the target gene in comparison with the reference. Traditionally most commonly used reference genes are the “ house-keeping genes”, involved in basic cellular processes. However, expression levels of such genes often vary in response to experimental conditions, forcing the researchers to validate the reference genes for every experimental platform. This study presents a data science driven unbiased genome-wide search for the selection of reference genes by assessing variation of >50,000 genes in a publicly available RNA- seq dataset of cotton species Gossypium hirsutum . Result: Five genes ( TMN5, TBL6, UTR5B, AT1g65240 and CYP76B6 ) identified by data-science driven analysis, along with two commonly used reference genes found in literature ( PP2A1 and UBQ14 ) were taken through qPCR in a set of 33 experimental samples consisting of different tissues (leaves, square, stem and root), different stages of leaf (young and mature) and square development (small, medium and large) in both transgenic and non-transgenic plants. Expression stability of the genes was evaluated using four algorithms - geNorm , BestKeeper , NormFinder and RefFinder. Conclusion: Based on the results we recommend the usage of TMN5 and TBL6 as the optimal candidate reference genes in qPCR experiments with normal and transgenic cotton plant tissues. AT1g65240 and PP2A1 can also be used if expression study includes squares. This study, for the first time successfully displays a data science driven genome-wide search method followed by experimental validation as a method of choice for selection of stable reference genes over the selection based on function alone.

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Genome wide search to identify reference genes candidates for gene expression analysis in Gossypium hirsutum

BMC Plant Biology ◽

10.1186/s12870-019-1988-3 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 3

Author(s):

P. K. Smitha ◽

K. Vishnupriyan ◽

Ananya S. Kar ◽

M. Anil Kumar ◽

Christopher Bathula ◽

...

Keyword(s):

Gossypium Hirsutum ◽

Reference Genes ◽

Data Science ◽

Natural Fiber ◽

Quantitative Polymerase Chain Reaction ◽

Critical Role ◽

Genome Wide ◽

Cotton Species ◽

Genome Wide Search ◽

Selection Of

Abstract Background Cotton is one of the most important commercial crops as the source of natural fiber, oil and fodder. To protect it from harmful pest populations number of newer transgenic lines have been developed. For quick expression checks in successful agriculture qPCR (quantitative polymerase chain reaction) have become extremely popular. The selection of appropriate reference genes plays a critical role in the outcome of such experiments as the method quantifies expression of the target gene in comparison with the reference. Traditionally most commonly used reference genes are the “house-keeping genes”, involved in basic cellular processes. However, expression levels of such genes often vary in response to experimental conditions, forcing the researchers to validate the reference genes for every experimental platform. This study presents a data science driven unbiased genome-wide search for the selection of reference genes by assessing variation of > 50,000 genes in a publicly available RNA-seq dataset of cotton species Gossypium hirsutum. Result Five genes (TMN5, TBL6, UTR5B, AT1g65240 and CYP76B6) identified by data-science driven analysis, along with two commonly used reference genes found in literature (PP2A1 and UBQ14) were taken through qPCR in a set of 33 experimental samples consisting of different tissues (leaves, square, stem and root), different stages of leaf (young and mature) and square development (small, medium and large) in both transgenic and non-transgenic plants. Expression stability of the genes was evaluated using four algorithms - geNorm, BestKeeper, NormFinder and RefFinder. Conclusion Based on the results we recommend the usage of TMN5 and TBL6 as the optimal candidate reference genes in qPCR experiments with normal and transgenic cotton plant tissues. AT1g65240 and PP2A1 can also be used if expression study includes squares. This study, for the first time successfully displays a data science driven genome-wide search method followed by experimental validation as a method of choice for selection of stable reference genes over the selection based on function alone.

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Genome Wide Search to Identify Reference Genes candidates for Gene Expression Analysis in Gossypium hirsutum

10.21203/rs.2.10200/v1 ◽

2019 ◽

Author(s):

Smitha P K ◽

Vishnupriyan K ◽

Ananya S. Kar ◽

Anil Kumar M ◽

Christopher Bathula ◽

...

Keyword(s):

Gossypium Hirsutum ◽

Reference Genes ◽

Data Science ◽

Experimental Validation ◽

Quantitative Polymerase Chain Reaction ◽

Critical Role ◽

Genome Wide ◽

Cotton Species ◽

Genome Wide Search ◽

Selection Of

Abstract Background: With the advent of newer breeds and transgenic varieties of commercial crops, qPCR (quantitative polymerase chain reaction) experiments have become extremely popular for quick expression checks. Selection of appropriate reference genes plays a critical role in quantifying the expression of target gene. Most commonly used reference genes in expression studies are the “house-keeping genes”, involved in basic cellular processes. However, expression levels of such genes often vary in response to experimental conditions, forcing the researchers to validate the reference genes in every experiment. This study presents a data science driven unbiased genome-wide search results for selection of reference genes by assessing variation of >50,000 genes in a publicly available RNA-seq dataset of cotton species Gossypium hirsutum. Selected candidate genes were validated experimentally across 33 samples from normal and transgenic G. hirsutum plants, harvested from different areas of the plant at different time points under various developmental conditions. Experimental validation also includes commonly used genes from literature to suggest the most stable set of 5 genes to be used for assessment of quantitative expression in cotton plants (Fig.1). Result: Five genes (TMN5, TBL6, UTR5B, AT1g65240, CYP76B6) identified by data-driven analysis, along with two commonly used reference genes for cotton found in literature (GhPP2A1 and GhuBQ14) were validated using qPCR in a set of 33 experimental samples consisting of different tissues (leaves, square, stem and root), different stages of leaf (young and mature) and square development (small, medium and large) in both transgenic and non-transgenic plants. Expression stability of the genes was evaulated using four different algorithms - DeltaCT, Genorm, BestKeeper and Normfinder. GhPP2A1 and TMN5 were identified as the most stable genes, followed by GhuBQ14 across all the samples tested. Conclusion: This study, for the first time successfully displays a data science driven genome-wide search method followed by experimental validation as a method of choice for selection of stable reference genes for experiment with cotton species. Based on the results we recommend use of GhPP2A1, TMN5 and GhuBQ14 as the optimal candidate reference genes in qPCR experiments with normal or transgenic cotton plant tissues.

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Genome-wide diversity analysis for signatures of selection of Bos indicus adaptability under extreme agro-climatic conditions of temperate and tropical ecosystems

Animal Gene ◽

10.1016/j.angen.2021.200115 ◽

2021 ◽

pp. 200115

Author(s):

Shivam Bhardwaj ◽

Sanjeev Singh ◽

Indrajit Ganguly ◽

A.K. Bhatia ◽

Vijay K. Bharti ◽

...

Keyword(s):

Bos Indicus ◽

Climatic Conditions ◽

Diversity Analysis ◽

Tropical Ecosystems ◽

Genome Wide ◽

Signatures Of Selection ◽

Selection Of

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Genome-wide search and structural and functional analyses for late embryogenesis-abundant (LEA) gene family in poplar

BMC Plant Biology ◽

10.1186/s12870-021-02872-3 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Zihan Cheng ◽

Xuemei Zhang ◽

Wenjing Yao ◽

Kai Zhao ◽

Lin Liu ◽

...

Keyword(s):

Gene Family ◽

Higher Plants ◽

Abiotic Stress Tolerance ◽

Gene Families ◽

Regulatory Elements ◽

Late Embryogenesis Abundant ◽

Genome Wide ◽

Lea Gene ◽

Late Embryogenesis ◽

Genome Wide Search

Abstract Background The Late Embryogenesis-Abundant (LEA) gene families, which play significant roles in regulation of tolerance to abiotic stresses, widely exist in higher plants. Poplar is a tree species that has important ecological and economic values. But systematic studies on the gene family have not been reported yet in poplar. Results On the basis of genome-wide search, we identified 88 LEA genes from Populus trichocarpa and renamed them as PtrLEA. The PtrLEA genes have fewer introns, and their promoters contain more cis-regulatory elements related to abiotic stress tolerance. Our results from comparative genomics indicated that the PtrLEA genes are conserved and homologous to related genes in other species, such as Eucalyptus robusta, Solanum lycopersicum and Arabidopsis. Using RNA-Seq data collected from poplar under two conditions (with and without salt treatment), we detected 24, 22 and 19 differentially expressed genes (DEGs) in roots, stems and leaves, respectively. Then we performed spatiotemporal expression analysis of the four up-regulated DEGs shared by the tissues, constructed gene co-expression-based networks, and investigated gene function annotations. Conclusion Lines of evidence indicated that the PtrLEA genes play significant roles in poplar growth and development, as well as in responses to salt stress.

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Epigenome-Wide Study Identified Methylation Sites Associated with the Risk of Obesity

Nutrients ◽

10.3390/nu13061984 ◽

2021 ◽

Vol 13 (6) ◽

pp. 1984

Author(s):

Majid Nikpay ◽

Sepehr Ravati ◽

Robert Dent ◽

Ruth McPherson

Keyword(s):

Quantitative Trait Locus ◽

Quantitative Trait ◽

Rare Variants ◽

Genome Wide ◽

A Genome ◽

Genome Wide Search ◽

Risk Snps ◽

Trait Locus ◽

Genomic Regions ◽

Eqtl Data

Here, we performed a genome-wide search for methylation sites that contribute to the risk of obesity. We integrated methylation quantitative trait locus (mQTL) data with BMI GWAS information through a SNP-based multiomics approach to identify genomic regions where mQTLs for a methylation site co-localize with obesity risk SNPs. We then tested whether the identified site contributed to BMI through Mendelian randomization. We identified multiple methylation sites causally contributing to the risk of obesity. We validated these findings through a replication stage. By integrating expression quantitative trait locus (eQTL) data, we noted that lower methylation at cg21178254 site upstream of CCNL1 contributes to obesity by increasing the expression of this gene. Higher methylation at cg02814054 increases the risk of obesity by lowering the expression of MAST3, whereas lower methylation at cg06028605 contributes to obesity by decreasing the expression of SLC5A11. Finally, we noted that rare variants within 2p23.3 impact obesity by making the cg01884057 site more susceptible to methylation, which consequently lowers the expression of POMC, ADCY3 and DNAJC27. In this study, we identify methylation sites associated with the risk of obesity and reveal the mechanism whereby a number of these sites exert their effects. This study provides a framework to perform an omics-wide association study for a phenotype and to understand the mechanism whereby a rare variant causes a disease.

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Genome-Wide Search for Local DNA Segments with Anomalous GC-Content

Journal of Computational Biology ◽

10.1089/cmb.2008.0159 ◽

2009 ◽

Vol 16 (4) ◽

pp. 555-564 ◽

Cited By ~ 1

Author(s):

Andrey Ilatovskiy ◽

Michael Petukhov

Keyword(s):

Gc Content ◽

Genome Wide ◽

Genome Wide Search

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Molecular cloning and biochemical characterization of sialidases from zebrafish (Danio rerio)

Biochemical Journal ◽

10.1042/bj20070627 ◽

2007 ◽

Vol 408 (3) ◽

pp. 395-406 ◽

Cited By ~ 20

Author(s):

Marta Manzoni ◽

Paolo Colombi ◽

Nadia Papini ◽

Luana Rubaga ◽

Natascia Tiso ◽

...

Keyword(s):

Danio Rerio ◽

Biochemical Characterization ◽

Chromosome 21 ◽

Ph Optimum ◽

Reverse Transcription Pcr ◽

Genome Wide ◽

Genome Wide Search ◽

Putative Orthologues

Sialidases remove sialic acid residues from various sialo-derivatives. To gain further insights into the biological roles of sialidases in vertebrates, we exploited zebrafish (Danio rerio) as an animal model. A zebrafish transcriptome- and genome-wide search using the sequences of the human NEU polypeptides as templates revealed the presence of seven different genes related to human sialidases. neu1 and neu4 are the putative orthologues of the mammalian sialidases NEU1 and NEU4 respectively. Interestingly, the remaining genes are organized in clusters located on chromosome 21 and are all more closely related to mammalian sialidase NEU3. They were thus named neu3.1, neu3.2, neu3.3, neu3.4 and neu3.5. Using RT–PCR (reverse transcription–PCR) we detected transcripts for all genes, apart from neu3.4, and whole-mount in situ hybridization experiments show a localized expression pattern in gut and lens for neu3.1 and neu4 respectively. Transfection experiments in COS7 (monkey kidney) cells demonstrate that Neu3.1, Neu3.2, Neu3.3 and Neu4 zebrafish proteins are sialidase enzymes. Neu3.1, Neu3.3 and Neu4 are membrane-associated and show a very acidic pH optimum below 3.0, whereas Neu3.2 is a soluble sialidase with a pH optimum of 5.6. These results were further confirmed by subcellular localization studies carried out using immunofluorescence. Moreover, expression in COS7 cells of these novel zebrafish sialidases (with the exception of Neu3.2) induces a significant modification of the ganglioside pattern, consistent with the results obtained with membrane-associated mammalian sialidases. Overall, the redundancy of sialidases together with their expression profile and their activity exerted on gangliosides of living cells indicate the biological relevance of this class of enzymes in zebrafish.

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