Introduction to Genome Wide Identification

However, conventional approaches for genome-wide identification of TE insertion sites are costly and laborious.

In this review, we summarize recent milestones in characterizing the human genetic basis of DNA methylation variation over the last decade, including heritability findings and genome-wide identification of meQTLs.

DrugCHIPER-CS as a computational approach can speed the genome-wide identification of drug target on jamu formula efficiently.

As detailed in this report, the data generated from both genome-wide identification and expression analysis of lipoxygenase genes suggest the putative functions of two 13-LOXs ( SbLOX9 and SbLOX5 ) and three 9-LOXs ( SbLOX1, SbLOX3, and SbLOXo ) in biosynthesis of jasmonic acid, green leaf volatiles and death acids, and all of them are involved in defense-related functions in plants.

Currently, genome-wide identification of non-coding regulatory elements is an active area of research with significant progress made in humans, mice, and other model organisms.

Genome-wide identification and characterization of MITEs provide essential information for understanding genome structure and evolution.

In the present study, comprehensive analyses, including genome-wide identification, phylogeny, conserved domain/motif, gene structure, chromosomal location, subcellular localization, gene duplication, and expression patterns of the SOCS gene family in grass carp, were performed, based on genomic and transcriptomic data.

At present, a comprehensive investigation into the genome-wide identification and classification of MADS-box genes in foxtail millet (Setaria italica L.

Conclusions: This study provides the genome-wide identification and functional characterization of lncRNAs associated with 20E-induced autophagy in the fat body of B.

OBJECTIVE: Current work aims for a genome-wide identificationof CAD family and its expression correlation with fruit firmness in strawberry varieties.

Here, we performed genome-wide identification and comparative analysis of flowering-time genes in three palnt families i.

Genome-wide identification of regulatory elements (REs) responsible for regulating gene activity is key to further mechanistic studies.

This study was aimed at the genome-wide identification, a comprehensive in silico characterization of NHX genes from soybean ( Glycine max L.

Existing experimental methods are time-consuming and expensive, highlighting the need for computational approaches to accelerate the genome-wide identification of enhancers.

MAIN CONCLUSION Genome-wide identification, expression analysis of the MYC family in Camellia sinensis, and potential functional characterization of CsMYC2.

Upscaled high-throughput versions of CAGE have enabled the genome-wide identification of transcription start sites, including transcriptionally active promoters and enhancers.

In this study, we conducted genome-wide identification and characterization of OR genes in the snow leopard and compared them to all other Panthera species.

Whereas most studies of TGLs have focused on seed oil metabolism and biofuel in plants, limited information is available regarding the genome-wide identification and characterization of the TGL gene family in tomato (Solanum lycopersicum L.

Conclusion As NAC genes are known to play role in several physiological and biological activities, a more comprehensive study on genome-wide identification and expression analyses of the NAC proteins have been carried out in chickpea, pigeonpea and groundnut.

Summary Translation initiation site (TIS) profiling allows for the genome-wide identification of TISs in vivo by exclusively capturing mRNA fragments within ribosomes that have just completed translation initiation.

MAIN CONCLUSION Genome-wide identification reveals 55 PvuGRAS genes belonging to 16 subfamilies and their gene structures and evolutionary relationships were characterized.

Therefore, genome-wide identification of MITE insertions can help to shed light on their copy number variation and genome insertion features.

In this paper, to gain more insights into the regulatory mechanism of miRNAs in apple fruit ripening, a genome-wide identification of the sRNAome was implemented in the postharvest ‘Qinguan’ apple fruit.

Though many omics approaches have been employed to study in planta survival strategies, the direct genome-wide identification of R.

We performed genome-wide identification and expression analysis of the STP gene family to investigate the STPSs’ potential roles in the growth of wheat seedlings under stress.

The development of high throughput genetic tools is needed to dissect the function of multigene families, targeting several genes in a specific pathway, and finally genome-wide identification of essential genes to find novel drug targets.

Overall, genome-wide identification approach was used to further analyze the related functions of the RF gene family, which may include the response to drought stress, in cotton.

Here, we performed genome-wide identification and evolutionary analysis of the REM gene family in Rosaceae.

Results Here, we have performed a genome-wide identification of FCS-like zinc finger (FLZ) proteins and assessed their involvement in submergence response in rice.

The transcription factor Scleraxis (Scx) is expressed throughout tendon development and plays essential roles in both embryonic tendon development and adult tendon healing, but few direct target genes of Scx in tendon development have been reported and genome-wide identification of Scx direct target genes in vivo has been lacking.

A genome-wide identification and expression analysis of multidrug and toxic compound extrusion (MATE) gene family in potato was carried out to explore the response of MATE proteins to heavy meta stress.

We used genome-wide identification, phylogenetic analysis, chromosomal distribution and collinearity to examine potential functions of Lhc superfamily genes in upland cotton.

The genome-wide identification and expression analysis of genes related to the branched-chain amino acids (BCAA) synthesis pathway were carried out.

Results: In this study, genome-wide identification was carried out on G-type lectin gene family in Fragaria vesca.

Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes.

Results To investigate the roles played by the AHL gene family in soybean, genome-wide identification, expression patterns and gene structures were performed to analyze.

Further, genome-wide identification of OsLEC1 binding sites demonstrated that OsLEC1 directly bound to genes involved in photosynthesis, photomorphogenesis, as well as abscisic acid (ABA) and gibberellin (GA) pathways, in seed maturation.

Various studies have demonstrated multiple cellular functions of Hsps in living organisms as an important biomarker in response to abiotic and biotic stressors, however, full genome-wide identification of Hsps, particularly in aquatic invertebrates, has not been reported.

In this study, the genome-wide identification of SOD genes and their expression patterns under abiotic stresses has been done in watermelon and melon.

The genome-wide identification of TaNRAMP1 (natural resistance-associated macrophage protein 1), known as high-affinity Mn transporter, showed several polymorphisms within genome A, B, and D.

In this study, we characterized 37 VrDIR genes in mungbean using a genome-wide identification method.

Genome-wide identification and expression analysis of SLAC/SLAH gene family members were performed in B.

The PYL gene family has been identified and analyzed in many species, however, there is no report about the research on the whole genome-wide identification of the alfalfa (Medicago sativa L.

In this study, we have carried out genome-wide identification and bioinformatics characterization of basic leucine zipper domain proteins (bZIPs) from cultivated cotton species Gossypium hirsutum along with two sub-genome species of allotetraploid cotton, Gossypium arboreum and Gossypium raimondii.

Herein, our study aimed to perform a genome-wide identification of the PUT gene family in C.

The current experimental methods provide a genome-wide identification of epigenetic modifications; however, they are expensive and time-consuming.

aralocaspica and comparatively analyze their expression and regulation patterns as well as the biochemical and enzymatic properties in this study, we characterized a bacterial-type PEPC (BTPC; SaPEPC-4) in addition to the two plant-type PEPCs (PTPCs; SaPEPC-1 and SaPEPC-2) using a genome-wide identification.

Thus, a comprehensive genome-wide identification analysis was performed to identify HSFs in the maize genome.

Here, we performed genome-wide identification of heat shock protein 70 family in the silkworm, Bombyx mori.

An accurate and reliable genome-wide identification of 6mA sites is crucial for systematically understanding its biological functions.

However, the increasing availability of reference genomes and bioinformatic tools provides better means for the genome-wide identification and analysis of MITEs and for the elucidation of their contribution to the evolution of plant genomes.

Here, we carried out genome-wide identification and expression analysis of the GLP gene family in cucumber to study their possible functions.

Genome-wide identification of MADS-Box transcription factors revealed loss of Mβ, and Mγ genes belonging to Type I subclass in the rattan lineage.

The genome-wide identification and co-expression analyses of M.

A genome-wide identification of the SDR gene family in M.

barbadense , respectively, via genome-wide identification.

The present study aimed to a comprehensive genome-wide identification and functional characterization of GST family in one of the economically important legume plants—Medicago truncatula.

Here, we conducted a genome-wide identification of R-loops and identified more than 700,000 R-loop peaks in the maize (Zea mays) genome.

Herein, a genome-wide identification and comprehensive bioinformatic analysis of 36 MDHAR family genes in four Gossypium species, Gossypium arboreum, G.

Herein, we performed genome-wide identification and characterization of ALMTs in B.

This is the first study to report a genome-wide identification of the MAPK, MAPKK, and MAPKK gene families in O.

Thus, a comprehensive analysis of 58 longan DEAD-box (DlDDX) genes characterization was performed by genome-wide identification and transcript abundance validation analysis.

Genome-wide identification and characterization of AP2/ERF genes has not yet been carried out in the oil palm genome.

reference genome has facilitated the genome-wide identification and characterization of NBS-encoding genes in radish.

The aim of the present study was to perform a whole-genome-wide identification of lncRNAs and mRNAs associated with DS.

In this study, genome-wide identification of G4 motifs in barley was performed, followed by a comparison of genomic distribution and molecular functions to other monocot species, such as wheat, maize, and rice.

In conclusion, the genome-wide identification analysis coupled with RNA-Seq expression data led to identifying candidate StbZIPs, which are dysregulated, and may play a pivotal role under various abiotic stress conditions.

This is the first genome-wide identification of transcriptional regulators of SSP genes in wheat, and the newly characterized transcriptional regulators will undoubtedly expand our knowledge of the transcriptional regulation of SSP synthesis.

In addition, we carried out a genome-wide identification and phylogenetic analysis of TGF-β superfamily in R.

Herein, this study aimed to discern gene(s) involved in petal coloration in Liriodendron via genome-wide identification, HPLC, and RT-qPCR assays.

Here, we identified a total of 23 ARF (EgARF) genes in oil palm through a genome-wide identification approach.

G protein-coupled receptors (GPCRs) are considered to have originated from early evolution of eukaryotic species, therefore, the genome-wide identification of GPCR genes can provide insight into the adaptive strategy and evolutionary tendency in an animal taxon.

However, there is no report on the genome-wide identification and comparison of CPs in the pollen coat and other tissues in maize.

Present study was aimed at genome-wide identification, comprehensive in silico characterization and involvement of NHX antiporters in plant development and abiotic stress responses of Indica rice (Oryza sativa subsp.

In addition, genome-wide identification of cytochrome P450s, glutathione S-transferases, and ATP-binding cassette transporters in E.

Here, we present genome-wide identification of AsA-GSH cycle genes (APX, MDHAR, DHAR, and GR) in several leguminous species and expression analyses in G.

The development of high-throughput sequencing and bioinformatics algorithms provides the possibility of genome-wide identification of alternative splicing events in eukaryotes.

However, limited information is available on genome-wide identification and characterization of the TPS family in Aquilaria trees.

Results: In this study, we performed a genome-wide identification of the TPP gene family in common wheat, and identified a total of 31 TPP genes.

Here, we performed genome-wide identification of the amino acid auxin permeases in the brown planthopper (BPH), Nilaparvata lugens, a devastating pest that feeds on the phloem sap of rice plants.

barbadense, respectively, via genome-wide identification.

In this study, we performed genome-wide identification of GST genes in Upland cotton and identified GST genes functioning in accumulation of anthocyanins.

In this review, we analyze the studies on genome-wide identifications of plant transporters like Sugars Will Eventually be Exported Transporters (SWEET), Multidrug and toxic compound extrusion (MATE) transporters, ATP-binding cassette (ABC) transporters, Natural resistance-associated macrophage proteins (NRAMP), and Sugar Transport Proteins (STPs), all having a significant role in plant disease resistance.

The genome-wide identification of enhancer elements and their activity status in a cellular context is therefore fundamental to understanding cell identity and function.

Chromatin immunoprecipitation followed by massively parallel, high throughput sequencing (ChIP-seq) is the method of choice for genome-wide identification of DNA segments bound by specific transcription factors or in chromatin with particular histone modifications.

MAIN CONCLUSION Genome-wide identification, tissue-specific and stress expression analyses and functional characterization of PbrATG8s genes were conducted and the role of PbrATG8c in Botryosphaeria dothidea resistance was further investigated.

To understand their role in floral transition-related pathways, a genome-wide identification was done in Cajanus cajan , identifying 102 members which were classified into two different groups based on their gene structure.

In this study, genome-wide identification and comprehensive analysis of SDR superfamily were carried out in 29 animal species based on the latest genome databases.

Conclusions This study provides the genome-wide identification and functional characterization of lncRNAs associated with 20E-induced autophagy in the fat body of B.

Results In this work, a genome-wide identification of the bHLH genes in Chinese white pear was performed, and we characterized the functional roles of these PbrbHLH genes in response to abiotic stresses.

We carried out a genome-wide identification of the MLO gene family in the Rosa chinensis genome, and screened for allelic variants among 22 accessions from seven different Rosa species using re-sequencing and transcriptome data.

Conclusion This study provides the first genome-wide identification of S.

MAIN CONCLUSION Genome-wide identification, analysis and functional characterization of an unreported VvBBX gene showed a response to light and positive correlation with anthocyanin content, but also inhibition of light-induced anthocyanin synthesis.

Genome-wide identification of DNA double-strand breaks (DSBs) induced by CRISPR-associated protein (Cas) systems is vital for profiling the off-target events of Cas nucleases.

The genome-wide identification and characterization of BnaPDFs will enrich understanding of their molecular characteristics and provide elite gene resources for genetic improvement of rapeseed resistance to nutrient stresses.

In order to gain insight into the participation of ZFPs in grapevine gametophyte development, we performed a genome-wide identification and characterization of genes encoding ZFP (VviZFP family).

Therefore, we performed genome-wide identification of the AnSnRK2 genes and analyzed their expression profiles under osmotic stresses including drought and salinity.

Epigenetic profiling by chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become a powerful tool for genome-wide identification of regulatory elements, for defining transcriptional regulatory networks and for screening for biomarkers.

Using genome-wide identification, transcriptome profile analysis, and phylogenetic relationships, this research provides a new perspective on the critical functions of ABC transporters in S.

In this review, we provide a comprehensive contemporary overview on our knowledge about these K+ transporter families in angiosperms, with a major focus on the genome-wide identification of K+ transporter families, subcellular localization, spatial expression, function and regulation.