scholarly journals PmiREN2.0: from data annotation to functional exploration of plant microRNAs

2021 ◽  
Author(s):  
Zhonglong Guo ◽  
Zheng Kuang ◽  
Yongxin Zhao ◽  
Yang Deng ◽  
Hao He ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Design Tools ◽  
Binding Motifs ◽  
Data Annotation ◽  
Genome Wide ◽  
A Genome ◽  
Plant Mirna ◽  
Regulatory Information ◽  
Mirna Evolution ◽  
New Discovery

Abstract Nearly 200 plant genomes have been sequenced over the last two years, and new functions of plant microRNAs (miRNAs) have been revealed. Therefore, timely update of the plant miRNA databases by incorporating miRNAs from the newly sequenced species and functional information is required to provide useful resources for advancing plant miRNA research. Here we report the update of PmiREN2.0 (https://pmiren.com/) with an addition of 19 363 miRNA entries from 91 plants, doubling the amount of data in the original version. Meanwhile, abundant regulatory information centred on miRNAs was added, including predicted upstream transcription factors through binding motifs scanning and elaborate annotation of miRNA targets. As an example, a genome-wide regulatory network centred on miRNAs was constructed for Arabidopsis. Furthermore, phylogenetic trees of conserved miRNA families were built to expand the understanding of miRNA evolution across the plant lineages. These data are helpful to deduce the regulatory relationships concerning miRNA functions in diverse plants. Beside the new data, a suite of design tools was incorporated to facilitate experimental practice. Finally, a forum named ‘PmiREN Community’ was added for discussion and resource and new discovery sharing. With these upgrades, PmiREN2.0 should serve the community better and accelerate miRNA research in plants.

scholarly journals Comprehensive Genome-Wide Analysis of The Catalase Enzyme Toolbox In Potato (Solanum Tuberosum L.)

2021 ◽  
Author(s):  
Rania Jbir Koubaa ◽  
Mariem Ayadi ◽  
Mohamed Najib Saidi ◽  
Safa Charfeddine ◽  
Radhia Gargouri Bouzid ◽  
...  
Keyword(s):  
Stress Responses ◽  
Expression Profiling ◽  
Phylogenetic Trees ◽  
Solanum Tuberosum L ◽  
Potato Cultivar ◽  
Promoter Sequence ◽  
3D Protein Structure ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Abstract As antioxidant enzymes, catalase (CAT) protects organisms from oxidative stress via the production of reactive oxygen species (ROS). These enzymes play important roles in diverse biological processes. However, little is known about the CAT genes in potato plants despite its important economical rank of this crop in the world. Yet, abiotic and biotic stresses severely hinder growth and development of the plants which affects the production and quality of the crop. To define the possible roles of CAT genes under various stresses, a genome-wide analysis of CAT gene family has been performed in potato plant.In this study, the StCAT gene’s structure, secondary and 3D protein structure, physicochemical properties, synteny analysis, phylogenetic tree and also expression profiling under various developmental and environmental cues were predicted using bioinformatics tools. The expression analysis by RT-PCR was performed using commercial potato cultivar. Three genes encoding StCAT that code for three proteins each of size 492 aa, interrupted by seven introns have been identified in potatoes. StCAT proteins were found to be localized in the peroxisome which is judged as the main H2O2 cell production site during different processes. Many regulating cis-elements related to stress responses and plant hormones signaling were found in the promoter sequence of each gene. The analysis of motifs and phylogenetic trees showed that StCAT are closer to their homologous in S. lycopersicum and share a 41% – 95% identity with other plants’ CATs. Expression profiling revealed that StCAT1 is the constitutively expressive member; while StCAT2 and StCAT3 are the stress-responsive members.

scholarly journals Hoxa1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on Hoxa1 targets

2016 ◽  
Author(s):  
Bony De Kumar ◽  
Hugo J. Parker ◽  
Ariel Paulson ◽  
Mark E. Parrish ◽  
Irina Pushel ◽  
...  
Keyword(s):  
Es Cells ◽  
Hox Proteins ◽  
Binding Motifs ◽  
Functional Roles ◽  
Regulatory Interactions ◽  
Mouse Es Cells ◽  
Genome Wide ◽  
A Genome ◽  
Combinatorial Interactions ◽  
Insight Into

AbstractHoxa1 has diverse functional roles in differentiation and development. We have identified and characterized properties of regions bound by Hoxa1 on a genome-wide basis in differentiating mouse ES cells. Hoxa1 bound regions are enriched for clusters of consensus binding motifs for Hox, Pbx and Meis and many display co-occupancy of Pbx and Meis. Pbx and Meis are members of the TALE family and genome-wide analysis of multiple TALE members (Pbx, Meis, TGIF, Prep1 and Prep2) show that nearly all Hoxa1 targets display occupancy of one or more TALE members. The combinatorial binding patterns of TALE proteins defines distinct classes of Hoxa1 targets and indicates a role as cofactors in modulating the specificity of Hox proteins. We also discovered extensive auto- and cross-regulatory interactions among the Hoxa1 and TALE genes. This study provides new insight into a regulatory network involving combinatorial interactions between Hoxa1 and TALE proteins.

scholarly journals Genome-wide reconstruction of rediploidization following autopolyploidization across one hundred million years of salmonid evolution

2021 ◽  
Author(s):  
Manu Kumar Gundappa ◽  
Thu-Hien To ◽  
Lars Grønvold ◽  
Samuel A M Martin ◽  
Sigbjørn Lien ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Divergence ◽  
Meiotic Pairing ◽  
Genome Wide ◽  
A Genome ◽  
Clock Analysis ◽  
Multiple Species ◽  
Genomic Regions ◽  
Genome Assemblies

The long-term evolutionary impacts of whole genome duplication (WGD) are strongly influenced by the ensuing rediploidization process. Following autopolyploidization, rediploidization involves a transition from tetraploid to diploid meiotic pairing, allowing duplicated genes (ohnologues) to diverge genetically and functionally. Our understanding of autopolyploid rediploidization has been informed by a WGD event ancestral to salmonid fishes, where large genomic regions are characterized by temporally delayed rediploidization, allowing lineage-specific ohnologue sequence divergence in the major salmonid clades. Here, we investigate the long-term outcomes of autopolyploid rediploidization at genome-wide resolution, exploiting a recent 'explosion' of salmonid genome assemblies, including a new genome sequence for the huchen (Hucho hucho). We developed a genome alignment approach to capture duplicated regions across multiple species, allowing us to create 121,864 phylogenetic trees describing ohnologue divergence across salmonid evolution. Using molecular clock analysis, we show that 61% of the ancestral salmonid genome experienced an initial 'wave' of rediploidization in the late Cretaceous (85-106 Mya). This was followed by a period of relative genomic stasis lasting 17-39 My, where much of the genome remained in a tetraploid state. A second rediploidization wave began in the early Eocene and proceeded alongside species diversification, generating predictable patterns of lineage-specific ohnologue divergence, scaling in complexity with the number of speciation events. Finally, using gene set enrichment, gene expression, and codon-based selection analyses, we provide insights into potential functional outcomes of delayed rediploidization. Overall, this study enhances our understanding of delayed autopolyploid rediploidization and has broad implications for future studies of WGD events.

scholarly journals Genomic signatures of pre-resistance in Mycobacterium tuberculosis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Arturo Torres Ortiz ◽  
Jorge Coronel ◽  
Julia Rios Vidal ◽  
Cesar Bonilla ◽  
David A. J. Moore ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Mycobacterium Tuberculosis ◽  
Phylogenetic Trees ◽  
Resistance Mutations ◽  
Resistance Evolution ◽  
Genomic Signatures ◽  
Genome Wide ◽  
A Genome ◽  
Lineage 2 ◽  
Emergence Of Resistance

AbstractRecent advances in bacterial whole-genome sequencing have resulted in a comprehensive catalog of antibiotic resistance genomic signatures in Mycobacterium tuberculosis. With a view to pre-empt the emergence of resistance, we hypothesized that pre-existing polymorphisms in susceptible genotypes (pre-resistance mutations) could increase the risk of becoming resistant in the future. We sequenced whole genomes from 3135 isolates sampled over a 17-year period. After reconstructing ancestral genomes on time-calibrated phylogenetic trees, we developed and applied a genome-wide survival analysis to determine the hazard of resistance acquisition. We demonstrate that M. tuberculosis lineage 2 has a higher risk of acquiring resistance than lineage 4, and estimate a higher hazard of rifampicin resistance evolution following isoniazid mono-resistance. Furthermore, we describe loci and genomic polymorphisms associated with a higher risk of resistance acquisition. Identifying markers of future antibiotic resistance could enable targeted therapy to prevent resistance emergence in M. tuberculosis and other pathogens.

Establishment of a genome-wide RNAi screen; Identification of novel genes involved in clonal maintenance of ALL

2014 ◽  
Vol 226 (03) ◽  
Author(s):  
F Ponthan ◽  
D Pal ◽  
J Vormoor ◽  
O Heidenreich
Keyword(s):  
Rnai Screen ◽  
Novel Genes ◽  
Genome Wide ◽  
A Genome

A genome-wide linkage scan for familial partial lipodystrophy susceptibility genes in a German kindreds

2007 ◽  
Vol 30 (4) ◽  
pp. 86
Author(s):  
M. Lanktree ◽  
J. Robinson ◽  
J. Creider ◽  
H. Cao ◽  
D. Carter ◽  
...  
Keyword(s):  
Subcutaneous Fat ◽  
Visceral Obesity ◽  
Fat Distribution ◽  
Dominant Negative ◽  
Molecular Forms ◽  
Partial Lipodystrophy ◽  
Genome Wide ◽  
A Genome ◽  
Familial Partial Lipodystrophy ◽  
Promoter Mutations

Background: In Dunnigan-type familial partial lipodystrophy (FPLD) patients are born with normal fat distribution, but subcutaneous fat from extremities and gluteal regions are lost during puberty. The abnormal fat distribution leads to the development of metabolic syndrome (MetS), a cluster of phenotypes including hyperglycemia, dyslipidemia, hypertension, and visceral obesity. The study of FPLD as a monogenic model of MetS may uncover genetic risk factors of the common MetS which affects ~30% of adult North Americans. Two molecular forms of FPLD have been identified including FPLD2, resulting from heterozygous mutations in the LMNA gene, and FPLD3, resulting from both heterozygous dominant negative and haploinsufficiency mutations in the PPARG gene. However, many patients with clinically diagnosed FPLD have no mutation in either LMNA or PPARG, suggesting the involvement of additional genes in FPLD etiology. Methods: Here, we report the results of an Affymetrix 10K GeneChip microarray genome-wide linkage analysis study of a German kindred displaying the FPLD phenotype and no known lipodystrophy-causing mutations. Results: The investigation identified three chromosomal loci, namely 1q, 3p, and 9q, with non-parametric logarithm of odds (NPL) scores >2.7. While not meeting the criteria for genome-wide significance, it is interesting to note that the 1q and 3p peaks contain the LMNA and PPARG genes respectively. Conclusions: Three possible conclusions can be drawn from these results: 1) the peaks identified are spurious findings, 2) additional genes physically close to LMNA, PPARG, or within 9q, are involved in FPLD etiology, or 3) alternative disease causing mechanisms not identified by standard exon sequencing approaches, such as promoter mutations, alternative splicing, or epigenetics, are also responsible for FPLD.

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