scholarly journals Genome-Wide Exploration of Thaumatin-like Protein (TLP) Gene Family in Cereals

2019 ◽  
Author(s):  
Irfan Iqbal ◽  
Rajiv Kumar Tripathi ◽  
Olivia Wilkins ◽  
Jaswinder Singh
Keyword(s):  
Seed Germination ◽  
Gene Family ◽  
Differential Expression ◽  
Brachypodium Distachyon ◽  
Transcript Abundance ◽  
Enzyme Inactivation ◽  
Abiotic Stress Response ◽  
Hordeum Vulgare L ◽  
Barley Genome ◽  
Pathogenesis Related Protein

Abstract Background: TLP genes are the members of a conserved pathogenesis-related protein 5 (PR-5) gene family. They play role in abiotic stress response, hormone signaling, cell death, cold tolerance, enzyme inactivation, fruit maturation and seed germination. In this study, we characterized the TLP gene family in barley with specific emphasis on germination and malting. Results: We identified 19 TLP genes from the reference genome of Hordeum vulgare L. cv. Morex and 37, 28 and 35 TLP genes from the Oryza sativa, Brachypodium distachyon and Sorghum bicolor genome respectively. Comparative phylogenetic analysis and thaumatin domain organization of TLPs using the conserved region classified the TLP family into nine groups. Data revealed that localized gene duplications contributed to the expansion of the TLP gene family in cereals with diverse exon/intron structures. In the barley genome, most HvTLPs were localized on chromosome 5H. The differential spatiotemporal expression pattern of HvTLP genes in barley indicate that TLPs have been expressed predominantly in the embryo, developing grains, root and shoot tissues. Additionally, transcript abundance of HvTLP genes was measured between 16 hrs. to 96 hrs. of grain germination. Differential expression of HvTLP14, HvTLP17 and HvTLP18 in the malting variety (Morex), as compared to the feed variety (Steptoe) at different stages of seed germination indicates their possible role in malting. Conclusion: Barley genome contains higher number (19) of TLP genes as previously thought (8). This study provides a description of the TLP gene family in barley and their differential expression between 16-96 hrs. of germination. The results indicate their possible involvement in the malting process. Keywords: Cereals, Barley, Thaumatin like-proteins, Phylogenetics, Expression analysis

scholarly journals Global analysis of SBP gene family in Brachypodium distachyon reveals its association with spike development

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Rajiv K. Tripathi ◽  
William Overbeek ◽  
Jaswinder Singh
Keyword(s):  
Gene Family ◽  
Large Scale ◽  
Global Analysis ◽  
Brachypodium Distachyon ◽  
Transcript Abundance ◽  
Transport Pathways ◽  
Protein Protein Interaction ◽  
Biological Pathway Analysis ◽  
Spike Development ◽  
Transcript Cleavage

Abstract SQUAMOSA-promoter binding like proteins (SBPs/SPLs) are plant specific transcription factors targeted by miR156 and involved in various biological pathways, playing multi-faceted developmental roles. This gene family is not well characterized in Brachypodium. We identified a total of 18 SBP genes in B.distachyon genome. Phylogenetic analysis revealed that SBP gene family in Brachypodium expanded through large scale duplication. A total of 10 BdSBP genes were identified as targets of miR156. Transcript cleavage analysis of selected BdSBPs by miR156 confirmed their antagonistic connection. Alternative splicing was observed playing an important role in BdSBPs and miR156 interaction. Characterization of T-DNA Bdsbp9 mutant showed reduced plant growth and spike length, reflecting its involvement in the spike development. Expression of a majority of BdSBPs elevated during spikelet initiation. Specifically, BdSBP1 and BdSBP3 differentially expressed in response to vernalization. Differential transcript abundance of BdSBP1,BdSBP3,BdSBP8,BdSBP9,BdSBP14,BdSBP18 and BdSBP23 genes was observed during the spike development under high temperature. Co-expression network, protein–protein interaction and biological pathway analysis indicate that BdSBP genes mainly regulate transcription, hormone, RNA and transport pathways. Our work reveals the multi-layered control of SBP genes and demonstrates their association with spike development and temperature sensitivity in Brachypodium.

Genome-wide Characterization of Major Intrinsic Protein (MIP) Gene Family in Brachypodium distachyon

2018 ◽  
Vol 13 (5) ◽  
pp. 536-552 ◽  
Author(s):  
Ankush Ashok Saddhe ◽  
Shweta ◽  
Kareem A. Mosa ◽  
Kundan Kumar ◽  
Manoj Prasad ◽  
...  
Keyword(s):  
Gene Family ◽  
Brachypodium Distachyon ◽  
Major Intrinsic Protein ◽  
Intrinsic Protein ◽  
Genome Wide

scholarly journals Insight into the bZIP Gene Family in Solanum tuberosum: Genome and Transcriptome Analysis to Understand the Roles of Gene Diversification in Spatiotemporal Gene Expression and Function

2020 ◽  
Vol 22 (1) ◽  
pp. 253
Author(s):  
Venura Herath ◽  
Jeanmarie Verchot
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Functional Groups ◽  
Leucine Zipper ◽  
Expression Profiles ◽  
Crop Improvement ◽  
Potato Virus X ◽  
Tissue Growth ◽  
Abiotic Stress Response ◽  
Sequence Alignments

The basic region-leucine zipper (bZIP) transcription factors (TFs) form homodimers and heterodimers via the coil–coil region. The bZIP dimerization network influences gene expression across plant development and in response to a range of environmental stresses. The recent release of the most comprehensive potato reference genome was used to identify 80 StbZIP genes and to characterize their gene structure, phylogenetic relationships, and gene expression profiles. The StbZIP genes have undergone 22 segmental and one tandem duplication events. Ka/Ks analysis suggested that most duplications experienced purifying selection. Amino acid sequence alignments and phylogenetic comparisons made with the Arabidopsis bZIP family were used to assign the StbZIP genes to functional groups based on the Arabidopsis orthologs. The patterns of introns and exons were conserved within the assigned functional groups which are supportive of the phylogeny and evidence of a common progenitor. Inspection of the leucine repeat heptads within the bZIP domains identified a pattern of attractive pairs favoring homodimerization, and repulsive pairs favoring heterodimerization. These patterns of attractive and repulsive heptads were similar within each functional group for Arabidopsis and S. tuberosum orthologs. High-throughput RNA-seq data indicated the most highly expressed and repressed genes that might play significant roles in tissue growth and development, abiotic stress response, and response to pathogens including Potato virus X. These data provide useful information for further functional analysis of the StbZIP gene family and their potential applications in crop improvement.

INHERITANCE AND LINKAGE STUDIES WITH THE GRANDPA GENE IN BARLEY, HORDEUM VULGARE L.

1971 ◽  
Vol 13 (3) ◽  
pp. 489-498
Author(s):  
R. W. Matchett ◽  
H. G. Nass ◽  
D. W. Robertson
Keyword(s):  
Hordeum Vulgare ◽  
Chromosomal Location ◽  
Gene Interactions ◽  
Chromosome 2 ◽  
Linkage Studies ◽  
Hordeum Vulgare L ◽  
Barley Genome ◽  
Chlorophyll Mutants ◽  
Mutant Genes ◽  
Linkage Association

This study was initiated to determine the chromosomal location of the grandpa (gp) gene within the barley genome. The gp gene was placed on the long arm of chromosome 2 as indicated by linkage association with liguleless (li).Tests of allelism showed the gp gene to the allelic with the gp-2 gene. Seven sources of "yellow" chlorophyll mutants when crossed to grandpa plants gave albino double recessive seedlings. Three other sources of "yellow" chlorophyll mutants in the double recessive combination with grandpa exhibited yellow and white bands on the leaves. Double recessive individuals carrying the mottled (mt2) and grandpa genes were also albino. This is evidence of gene interactions between chlorophyll mutant genes.

scholarly journals Independent origins of the Golgi phosphoprotein 3 oncoprotein gene

2021 ◽  
Author(s):  
Juan C. Opazo ◽  
Michael W. Vandewege ◽  
Javier Gutierrez ◽  
Kattina Zavala ◽  
Luis Vargas-Chacoff ◽  
...  
Keyword(s):  
Gene Family ◽  
Transcript Abundance ◽  
Single Copy ◽  
Model Systems ◽  
Deep Roots ◽  
Starting Point ◽  
Amino Acid Divergence ◽  
Evolutionarily Conserved ◽  
History Of ◽  
Divergence Estimates

AbstractGolgi phosphoprotein 3 (GOLPH3) is considered the first oncoprotein of the Golgi apparatus. It was identified as an evolutionarily conserved protein upon its discovery about 20 years ago, but its function remains puzzling in normal and cancer cells. The GOLPH3 gene is part of a group of genes that also includes the GOLPH3L gene. Because cancer has deep roots in multicellular evolution, studying the evolution of the GOLPH3 gene family in non-model species represents an opportunity to identify new model systems that could help better understand the biology behind this group of genes. The main goal of this study is to explore the evolution of the GOLPH3 gene family in birds as a starting point to understand the evolutionary history of this oncoprotein. We identified a repertoire of three GOLPH3 genes in birds. We found duplicated copies of the GOLPH3 gene in all main groups of birds other than paleognaths, and a single copy of the GOLPH3L gene. We suggest there were at least three independent origins for GOLPH3 duplicates. Amino acid divergence estimates show that most of the variation is located in the N-terminal region of the protein. Our transcript abundance estimations show that one paralog is highly and ubiquitously expressed, and the others were variable. Our results are an example of the significance of understanding the evolution of the GOLPH3 gene family, especially for unraveling its structural and functional attributes.

scholarly journals Alignment and mapping methodology influence transcript abundance estimation

2019 ◽  
Author(s):  
Avi Srivastava ◽  
Laraib Malik ◽  
Hirak Sarkar ◽  
Mohsen Zakeri ◽  
Fatemeh Almodaresi ◽  
...  
Keyword(s):  
Differential Expression ◽  
Expression Analysis ◽  
Differential Expression Analysis ◽  
Computational Cost ◽  
Simulated Data ◽  
Transcript Abundance ◽  
Mapping Method ◽  
Rna Seq ◽  
Transcript Quantification ◽  
Quantification Model

AbstractBackgroundThe accuracy of transcript quantification using RNA-seq data depends on many factors, such as the choice of alignment or mapping method and the quantification model being adopted. While the choice of quantification model has been shown to be important, considerably less attention has been given to comparing the effect of various read alignment approaches on quantification accuracy.ResultsWe investigate the influence of mapping and alignment on the accuracy of transcript quantification in both simulated and experimental data, as well as the effect on subsequent differential expression analysis. We observe that, even when the quantification model itself is held fixed, the effect of choosing a different alignment methodology, or aligning reads using different parameters, on quantification estimates can sometimes be large, and can affect downstream differential expression analyses as well. These effects can go unnoticed when assessment is focused too heavily on simulated data, where the alignment task is often simpler than in experimentally-acquired samples. We also introduce a new alignment methodology, called selective alignment, to overcome the shortcomings of lightweight approaches without incurring the computational cost of traditional alignment.ConclusionWe observe that, on experimental datasets, the performance of lightweight mapping and alignment-based approaches varies significantly and highlight some of the underlying factors. We show this variation both in terms of quantification and downstream differential expression analysis. In all comparisons, we also show the improved performance of our proposed selective alignment method and suggest best practices for performing RNA-seq quantification.

Differential gene expression during seed germination in barley (Hordeum vulgare L.)

2002 ◽  
Vol 2 (1-2) ◽  
pp. 28-39 ◽  
Author(s):  
E. Potokina ◽  
N. Sreenivasulu ◽  
L. Altschmied ◽  
W. Michalek ◽  
A. Graner
Keyword(s):  
Gene Expression ◽  
Hordeum Vulgare ◽  
Seed Germination ◽  
Differential Gene Expression ◽  
Hordeum Vulgare L ◽  
Differential Gene
Sign in / Sign up

Export Citation Format

Share Document