scholarly journals Ozone Stress Responsive Gene Database (OSRGD ver. 1.1): a literature curated database for crop improvement

2021 ◽  
Author(s):  
Prachi Yadav ◽  
Usha Mina
Keyword(s):  
Gene Expression ◽  
Plant Species ◽  
Crop Improvement ◽  
Data Repository ◽  
Foliar Injury ◽  
Keyword Query ◽  
Biological Insight ◽  
Ozone Stress ◽  
Responsive Gene ◽  
Specific Species

Ozone (O3) is a major abiotic stress which severely affects the growth and development of plants. In order to cope up with ozone stress, plants exhibit a plethora of morphological, physiological and molecular changes. Various molecular studies have been performed and a variety of genes exhibiting expression in response to ozone stress have been identified. However, no existing database has been designed yet to present information on ozone stress responsive genes differentially expressed across different plant species. The lack of a curated database limits the research potential in the area and therefore a cohesive database should be designed as a data repository of the ozone responsive genes. OSRGD ver. 1.1 is a user friendly web interface to explore ozone stress specific transcriptome dataset of different plant species. It allows users to retrieve the ozone stress responsive gene data by keyword based search. Each entry upon keyword query contains detailed information about the specific species, its foliar injury symptoms, pattern of gene expression, and platform used for gene expression analysis with reference literature. This comprehensive biocuration will offer researchers a better biological insight into plants response to ozone stress which will focus on development of climate smart crops through crop breeding.

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.

scholarly journals Comparative Transcriptome Atlases Reveal Altered Gene Expression Modules between Two Cleomaceae C3 and C4 Plant Species

2014 ◽  
Vol 26 (8) ◽  
pp. 3243-3260 ◽  
Author(s):  
Canan Külahoglu ◽  
Alisandra K. Denton ◽  
Manuel Sommer ◽  
Janina Maß ◽  
Simon Schliesky ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plant Species ◽  
Comparative Transcriptome ◽  
C4 Plant ◽  
Altered Gene Expression ◽  
Altered Gene

scholarly journals Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Hui Li ◽  
Xingyu Yang ◽  
Yue Zhang ◽  
Zhiyan Gao ◽  
Yuting Liang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plant Species ◽  
Aquatic Plant ◽  
Molecular Breeding ◽  
Nelumbo Nucifera ◽  
Sequence Analyses ◽  
Genome Database ◽  
Future Studies ◽  
Sacred Lotus ◽  
Coexpression Networks

AbstractSacred lotus (Nelumbo nucifera, or lotus) is one of the most widely grown aquatic plant species with important uses, such as in water gardening and in vegetable and herbal medicine. A public genomic database of lotus would facilitate studies of lotus and other aquatic plant species. Here, we constructed an integrative database: the Nelumbo Genome Database (NGD, http://nelumbo.biocloud.net). This database is a collection of the most updated lotus genome assembly and contains information on both gene expression in different tissues and coexpression networks. In the NGD, we also integrated genetic variants and key traits from our 62 newly sequenced lotus cultivars and 26 previously reported cultivars, which are valuable for lotus germplasm studies. As applications including BLAST, BLAT, Primer, Annotation Search, Variant and Trait Search are deployed, users can perform sequence analyses and gene searches via the NGD. Overall, the valuable genomic resources provided in the NGD will facilitate future studies on population genetics and molecular breeding of lotus.

scholarly journals Arabidopsis DREB2A-Interacting Proteins Function as RING E3 Ligases and Negatively Regulate Plant Drought Stress–Responsive Gene Expression

2008 ◽  
Vol 20 (6) ◽  
pp. 1693-1707 ◽  
Author(s):  
Feng Qin ◽  
Yoh Sakuma ◽  
Lam-Son Phan Tran ◽  
Kyonoshin Maruyama ◽  
Satoshi Kidokoro ◽  
...  
Keyword(s):  
Gene Expression ◽  
Drought Stress ◽  
Interacting Proteins ◽  
E3 Ligases ◽  
Responsive Gene ◽  
Ring E3 Ligases ◽  
Ring E3
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