CerealESTDb: A Comprehensive Resource for Abiotic Stress-Responsive Annotated ESTs With Predicted Genes, Gene Ontology, and Metabolic Pathways in Major Cereal Crops

Abstract

Cereals are the most important food crops and are considered key contributors to global food security. Loss due to abiotic stresses in cereal crops is limiting potential productivity in a significant manner. The primary reasons for abiotic stresses are abrupt temperature, variable rainfall, and declining nutrient status of the soil. Varietal development is the key to sustaining productivity under influence of multiple abiotic stresses and must be studied in context with genomics and molecular breeding. Recently, advances in a plethora of Next Generation Sequencing (NGS) based methods have accelerated the enormous genomic data generation associated with stress-induced transcripts such as microarray, RNAseq, Expressed Sequenced Tag (ESTs), etc. Many databases related to microarray and RNA-seq based transcripts have been developed and profusely utilized. However, an abundant amount of transcripts related to abiotic stresses in various cereal crops arising from EST technology are available but still remain underutilized in absence of a consolidated database. In this study, an attempt has been made with a primary goal to integrate, analyse, and characterise the available resources of ESTs responsive to abiotic stresses in major cereals. The developed CerealESTdb presents a customisable search in two different ways in the form of searchable content for easy access and potential use. This database comprises ESTs from four major cereal crops, namely rice (Oryza sativa L.), wheat (Triticum aestivum L.), sorghum (Sorghum bicolour L.), and maize (Zea mays L.), under a set of abiotic stresses. The current statistics of this cohesive database consists of 55,826 assembled EST sequences, 51,791 predicted genes models, and their 254,609 gene ontology terms including extensive information on 1,746 associated metabolic pathways. We anticipate that developed CerealESTdb will be helpful in deciphering the knowledge of complex biological phenomena under abiotic stresses to accelerate the molecular breeding programs towards the development of crop cultivars resilient to abiotic stresses. The CerealESTdb is publically available with the URL http://cabgrid.res.in/CerealESTDb.

Comprehensive in silico analysis of the underutilized crop tef (Eragrostis tef (Zucc.) Trotter) genome reveals drought tolerance signatures

“…To identify drought-responsive coding and regulatory elements in tef, sequences were retrieved were retrieved from two databases: Drought Stress Gene Database [65] and CrealESTDb which is a resource for abiotic stress-responsive annotated ESTs [63]. Furthermore, we retrieved 175 previously reported drought-responsive genes in tef [66] from the NCBI database.…”

“…capsularis and C . olitorius , respectively [ 56 ] 3 Identification of candidate genes regulating drought tolerance in pearl millet 74 drought-responsive genes separated into five phylogenic groups [ 57 ] 4 In-Silico study of Brassinosteroid (BR) signaling genes in rice 39 BR signaling genes [ 58 ] 5 Genome-wide in silico identification and characterization of sodium-proton (Na + /H +) antiporters in Indica rice sixteen NHX orthologous [ 59 ] 6 In silico identification and annotation of drought responsive candidate genes in Solanaceous 109 drought responsive unigenes [ 60 ] 7 In silico identification of Rare Cold Inducible 2 (RCI2) gene family in cucumber Four RCI2 genes 8 In silico identification and expression analysis of nuclear factor Y (Nf-Y) in cucumber 27 CsaNF-Y members [ 61 ] 9 Genome-wide In silico identification and comparative analysis of Dof gene family in Brassica napus 117 Brassica napus Dof genes ( BnaDofs ) [ 62 ] 10 Genome-wide identification and in silico analysis of nitrate transporters in hexaploid wheat 412 nitrate transporter genes [ 63 ] 11 VOZS identification from tef [ Eragrostis tef (Zucc.) Trotter] using in silico tools Four VOZs from tef …”

Rice Responses to Water Limiting Conditions: Improving Stress Management by Exploiting Genetics and Physiological Processes

“…New agronomic methods and breeding technologies, as well as the development of genetic diversity and the use of genomic resources, are needed to discover and integrate different gene functions useful to cope with water stress [135]. A CerealESTdb, based on rice, maize, wheat, and sorghum Expressed Sequence Tags (EST) whose expression is modulated under various abiotic stresses, including water stress, provides an updated picture of genes involved in the response to this stress and supports in accelerating efforts to develop abiotic stress-resistant cultivars without compromising the nutritional quality through introgression and gene pyramiding [136]. In addition, advances in next-generation sequencing (NGS) technologies and the reduction in genome sequencing costs have allowed the decoding of many crop genomes and the development of molecular markers to select and improve traits [137].…”

Conventional and Omics Approaches for Understanding the Abiotic Stress Response in Cereal Crops—An Updated Overview

“…This database consists of 55,826 assembled EST sequences, 51,791 predicted genes models, and their 254,609 gene ontology terms including extensive information on 1746 associated metabolic pathways. The CerealESTdb is publicly available with the URL (accessed on 5 October 2022) [ 129 ].…”