Genome- and Transcriptome-Wide Identification of C3Hs in Common Bean (Phaseolus vulgaris L.) and Structural and Expression-Based Analyses of Their Functions During the Sprout Stage Under Salt-Stress Conditions

Abstract

CCCH (C3H) zinc-finger proteins are involved in plant biotic and abiotic stress responses, growth and development, and disease resistance. However, studies on C3H genes in Phaseolus vulgaris L. (common bean) are limited. Here, 29 protein-encoding C3H genes, located on 11 different chromosomes, were identified in P. vulgaris . A phylogenetic analysis categorized the PvC3H s into seven subfamilies on the basis of distinct features, such as exon–intron structure, cis -regulatory elements, and MEME motifs. A collinearity analysis revealed connections among the PvC3H s in the same and different species. The PvC3H genes showed tissue-specific expression patterns during the sprout stage, as assessed by real-time quantitative PCR (RT-qPCR). Using RNA-sequencing and RT-qPCR data, PvC3H s were identified as being enriched through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses in binding, channel activity, and the spliceosome pathway. These results provide useful information and a rich resource that can be exploited to functionally characterize and understand PvC3H s. These PvC3Hs , especially those enriched in binding, channel activity, and the spliceosome pathway will further facilitate the molecular breeding of common bean and provide insights into the correlations between PvC3Hs and salt-stress responses during the sprout stage.

Transcriptome-based analysis of salt-related genes during the sprout stage of common bean (Phaseolus vulgaris) under salt stress conditions

“…drought, cold and heat) because plants are already exposed to it during the sprouting period, which is when plants are most susceptible to abiotic stresses [42]. Therefore, there is an urgent need for improving the salt tolerance of common bean during the sprout stage [21]. Radicle length has been used as a physiological indicator of salt-induced damage in the sprout stage of Medicago sativa [43] and Glycyrrhiza uralensis [44].…”

“…Each sample was immediately frozen in liquid nitrogen and then ground to a powder. Total RNA was extracted from all samples using the method of TRIzol (Transgen, Beijing, China), while the method was as previously described [21]. The RNA quality was assessed by 1% agarose gel electrophoresis and by an analysis using a NanoDrop spectrophotometer [22], which was also used for determining the RNA concentration and purity.…”

Genome-wide identification of the CCCH gene family in rose (Rosa chinensis Jacq.) reveals its potential functions

“…The 31 RcC3H members were divided into 11 subgroups. Similarly, the C3H family genes in other different species were also divided into 11 subgroups as CCCH-type zinc finger gene family in Arabidopsis and rice (Oryza sativa L.) [5], common bean (Phaseolus vulgaris L.) [20], citrus (Clementine mandarin) [16], Brassica rapa [15], chickpea (Cicer arietinum L.) [30] and Tetraploid switchgrass [31].…”

“…The CCCH as an important gene family is currently reported in Arabidopsis and rice (Oryza sativa) [5], maize (Zea mays) [14], chinese cabbage (Brassica rapa) [15], citrus (Clementine mandarin) [16], tomato (Solanum lycopersicum) [17], poplar (Populus trichocarpa) [18], alfalfa (Medicago truncatula) [19] and common bean (Phaseolus vulgaris L.) [20]. Although the CCCH gene has been a hot spot in plant gene research, the comprehensive identification and analysis of the CCCH gene family in rose is rarely reported.…”

CCCH Zinc Finger Genes in Barley: Genome-Wide Identification, Evolution, Expression and Haplotype Analysis

“…Genome assemblies have been used for the global identi cation and characterization of genes in numerous plant species. Genome-wide identi cation and characterization of CCCH genes have been carried out in Arabidopsis, rice [11], maize [13], poplar [35], tomato [36], Medicago truncatula [37], grape [38], citrus [39], switchgrass [40], Brassica rapa [41], and recently in the common bean [42], moso bamboo [43], wheat [44], and soybean [45]. However, CCCH genes have not yet been identi ed in barley (Hordeum vulgare), and their biological functions and evolutionary history remain poorly understood.…”