Systematic analysis of the basic/helix-loop-helix (bHLH) transcription factor family in pummelo (Citrus grandis) and identification of the key members involved in the response to iron deficiency

Abstract

Background Iron (Fe) deficiency is a common problem in citrus production. As the second largest superfamily of transcription factors (TFs), the basic/helix-loop-helix (bHLH) proteins have been shown to participate in the regulation of Fe homeostasis and a series of other biological and developmental processes in plants. However, this family of members in citrus and their functions in citrus Fe deficiency are still largely unknown. Results In this study, we identified a total of 128 CgbHLHs from pummelo ( Citrus grandis ) genome that were classified into 18 subfamilies by phylogenetic comparison with Arabidopsis thaliana bHLH proteins. All of these CgbHLHs were randomly distributed on nine known (125 genes) and one unknown (3 genes) chromosomes, and 12 and 47 of them were identified to be tandem and segmental duplicated genes, respectively. Sequence analysis showed detailed characteristics of their intron-exon structures, bHLH domain and conserved motifs. Gene ontology (GO) analysis suggested that most of CgbHLHs were annotated to the nucleus, DNA-binding transcription factor activity, response to abiotic stimulus, reproduction, post-embryonic development, flower development and photosynthesis. In addition, 27 CgbHLH proteins were predicted to have direct or indirect protein-protein interactions. Based on GO annotation, RNA sequencing data in public database and qRT-PCR results, several of CgbHLHs were identified as the key candidates that respond to iron deficiency. Conclusions In total, 128 CgbHLH proteins were identified from pummelo, and their detailed sequence and structure characteristics and putative functions were analyzed. This study provides comprehensive information for further functional elucidation of CgbHLH genes in citrus.

Automatic Identification of Players in the Flavonoid Biosynthesis with Application on the Biomedicinal Plant Croton tiglium

“…MYB sequences of A. thaliana [ 64 ], Vitis vinifera [ 120 ], Beta vulgaris [ 121 ], and Musa acuminata [ 122 ] were subject to KIPEs as baits. bHLH bait sequences were collected from A. thaliana [ 123 ], V. vinifera [ 124 ], Nelumbo nucifera [ 125 ], Citrus grandis [ 126 ], M. acuminata [ 127 ], and Solanum melongena [ 128 ]. WD40 sequences of A. thaliana [ 129 ], Triticum aestivum [ 130 ], and Setaria italica [ 131 ] were collected as bait sequences for the identification of the WD40 protein TTG1.…”

Phytochemical and Therapeutic Potential ofCitrus grandis(L.) Osbeck: A Review

“…30,31 Shaddock. 32,33 Pummelo, [34][35][36] Jambola. 25,37,38 Chakota, 39 Mato Peiyu 40 Papanus, 39 Tomentosa, 41 Jamboa, Pompelmoes, Pamplemousse, Bali lemon, Betabi lebu, and Panis.…”