Genome-wide analyses of the bHLH gene family reveals structural and functional characteristics in the aquatic plantNelumbo nucifera

Abstract

Lotus (Nelumbo nucifera Gaertn.) is an economically important aquatic plant with multiple applications, but water salinity and cold stress seriously affect lotus yield and distribution. The basic helix-loop-helix (bHLH) transcription factors (TFs) play a vital role in plant growth and development, metabolic regulation processes and responses to environmental changes. However, systematic analyses of the bHLH TF family in lotus has not yet been reported. Here, we report the identification and description of bHLH genes in lotus (NnbHLHs) with a focus on functional prediction, particularly for those involved in stress resistance. In all, 115 NnbHLHs were identified in the lotus genome and classified into 19 subfamilies. The chromosomal distribution, physicochemical properties, bHLH domain, conserved motif compositions and evolution of these 115 NnbHLHs were further analyzed. To better understand the functions of the lotus bHLH family, gene ontology, cis-element, and phylogenetic analyses were conducted. NnbHLHs were predicted to be involved in plant development, metabolic regulation and responses to stress, in accordance with previous findings. Overall, 15 NnbHLHs were further investigated with functional prediction via quantitative real-time PCR analyses. Meanwhile, expression profiles of NnbHLHs in four tissues indicated that many NnbHLHs showed tissue preference in their expression. This study is supposed to provide a good foundation for further research into the functions and evolution of NnbHLHs, and identifies candidate genes for stress resistance in lotus.

Genome-Wide Identification and Characterization of the bHLH Transcription Factor Family in Pepper (Capsicum annuum L.)

“…We identified ten highly conserved motifs in the CabHLH proteins. Similar to the bHLHs of potato, lotus and Arabidopsis (Wang et al, 2018;Mao et al, 2019), motif 1 and motif 2 were present in almost all CabHLH proteins and represented the position of the bHLH domain, which is highly conserved among species. However, motif 9 and 10 were only present in subfamilies III (a + c) and VII, respectively.…”

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.…”

Genome-wide identification and characterization of cucumber bHLH family genes and the functional characterization of CsbHLH041 in NaCl and ABA tolerance in Arabidopsis and cucumber

“…Asterisks indicated a significant difference **p < 0.01 compared with the corresponding controls. The growth of Col-0 (WT) and CsbHLH041 transgenic lines after 200 mM NaCl (e) and 100 μM ABA (f) treatments genes in Nelumbo nucifera [45], 188 bHLH genes in apple [40], 167 bHLH genes in rice [12] and 159 bHLH genes in tomato [13]. The bHLH TFs have been involved in multiple biological processes in plants, especially in regulating defense against biotic and abiotic stresses [46].…”