Identification and Bioinformatics Analysis of bHLH Transcription Factor Family in Lactuca sativa L.

doi:10.11924/j.issn.1000-6850.casb2022-0214

Abstract

Abstract:

The aim of this study is to conduct genome-wide identification and systematic analysis of lettuce (Lactuca sativa L.) bHLH transcription factors in order to provide a theoretical basis for studying the biological function of lettuce bHLH gene family. The Hidden Markov Model profiles of the bHLH domains downloaded from Pfam were used to search the database using HMMER ver. 3.0. and SMART. The obtained amino acid sequences were analyzed by bioinformatics using software such as ExPASy ProtParam tool, DNAMAN 5.0, ClustalX and MEGA 7.0. In this study, 135 bHLH transcription factors were identified from lettuce and the relative molecular weight of the encoding proteins ranged from 17843.82 Da to 75409.15 Da with theoretical isoelectric points of 0.63-9.51, among which there were 92 acidic proteins and 43 basic proteins. In addition, 123 bHLH proteins were unstable proteins and all 135 bHLH proteins were hydrophilic proteins. Each family member contained an N-terminal basic structural domain and a C-terminal HLH structural domain, where the N-terminal could bind specific DNA cis-elements and the C-terminal could maintain the stability of the bHLH protein secondary structure. The 135 bHLH proteins could be divided into 10 sub-families by phylogenetic analysis. In conclusion, 135 bHLH transcription factors in lettuce are identified by genome-wide screening, and the study can provide reference for exploring the biological function of lettuce bHLH gene family.

Key words: lettuce, bHLH, phylogeny analysis, sequence alignment, genome-wide identification

SUI Xinyi, ZHAO Xiaogang, MAO Xin, LI Yaling, WEN Xiangzhen. Identification and Bioinformatics Analysis of bHLH Transcription Factor Family in Lactuca sativa L.[J]. Chinese Agricultural Science Bulletin, 2023, 39(3): 104-110.

Figures/Tables 5

References 32

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