Genome-wide identification and expression analysis of bHLH transcription factors reveal their putative regulatory effects on petal nectar spur development in <i>Aquilegia</i>

Li, Xueyan; Huang, Hui; Zhang, Zhiqiang

doi:10.1101/2022.04.20.488976

Cited by 3 publications

(4 citation statements)

References 68 publications

(95 reference statements)

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“…Consistent with this function, analyses of the animal bHLH residues have shown less sequence variability for buried helix positions than for exposed [19]. The loop region shows high variation regarding length and sequence [1,[8][9][10][11]17]. In eukaryotes, the minimum found loop length is five amino acids long [4,19].…”

mentioning

confidence: 71%

“…In plants, the basic region of a bHLH is represented by the first 10 to 19 amino acids [1,[9][10][11][12]21]. Conserved positions in this region determine the DNA binding behaviour [4][5][6]22].…”

Section: Introductionmentioning

confidence: 99%

“…The loop region shows high variation regarding length and sequence [1,[9][10][11][12]21]. In eukaryotes, the minimum found loop length is five amino acids long [4,23].…”

Section: Introductionmentioning

confidence: 99%

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Automatic annotation of the bHLH gene family in plants

Thoben

Pucker

2023

Preprint

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Background: The bHLH transcription factor family is named after the basic helix-loop-helix (bHLH) domain that is a characteristic element of their members. Understanding the function and characteristics of this family is important for the examination of a wide range of functions. As the availability of genome sequences and transcriptome assemblies has increased significantly, the need for automated solutions that provide reliable functional annotations is emphasised. Results: A phylogenetic approach was adapted for the automatic identification and functional annotation of the bHLH transcription factor family. The bHLH_annotator for the automated functional annotation of bHLHs was implemented in Python3. Sequences of bHLHs described in literature were collected to represent the full diversity of bHLH sequences. Previously described orthologs form the basis for the functional annotation assignment to candidates which are also screened for bHLH-specific motifs. The pipeline was successfully deployed on the two Arabidopsis thaliana accessions Col-0 and Nd-1, the monocot species Dioscorea dumetorum, and a transcriptome assembly of Croton tiglium. Depending on the applied search parameters for the initial candidates in the pipeline, species-specific candidates or members of the bHLH family which experienced domain loss can be identified. Conclusions: The bHLH_annotator allows a detailed and systematic investigation of the bHLH family in land plant species and classifies candidates based on bHLH-specific characteristics, which distinguishes the pipeline from other established functional annotation tools. This provides the basis for the functional annotation of the bHLH family in land plants and the systematic examination of a wide range of functions regulated by this transcription factor family.

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mentioning

confidence: 71%

Section: Introductionmentioning

confidence: 99%

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Automatic annotation of the bHLH gene family in plants

Thoben

Pucker

2023

Preprint

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“… Phylogenetic analysis of the species based on genome-wide association study of the basic helix-loop-helix (bHLH) family. The total number of bHLH transcription factors identified from the genome of each species are indicated [ 5 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 ]. …”

Section: Figurementioning

confidence: 99%

Basic Helix-Loop-Helix Transcription Factors: Regulators for Plant Growth Development and Abiotic Stress Responses

Zuo

Lee

Kang

2023

IJMS

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Plant basic helix-loop-helix (bHLH) transcription factors are involved in many physiological processes, and they play important roles in the abiotic stress responses. The literature related to genome sequences has increased, with genome-wide studies on the bHLH transcription factors in plants. Researchers have detailed the functionally characterized bHLH transcription factors from different aspects in the model plant Arabidopsis thaliana, such as iron homeostasis and abiotic stresses; however, other important economic crops, such as rice, have not been summarized and highlighted. The bHLH members in the same subfamily have similar functions; therefore, unraveling their regulatory mechanisms will help us to identify and understand the roles of some of the unknown bHLH transcription factors in the same subfamily. In this review, we summarize the available knowledge on functionally characterized bHLH transcription factors according to four categories: plant growth and development; metabolism synthesis; plant signaling, and abiotic stress responses. We also highlight the roles of the bHLH transcription factors in some economic crops, especially in rice, and discuss future research directions for possible genetic applications in crop breeding.

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Automatic annotation of the bHLH gene family in plants

Thoben,

Pucker

2023

BMC Genomics

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Background The bHLH transcription factor family is named after the basic helix-loop-helix (bHLH) domain that is a characteristic element of their members. Understanding the function and characteristics of this family is important for the examination of a wide range of functions. As the availability of genome sequences and transcriptome assemblies has increased significantly, the need for automated solutions that provide reliable functional annotations is emphasised. Results A phylogenetic approach was adapted for the automatic identification and functional annotation of the bHLH transcription factor family. The bHLH_annotator, designed for the automated functional annotation of bHLHs, was implemented in Python3. Sequences of bHLHs described in literature were collected to represent the full diversity of bHLH sequences. Previously described orthologs form the basis for the functional annotation assignment to candidates which are also screened for bHLH-specific motifs. The pipeline was successfully deployed on the two Arabidopsis thaliana accessions Col-0 and Nd-1, the monocot species Dioscorea dumetorum, and a transcriptome assembly of Croton tiglium. Depending on the applied search parameters for the initial candidates in the pipeline, species-specific candidates or members of the bHLH family which experienced domain loss can be identified. Conclusions The bHLH_annotator allows a detailed and systematic investigation of the bHLH family in land plant species and classifies candidates based on bHLH-specific characteristics, which distinguishes the pipeline from other established functional annotation tools. This provides the basis for the functional annotation of the bHLH family in land plants and the systematic examination of a wide range of functions regulated by this transcription factor family.

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Genome-wide identification and expression analysis of bHLH transcription factors reveal their putative regulatory effects on petal nectar spur development in Aquilegia

Cited by 3 publications

References 68 publications

Automatic annotation of the bHLH gene family in plants

Automatic annotation of the bHLH gene family in plants

Basic Helix-Loop-Helix Transcription Factors: Regulators for Plant Growth Development and Abiotic Stress Responses

Automatic annotation of the bHLH gene family in plants

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