Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants

Feng, Shuyan; Li, Nan; Chen, Huilong; Liu, Zhuo; Li, Chunjin; Zhou, Rong; Zhang, Yingchao; Cao, Rui; Ma, Xiao; Song, Xiaoming

doi:10.1186/s43897-024-00090-7

Cited by 4 publications

(1 citation statement)

References 63 publications

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“…From a duplication perspective, gene production can be traced to a variety of duplication mechanisms, such as WGD and tandem duplication ( Chen et al, 2023 ; Feng et al, 2024 ). By duplication origin analysis, we found that the seven NLP genes in foxtail millet were derived from dispersed duplication ( Si1G094300.1 , Si2G298700.1 , Si6G248300.1 , Si8G074000.1 , and Si9G553000.1 ) and WGD or segmental duplication ( Si3G084600.1 and Si5G004100.1 ).…”

Section: Discussionmentioning

confidence: 99%

Identification, molecular evolution, codon bias, and expansion analysis of NLP transcription factor family in foxtail millet (Setaria italica L.) and closely related crops

Chen,

Liu,

Chen

et al. 2024

Front. Genet.

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The NODULE-INCEPTION-like protein (NLP) family is a plant-specific transcription factor (TF) family involved in nitrate transport and assimilation in plants, which are essential for improving plant nitrogen use efficiency. Currently, the molecular nature and evolutionary trajectory of NLP genes in the C4 model crop foxtail millet are unknown. Therefore, we performed a comprehensive analysis of NLP and molecular evolution in foxtail millet by scanning the genomes of foxtail millet and representative species of the plant kingdom. We identified seven NLP genes in the foxtail millet genome, all of which are individually and separately distributed on different chromosomes. They were not structurally identical to each other and were mainly expressed on root tissues. We unearthed two key genes (Si5G004100.1 and Si6G248300.1) with a variety of excellent characteristics. Regarding its molecular evolution, we found that NLP genes in Gramineae mainly underwent dispersed duplication, but maize NLP genes were mainly generated via WGD events. Other factors such as base mutations and natural selection have combined to promote the evolution of NLP genes. Intriguingly, the family in plants showed a gradual expansion during evolution with more duplications than losses, contrary to most gene families. In conclusion, this study advances the use of NLP genetic resources and the understanding of molecular evolution in cereals.

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Section: Discussionmentioning

confidence: 99%

Identification, molecular evolution, codon bias, and expansion analysis of NLP transcription factor family in foxtail millet (Setaria italica L.) and closely related crops

Chen,

Liu,

Chen

et al. 2024

Front. Genet.

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Genome-wide characterization of auxin response factor (ARF) genes in bermudagrass and ectopically functional analysis of CdARF6-B2 gene in Arabidopsis

Chen,

Zhang

2024

Physiol Mol Biol Plants

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SoIR: a comprehensive Solanaceae information resource for comparative and functional genomic study

Liu,

Shen,

et al. 2024

Nucleic Acids Research

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The Solanaceae family, which includes economically important crops such as tomatoes, potatoes and peppers, has experienced a rapid expansion in genomic data due to advancements in sequencing technologies. However, existing databases are limited by incomplete species representation, a lack of comprehensive comparative genomic tools and the absence of systematic pan-genomic analyses. To address these gaps, we developed the Solanaceae Information Resource (SoIR, https://soir.bio2db.com), a comprehensive genomics database for the Solanaceae family. SoIR integrates genomic data from 81 species and transcriptomic data from 41 species, encompassing a total of 3 908 408 gene annotations derived from Gene Ontology, nonredundant protein, Pfam, Swiss-Prot and TrEMBL databases. The resource also includes 3 437 115 CRISPR guide sequences, 212 395 transcription factors and 19 086 genes associated with methylation modification. In addition to species-specific analyses, SoIR provides extensive bioinformatics tools for investigating gene family evolution, phylogenetic relationships and karyotype reconstruction across 25 fully sequenced genomes. With advanced tools such as Blast, Synteny and Sequence Alignment, the platform provides users with interactive and intuitive visualizations for conducting cross-species comparative genomics. As the first comprehensive pan-genomic resource for the entire Solanaceae family, SoIR facilitates in-depth cross-species analysis, supporting global research initiatives in plant evolution, functional genomics and crop improvement.

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Large-scale analysis of the ARF and Aux/IAA gene families in 406 horticultural and other plants

Cited by 4 publications

References 63 publications

Identification, molecular evolution, codon bias, and expansion analysis of NLP transcription factor family in foxtail millet (Setaria italica L.) and closely related crops

Identification, molecular evolution, codon bias, and expansion analysis of NLP transcription factor family in foxtail millet (Setaria italica L.) and closely related crops

Genome-wide characterization of auxin response factor (ARF) genes in bermudagrass and ectopically functional analysis of CdARF6-B2 gene in Arabidopsis

SoIR: a comprehensive Solanaceae information resource for comparative and functional genomic study

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