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. 2024 May 21:15:1395224.
doi: 10.3389/fgene.2024.1395224. eCollection 2024.

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

Huilong Chen #  1 , Fang Liu #  1 , Jing Chen  1 , Kexin Ji  1 , Yutong Cui  2 , Weina Ge  1 , Zhenyi Wang  1
Affiliations

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

Huilong Chen et al. Front Genet. .

Abstract

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.

Keywords: NODULE-INCEPTION-like protein; codon bias; foxtail millet; molecular evolution; structure; transcription factor.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Prediction of the tertiary structure of NLP family proteins in foxtail millet. Note: Helix-blue; sheet-red; turn-yellow; coil-green.
FIGURE 2
FIGURE 2
Analysis of promoter in foxtail millet NLP genes. (A) Distribution of promoter elements of the NLP gene family in foxtail millet. (B) Number of promoter elements of the NLP gene family in foxtail millet.
FIGURE 3
FIGURE 3
Tissue expression analysis of NLP gene family in foxtail millet and rice. (A) Tissue expression profile of foxtail millet NLP genes. (B) Tssue expression profile of rice NLP genes. Note: Lines represent orthologous gene pairs identified by OrthoMCL software. Red indicates that the expression level of the orthologous pair is higher, and blue indicates that the expression level of the orthologous pair is relatively low.
FIGURE 4
FIGURE 4
Protein interactions analysis of foxtail millet NLP gene family.
FIGURE 5
FIGURE 5
Chromosome distribution. Note: The horizontal axis is the four species of foxtail millet, rice, sorghum and maize, and the vertical axis is the number of NLP genes. Os, Si, Sb and Zm are abbreviations of rice, foxtail millet, sorghum and maize, respectively.
FIGURE 6
FIGURE 6
ENC-plot diagram.
FIGURE 7
FIGURE 7
Optimal codon Venn diagram of NLP family in foxtail millet and closely related crops. Note: Os, Si, Sb and Zm are abbreviations of rice, foxtail millet, sorghum and maize, respectively.
FIGURE 8
FIGURE 8
Phylogenetic tree of NLP gene family. Note: Gene IDs show their respective sources: Os represents rice, Si represents foxtail millet, Sb represents sorghum, Zm represents maize, Am represents A. trichopoda, At represents A. thaliana, Sm represents S. moellendorfii, Cb represents C. braunii, Pp represents P. patens, Ol represents O. lucimarinus. We use shape and color to distinguish different species. Green circles, yellow circles, black circles, pink circles, blue stars, orange circles, purple circles, brown circles and red triangles represent sorghum, maize, rice, A. trichopoda, A. thaliana, P. patens, S. moellendorfii, O. lucimarinus and foxtail millet, respectively. The number on the branch is the bootstrap value.
FIGURE 9
FIGURE 9
NLP family homology map and radar map. (A) Orthologous networks of NLP gene families in representative plants. (B) Paralogous homology radargram of NLP gene families in representative plants.
FIGURE 10
FIGURE 10
Polyploidy and amplification analysis of the NLP family in plants.
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