Genome-wide identification and expression analysis of NIN-like protein (NLP) genes: Exploring their potential roles in nitrate response in tea plant (Camellia sinensis)

Li, Da; Jin, Ya; Lu, Qin-Hua; Ren, Ning; Wang, Ying-Qi; Li, Qing-Sheng

doi:10.1016/j.plaphy.2024.108340

Cited by 3 publications

(3 citation statements)

References 46 publications

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“…Nitrogen is an important component of amino acids, nucleotides, chlorophyll, and hormones, and it is also an essential nutrient for all organisms ( Tegeder and Masclaux-Daubresse, 2018 ; Li D. et al, 2024 ). The growth and development of crops depend on their ability to take up and utilize nitrogen.…”

Section: Introductionmentioning

confidence: 99%

“…Moreover, the N-terminus of NLP has a highly conserved cGMP phosphodiesterase domain in addition to the RWP-RK domain, which may be involved in signal transduction or dimerization ( Yu et al, 2023 ). There have been many genome-wide studies of the NLP gene family, such as Arabidopsis thaliana ( Schauser et al, 2005 ), rice ( Oryza sativa ) ( Schauser et al, 2005 ), pepper ( Wu et al, 2023 ), alfalfa ( Wu et al, 2023 ), cucumber seedlings ( Li Y. et al, 2024 ), tea tree ( Li D. et al, 2024 ), Physcomitrella patens ( Crawford, 1995 ), wheat ( Kumar et al, 2018 ), maize ( Zea mays ) ( Ge et al, 2018 ), Brassica napus ( Feng et al, 2020 ), Chinese cabbage ( Chen et al, 2022a ) and so on. Evolutionary studies of the Chinese cabbage NLP family have revealed that the origins of duplication of the NLP gene family in the genus Brassica were almost exclusively derived from the WGD type ( Chen et al, 2022a ), yet the molecular evolutionary characterization of the other plant taxa is not known.…”

Section: Introductionmentioning

confidence: 99%

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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: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

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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“…Moreover, overexpression of ZbAGL11 (a class D MADS-box transcription factor) in Arabidopsis can induce apomixis after emasculation [ 26 ]. To date, analysis of the RWP-RK family has only been conducted for a few species such as soybean, tea, and Brassica napus [ 5 , 27 , 28 ]. These studies analyze the function of RWP-RK transcription factors in defense responses and nitrate responses based on genetic information analysis and RNA sequencing.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of the RWP-RK Proteins in Zanthoxylum armatum

Zheng,

Duan,

Zheng

et al. 2024

Genes

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Apomixis is a common reproductive characteristic of Zanthoxylum plants, and RWP-RKs are plant-specific transcription factors known to regulate embryonic development. However, the genome-wide analysis and function prediction of RWP-RK family genes in Z. armatum are unclear. In this study, 36 ZaRWP-RK transcription factors were identified in the genome of Z. armatum, among which 15 genes belonged to the RKD subfamily and 21 belonged to the NLP subfamily. Duplication events of ZaRWP-RK genes were mainly segmental duplication, and synteny analysis revealed a close phylogenetic relationship between Z. armatum and Arabidopsis. The analysis of cis-elements indicated that ZaRWP-RK genes may be involved in the regulation of the embryonic development of Z. armatum by responding to plant hormones such as abscisic acid, auxin, and gibberellin. Results of a real-time PCR showed that the expression levels of most ZaRWP-RK genes were significantly increased from flowers to young fruits. Protein–protein interaction network analysis further revealed the potential roles of the ZaRWP-RK proteins in apomixis. Collectively, this study is expected to improve our understanding of ZaRWP-RK transcription factors and provide a theoretical basis for future investigations into the ZaRWP-RK genes and their regulatory mechanisms in the apomixis process of Z. armatum.

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Genome-wide identification of SWEET gene family and the sugar transport function of three candidate genes during female flower bud induction stage of Juglans sigillata Dode

Li,

Chen,

et al. 2024

Plant Physiology and Biochemistry

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Genome-wide identification and expression analysis of NIN-like protein (NLP) genes: Exploring their potential roles in nitrate response in tea plant (Camellia sinensis)

Cited by 3 publications

References 46 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 Identification and Characterization of the RWP-RK Proteins in Zanthoxylum armatum

Genome-wide identification of SWEET gene family and the sugar transport function of three candidate genes during female flower bud induction stage of Juglans sigillata Dode

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