Phylogeny and Expression Atlas of the NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY in Agave

Tan, Shibei; Liang, Yanqiong; Huang, Yanlei; Xi, Jingen; Xing, Huang; Yang, Xiaohan; Yi, Kexian

doi:10.3390/plants11111434

Cited by 6 publications

(8 citation statements)

References 47 publications

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“…There are two classification systems for the NPF gene family, as follows: one system is based on a phylogenetic analysis of 1077 sequences from 22 plant genomes and 24 nonplant sequences, dividing the family into 10 supergroups and 32 groups [ 45 ]; and the other system divides the NRT1/PTR family into eight subfamilies (NPF1-NPF8), based on an analysis of 2398 sequences from 33 full-sequence genomes [ 40 ]. Previous studies have generally conformed to the criteria of the latter division [ 8 , 11 , 38 , 46 , 47 , 48 , 49 , 50 , 51 , 52 ]. Recently, a new classification method appeared in Brassica napus .…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of NPF Genes in Cucumber (Cucumis sativus L.)

Zhang

Zheng

et al. 2023

Plants

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The NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family (NPF) proteins perform an essential role in regulating plant nitrate absorption and distribution and in improving plant nitrogen use efficiency. In this study, cucumber (Cucumis sativus L.) NPF genes were comprehensively analyzed at the whole genome level, and 54 NPF genes were found to be unevenly distributed on seven chromosomes in the cucumber genome. The phylogenetic analysis showed that these genes could be divided into eight subfamilies. We renamed all CsNPF genes according to the international nomenclature, based on their homology with AtNPF genes. By surveying the expression profiles of CsNPF genes in various tissues, we found that CsNPF6.4 was specifically expressed in roots, indicating that CsNPF6.4 may play a role in N absorption; CsNPF6.3 was highly expressed in petioles, which may be related to NO3− storage in petioles; and CsNPF2.8 was highly expressed in fruits, which may promote NO3− transport to the embryos. We further examined their expression patterns under different abiotic stress and nitrogen conditions, and found that CsNPF7.2 and CsNPF7.3 responded to salt, cold, and low nitrogen stress. Taken together, our study lays a foundation for further exploration of the molecular and physiological functions of cucumber nitrate transporters.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of NPF Genes in Cucumber (Cucumis sativus L.)

Zhang

Zheng

et al. 2023

Plants

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“…Additionally, more than half of the A. angustifolia unigenes have homologs in public databases, facilitating the prediction of agave gene functions based on sequence homology [11]. Various genes related to fiber traits have been identified in agave species, including CesA, SAUR and NPF families [11][12][13]. Moreover, our comparative analysis…”

Section: Features Of a Angustifolia Transcriptomementioning

confidence: 95%

“…The plants of A. deserti, A. tequilana, A. americana, A. hybrid H11648 and A. angustifolia were cultivated in the Wenchang experimental field (19.54 • N 110.77 • E) of Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences since 2013. The samples of young leaves were collected from three-year-old plants, as previously described [13]. The samples of each species were repeated three times with different individuals as biological replicates and soaked in liquid nitrogen for immediate freezing.…”

Section: Plant Materials and Rna Isolationmentioning

confidence: 99%

“…Five cellulose synthase A (CesA) genes have been identified by transcriptome mining in A. hybrid H11648 [11]. The expression patterns of SMALL AUXIN UP-REGULATED RNA (SAUR) and NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY (NPF) family genes have been well characterized, with several genes from the SAUR and NPF families identified as candidate regulators of leaf development [12,13]. Recent studies have revealed the expression patterns of cell wall-related genes in A. sisalana, A. fourcroydes, A. hybrid H11648 and A. tequilana [9,14].…”

Section: Introductionmentioning

confidence: 99%

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Transcriptome Sequencing of Agave angustifolia Reveals Conservation and Diversification in the Expression of Cinnamyl Alcohol Dehydrogenase Genes in Agave Species

Huang

Tan

et al. 2022

Agriculture

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Agave angustifolia is an important crassulacean acid metabolism plant species, with wide applications in beverage and sisal fiber production. In this study, we carried out a transcriptome analysis of A. angustifolia leaves, generating a total of 58,482,436 clean reads through Illumina paired-end sequencing. De novo transcriptome assembly generated 67,314 unigenes, with about half of them having homologs in four public databases. In the Nr database, Asparagus officinalis was shown to be most closely related to agave, and the early angiosperm Amborella trichopoda was selected as an outgroup species. We further identified five, two, seven, seven, seven, six and six CAD genes in asparagus, amborella, A. deserti, A. tequilana, A. americana, A. hybrid H11648 and A. angustifolia, respectively. The maximum likelihood phylogenetic tree revealed the species-specific expansion of CAD genes in arabidopsis, rice and agave. The expression analysis indicated the conservatively expressed CAD1/2/4/6, providing candidate targets for manipulation to improve lignin traits. The species-specific expression of CAD3/5/7 indicates the existence of different regulatory mechanisms controlling the expression of these genes in agave species. This study presents the first transcriptome dataset of A. angustifolia, facilitating future studies on lignin biosynthesis in agave.

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“…A. amaniensis and A. H11648 were planted and normally managed in the Wenchang experimental field (19.00° N, 110.33° E) of the Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences. Shoots, unexpanded leaves, and expanded leaves were collected separately from two-year-old plants at different stages of development [ 30 ].…”

Section: Methodsmentioning

confidence: 99%

Transcriptome Sequencing of Agave amaniensis Reveals Shoot-Related Expression Patterns of Expansin A Genes in Agave

Wang

Xing

Chen

et al. 2023

Plants

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Agave species are widely planted for fiber production. However, the molecular basis of agave fiber development has not been well understood. In this study, we performed a transcriptomic analysis in A. amaniensi, a well-known variety with high-quality fiber production. Approximately 43.87 million clean reads were obtained using Illumina sequencing. The de novo assembly produced 66,746 unigrams, 54% of which were annotated in a public database. In the Nr database, 21,490 unigenes of A. amaniensis were shown to be most closely related to Asparagus officinalis. Nine expansin A orthologs with full coding regions were obtained, which were named EXP1a, EXP1b, EXP2, EXP3, EXP4a, EXP4b, EXP11, EXP12, and EXP13. The maximum likelihood phylogenetic tree revealed the species-specific expansion of expansin genes in Arabidopsis, rice and agave. The expression analysis suggested the negative correlation between the expression of expansin genes and the leaf growth rate, except AhEXP11. Moreover, expansin genes were differentially affected by abiotic and biotic stresses. Notably, AhEXP2 expression level was highly upgraded after the infection of Phytophthora nicotiana. Nutrient deficiency also influent expansin genes expression. Together, our research will benefit future studies related to fiber development, disease resistance and nutrient usage in agave.

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Phylogeny and Expression Atlas of the NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY in Agave

Cited by 6 publications

References 47 publications

Genome-Wide Identification and Expression Analysis of NPF Genes in Cucumber (Cucumis sativus L.)

Genome-Wide Identification and Expression Analysis of NPF Genes in Cucumber (Cucumis sativus L.)

Transcriptome Sequencing of Agave angustifolia Reveals Conservation and Diversification in the Expression of Cinnamyl Alcohol Dehydrogenase Genes in Agave Species

Transcriptome Sequencing of Agave amaniensis Reveals Shoot-Related Expression Patterns of Expansin A Genes in Agave

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