Molecular evolution and species-specific expansion of the NAP members in plants

The MYB-related transcription factor family in rubber dandelion (Taraxacum kok-saghyz): An insight into a latex-predominant member, TkMYBR090

MYB-related (MYBR) proteins play diverse roles in plant growth and development. However, the MYBR genes in Taraxacum kok-saghyz, a promising alternative source of natural rubber, a valuable biopolymer, remain scarcely investigated. Here, a total of 122 MYBR genes, namely TkMYBRs, were identified and classified into the groups of GARP-like, CCA1-like/R-R, and a heterogenous one in T. kok-saghyz. Collinearity analysis revealed a high similarity in MYBRs across two Taraxacum species with contrasting rubber yield. TkMYBR090 showed predominant expression in latex, the cytoplasm of rubber-producing laticifers. Transient overexpression of TkMYBR090 in tobacco and T. kok-saghyz demonstrated its localizations in nucleus and cytoplasm. Yeast two-hybrid assay revealed that the C-terminus of TkMYBR090 possessed transcriptional activation activity. DAP-seq analysis identified 18,232 TkMYBR090-targeted candidate genes, and four significantly enriched TkMYBR090 DNA-binding promoter motifs that were validated by yeast one-hybrid assay. The binding of TkMYBR090 on the promoter of an ascorbate oxidase gene was verified by yeast one-hybrid and dual luciferase activity assays, suggesting a role in ROS metabolism. Such assumption was supported by heterologous expression assays of TkMYBR090 in tobacco and yeast. This study is beneficial to further functional dissection of MYBRs in T. kok-saghyz, especially the roles in development and function of rubber-producing laticifers.

LcMYB43 enhances monoterpene biosynthesis by activating 1-deoxy-D-xylulose-5-phosphate synthase gene expression in Litsea cubeba

MYB transcription factors are crucial regulators involved in various metabolic processes in plants, including terpene biosynthesis. Litsea cubeba, a member of the Lauraceae family, is rich in monoterpenes and regulates their biosynthesis via the key enzyme DXS in the MEP pathway. Seven DXS genes have been identified in this species, but the role of the MYB family in terpene biosynthesis remains unclear. This study conducted a genome-wide characterization of the R2R3-MYB gene family in L. cubeba, analyzing its phylogenetics, expression, and regulatory functions. A total of 129 R2R3-MYB members were identified, with expansion mechanisms involving tandem and segmental duplications. Expression analysis revealed that LcMYB43 activates LcDXS5, a key enzyme in monoterpene biosynthesis. Overexpression of LcMYB43 significantly increased monoterpene accumulation. Y1H, EMSA, and dual-luciferase assays showed that LcMYB43 directly binds to the CAACAG motif in the LcDXS5 promoter, activating its expression. These findings suggest that LcMYB43 enhances monoterpene biosynthesis by promoting LcDXS5 expression, providing new insights into the regulatory mechanisms of monoterpene biosynthesis.

Genome-Wide Identification, Gene Duplication, and Expression Pattern of NPC2 Gene Family in Parnassius glacialis

BACKGROUND

The Niemann-Pick C2 (NPC2) gene family plays an important role in olfactory communication, immune response, and the recognition of host plants associated with environmental adaptation for insects.

METHODS

In this study, we conducted a genomic analysis of the structural characteristics and physicochemical properties of the NPC2 genes of eleven butterfly species available, focusing on the alpine Parnassius species, especially Parnassius glacialis, to investigate their duplication and expression patterns.

RESULTS

Our results indicate that a significant expansion of NPC2 genes was detected in P. glacialis compared to other butterflies; in addition, the expansion of these unevenly distributed P. glacialis NPC2 chromosome genes was shaped by tandem duplication mediated by transposons. Furthermore, the PgNPC2 genes had relatively higher expression in P. glacialis antennae and other head tissues. These facts were verified by quantitative real-time PCR (qRT-PCR).

CONCLUSIONS

These findings suggest that the expansion of NPC2 genes may have contributed to the local adaptation of P. glacialis during its dispersal 'out of the Qinghai-Tibet Plateau', although further functional tests are needed to confirm their specific role in this adaptive process.

Evolution of NAC transcription factors from early land plants to domesticated crops

NAC [NO APICAL MERISTEM (NAM), ARABIDOPSIS TRANSCRIPTION ACTIVATOR FACTOR 1/2 (ATAF1/2), and CUP-SHAPED COTYLEDON (CUC2)] transcription factors are key regulators of plant growth, development, and stress responses but were also crucial players during land plant adaptation and crop domestication. Using representative members of green algae, bryophytes, lycophytes, gymnosperms, and angiosperms, we expanded the evolutionary history of NAC transcription factors to unveil the relationships among members of this gene family. We found a massive increase in the number of NAC transcription factors from green algae to lycophytes and an even larger increase in flowering plants. Many of the NAC clades arose later during evolution since we found eudicot- and monocot-specific clades. Cis-elements analysis in NAC promoters showed the presence of abiotic and biotic stress as well as hormonal response elements, which indicate the ancestral function of NAC transcription factor genes in response to environmental stimuli and in plant development. At the transcriptional level, the expression of NAC transcription factors was low or absent in male reproduction, particularly mature pollen, across the plant kingdom. We also identified NAC genes with conserved expression patterns in response to heat stress in Marchantia polymorpha and Oryza sativa. Our study provides further evidence that transcriptional mechanisms associated with stress responses and development emerged early during plant land adaptation and are still conserved in flowering plants and domesticated crops.

Genome-Wide Identification and Expression Analysis of MYB Transcription Factor Family in Response to Various Abiotic Stresses in Coconut (Cocos nucifera L.)

Abiotic stresses such as nitrogen deficiency, drought, and salinity significantly impact coconut production, yet the molecular mechanisms underlying coconut's response to these stresses are poorly understood. MYB proteins, a large and diverse family of transcription factors (TF), play crucial roles in plant responses to various abiotic stresses, but their genome-wide characterization and functional roles in coconut have not been comprehensively explored. This study identified 214 CnMYB genes (39 1R-MYB, 171 R2R3-MYB, 2 3R-MYB, and 2 4R-MYB) in the coconut genome. Phylogenetic analysis revealed that these genes are unevenly distributed across the 16 chromosomes, with conserved consensus sequences, motifs, and gene structures within the same subgroups. Synteny analysis indicated that segmental duplication primarily drove CnMYB evolution in coconut, with low nonsynonymous/synonymous ratios suggesting strong purifying selection. The gene ontology (GO) annotation of protein sequences provided insights into the biological functions of the CnMYB gene family. CnMYB47/70/83/119/186 and CnMYB2/45/85/158/195 were identified as homologous genes linked to nitrogen deficiency, drought, and salinity stress through BLAST, highlighting the key role of CnMYB genes in abiotic stress tolerance. Quantitative analysis of PCR showed 10 CnMYB genes in leaves and petioles and found that the expression of CnMYB45/47/70/83/85/119/186 was higher in 3-month-old than one-year-old coconut, whereas CnMYB2/158/195 was higher in one-year-old coconut. Moreover, the expression of CnMYB70, CnMYB2, and CnMYB2/158 was high under nitrogen deficiency, drought, and salinity stress, respectively. The predicted secondary and tertiary structures of three key CnMYB proteins involved in abiotic stress revealed distinct inter-proteomic features. The predicted interaction between CnMYB2/158 and Hsp70 supports its role in coconut's drought and salinity stress responses. These results expand our understanding of the relationships between the evolution and function of MYB genes, and provide valuable insights into the MYB gene family's role in abiotic stress in coconut.

A novel NAC transcription factor ZmNAC55 negatively regulates drought stress in Zea mays

Drought stress is a major limit on the maize growth and productivity, and understanding the drought response mechanism is one of the important ways to improve drought resistance in maize. However, more drought-related genes and their regulated mechanisms are still to be reported. Here, we identified a novel NAC transcription factor ZmNAC55 in Zea mays and comprehensively investigated the functions of ZmNAC55 under drought stress. ZmNAC55 belonged to the NAP subfamily. ZmNAC55 had a conserved NAC domain in the N-terminal region and a divergent TAR region in the C-terminal region. ZmNAC55 was a nuclear protein, and ZmNAC55 and its TAR region had the transcriptional activation activity. Furthermore, the expression level of ZmNAC55 in leaves could be highly induced by drought stress. ZmNAC55 overexpression in Arabidopsis conferred the drought-sensitive phenotype with higher water loss, lower survival rate, higher membrane ion leakage, and higher expression levels of some drought-related genes. Meanwhile, ZmNAC55 underexpression in maize enhanced drought tolerance with lower water loss, higher survival rate, lower membrane ion leakage and lower expression levels of some drought-related genes. In addition, ZmNAC55 appeared to be very key in regulating ROS production under drought stress. Moreover, ZmNAC55 could activate ZmHOP3 expression by binding to its promoter. A novel working model of ZmNAC55 under drought stress could be found in maize. Taken together, the NAC transcription factor ZmNAC55 could negatively regulate drought stress via increasing ZmHOP3 expression in maize. ZmNAC55 is a promising candidate for improving drought resistance in maize.

Genome-wide identification of the Pyrus R2R3-MYB gene family and PhMYB62 regulation analysis in Pyrus hopeiensis flowers at low temperature

The R2R3-MYB gene family play an important role in plant growth, development and stress responses. In this study, a total of 122 PcoR2R3-MYB genes were identified and grouped into 26 clades in pear. And these PcoMYBs were unevenly distributed among 17 chromosomes. The sequence characteristics, conversed motifs, exon/intron structures, classification, duplication events and cis-acting elements were also investigated. The gene duplication events showed that segmental duplication may play key roles in expansion of the PcoMYB gene family. Pyrus hopeiensis, which is a valuable wild resource, has strong cold resistance. An integrative analyses of miRNA and mRNA showed that PhMYB62 was involved in regulating low-temperature stress in P. hopeiensis flower organs. Subcellular localization analysis showed that PhMYB62 protein was specifically localized to the nucleus. The result of DAP-seq showed that PhMYB62 responded to low-temperature stress in P. hopeiensis by regulating TFs, which were associated with plant stress resistance, and POD, GAUT12, AUX28 and CHS genes. Subsequently, yeast one-hybrid verified that PhMYB62 could bind and activate the promoter of POD gene. The current study would provide a comprehensive information for further functional research on the stress-responsive R2R3-MYB gene candidates in pear, and may help to identify the genes associated with cold resistance for the cultivation of cold-resistant pear varieties.

OsNAC103, an NAC transcription factor negatively regulates plant height in rice

MAIN CONCLUSION

OsNAC103 negatively regulates rice plant height by influencing the cell cycle and crosstalk of phytohormones. Plant height is an important characteristic of rice farming and is directly related to agricultural yield. Although there has been great progress in research on plant growth regulation, numerous genes remain to be elucidated. NAC transcription factors are widespread in plants and have a vital function in plant growth. Here, we observed that the overexpression of OsNAC103 resulted in a dwarf phenotype, whereas RNA interference (RNAi) plants and osnac103 mutants showed no significant difference. Further investigation revealed that the cell length did not change, indicating that the dwarfing of plants was caused by a decrease in cell number due to cell cycle arrest. The content of the bioactive cytokinin N6-Δ2-isopentenyladenine (iP) decreased as a result of the cytokinin synthesis gene being downregulated and the enhanced degradation of cytokinin oxidase. OsNAC103 overexpression also inhibited cell cycle progression and regulated the activity of the cell cyclin OsCYCP2;1 to arrest the cell cycle. We propose that OsNAC103 may further influence rice development and gibberellin-cytokinin crosstalk by regulating the Oryza sativa homeobox 71 (OSH71). Collectively, these results offer novel perspectives on the role of OsNAC103 in controlling plant architecture.

Genome-Wide Identification, Characterization, and Expression Analysis of the NAC Gene Family in Litchi chinensis

NAC proteins play an essential role in the growth and development of litchi, especially during reproductive development. However, a comprehensive analysis of the litchi NAC gene family is currently absent. Based on information from the litchi genome, we found that the 112 NAC genes of litchi show an uneven distribution on the chromosomes. Phylogenetic and conserved structural domain analyses indicated that different types of variability were exhibited in the family of litchi NACs (LcNACs). Gene covariance analysis showed that the LcNACs showed better similarity in the same genus than with Arabidopsis. We further investigated the differential expression patterns of LcNACs in buds and rudimentary leaves of litchi. qRT-PCR results implied that they were involved in the process. Profiling of LcNAC promoter elements in litchi showed that they were extensively involved in light response, phytohormone regulation, abiotic stress response, and plant growth and development processes. This study provides new insights into the identification, structural characterization, tissue-specific expression analysis, and promoter response elements of LcNACs. It reveals the characteristics of the LcNACs and lays the foundation for the subsequent understanding of its biological functions and molecular regulatory mechanisms.

Genome-wide identification, molecular evolution and expression analysis of the non-specific lipid transfer protein (nsLTP) family in Setaria italica

BACKGROUND

Foxtail millet (Setaria italica L.) is a millet species with high tolerance to stressful environments. Plant non-specific lipid transfer proteins (nsLTPs) are a kind of small, basic proteins involved in many biological processes. So far, the genome of S. italica has been fully sequenced, and a comprehensive understanding of the evolution and expression of the nsLTP family is still lacking in foxtail millet.

RESULTS

Forty-five nsLTP genes were identified in S. italica and clustered into 5 subfamilies except three single genes (SinsLTP38, SinsLTP7, and SinsLTP44). The proportion of SinsLTPs was different in each subfamily, and members within the same subgroup shared conserved exon-intron structures. Besides, 5 SinsLTP duplication events were investigated. Both tandem and segmental duplication contributed to nsLTP expansion in S. italica, and the duplicated SinsLTPs had mainly undergone purifying selection pressure, which suggested that the function of the duplicated SinsLTPs might not diverge much. Moreover, we identified the nsLTP members in 5 other monocots, and 41, 13, 10, 4, and 1 orthologous gene pairs were identified between S. italica and S. viridis, S. bicolor, Z. mays, O. sativa, and B. distachyon, respectively. The functional divergence within the nsLTP orthologous genes might be limited. In addition, the tissue-specific expression patterns of the SinsLTPs were investigated, and the expression profiles of the SinsLTPs in response to abiotic stress were analyzed, all the 10 selected SinsLTPs were responsive to drought, salt, and cold stress. Among the selected SinsLTPs, 2 paired duplicated genes shared almost equivalent expression profiles, suggesting that these duplicated genes might retain some essential functions during subsequent evolution.

CONCLUSIONS

The present study provided the first systematic analysis for the phylogenetic classification, conserved domain and gene structure, expansion pattern, and expression profile of the nsLTP family in S. italica. These findings could pave a way for further comparative genomic and evolution analysis of nsLTP family in foxtail millet and related monocots, and lay the foundation for the functional analysis of the nsLTPs in S. italica.

LcNAC13 Is Involved in the Reactive Oxygen Species-Dependent Senescence of the Rudimentary Leaves in Litchi chinensis

Litchi is an important evergreen fruit tree. Floral formation in litchi is induced by low temperatures (LTs). However, unstable flowering is a challenge for litchi production in times of global warming and climate change. Previous studies have shown that the methyl viologen dichloride hydrate-generated reactive oxygen species (ROS) could promote flowering. Leaves in the panicles may affect the development of the inflorescence in litchi under high-temperature condition. In this study, potted litchi trees were transferred to growth chambers at LT and high temperature (HT). From a previous dataset of the RNA sequencing of the ROS-treated rudimentary leaves, a NAC transcription factor-encoding gene LcNAC13 was identified. By genetic transformation of LcNAC13 to Arabidopsis thaliana and tobacco, it was found that the ROS-induced senescence of the leaves was accelerated. Silencing LcNAC13 by virus-induced gene silencing (VIGS) delayed ROS-dependent senescence. Our results suggested that LcNAC13 regulates rudimentary leaf senescence. Our study provided a new target gene for the future molecular breeding of new cultivars that could flower under global warming conditions.

Genome-wide identification and molecular evolution analysis of the heat shock transcription factor (HSF) gene family in four diploid and two allopolyploid Gossypium species

Heat shock transcription factors (HSFs) can regulate plant development and stress response. The comprehensive evolutionary history of the HSF family remains elusive in cotton. In this study, each cotton species had 78 members in Gossypium barbadense and Gossypium hirsutum. The diploid species had 39 GaHSFs in Gossypium arboreum, 31 GrHSFs in Gossypium raimondii, 34 GtHSFs in Gossypium turneri, and 34 GlHSFs in Gossypium longicalyx. The HSF family in cotton can be classified into three subfamilies, with seven groups in subfamily A and five groups in subfamily B. Different groups exhibited distinct gene proportions, conserved motifs, gene structures, expansion rates, gene loss rates, and cis-regulatory elements. The paleohexaploidization event led to the expansion of the HSF family in cotton, and the gene duplication events in six Gossypium species were inherited from their common ancestor. The HSF family in diploid species had a divergent evolutionary history, whereas two cultivated tetraploids presented a highly conserved evolution of the HSF family. The HSF members in At and Dt subgenomes of the cultivated tetraploids showed a different evolution from their corresponding diploid donors. Some HSF members were regarded as key candidates for regulating cotton development and stress response. This study provided the comprehensive information on the evolutionary history of the HSF family in cotton.

Genome-wide survey, characterization, and expression analysis of bZIP transcription factors in Chenopodium quinoa

BACKGROUND

Chenopodium quinoa Willd. (quinoa) is a pseudocereal crop of the Amaranthaceae family and represents a promising species with the nutritional content and high tolerance to stressful environments, such as soils affected by high salinity. The basic leucine zipper (bZIP) transcription factor represents exclusively in eukaryotes and can be related to many biological processes. So far, the genomes of quinoa and 3 other Amaranthaceae crops (Spinacia oleracea, Beta vulgaris, and Amaranthus hypochondriacus) have been fully sequenced. However, information about the bZIPs in these Amaranthaceae species is limited, and genome-wide analysis of the bZIP family is lacking in quinoa.

RESULTS

We identified 94 bZIPs in quinoa (named as CqbZIP1-CqbZIP94). All the CqbZIPs were phylogenetically splitted into 12 distinct subfamilies. The proportion of CqbZIPs was different in each subfamily, and members within the same subgroup shared conserved exon-intron structures and protein motifs. Besides, 32 duplicated CqbZIP gene pairs were investigated, and the duplicated CqbZIPs had mainly undergone purifying selection pressure, which suggested that the functions of the duplicated CqbZIPs might not diverge much. Moreover, we identified the bZIP members in 3 other Amaranthaceae species, and 41, 32, and 16 orthologous gene pairs were identified between quinoa and S. oleracea, B. vulgaris, and A. hypochondriacus, respectively. Among them, most were a single copy being present in S. oleracea, B. vulgaris, and A. hypochondriacus, and two copies being present in allotetraploid quinoa. The function divergence within the bZIP orthologous genes might be limited. Additionally, 11 selected CqbZIPs had specific spatial expression patterns, and 6 of 11 CqbZIPs were up-regulated in response to salt stress. Among the selected CqbZIPs, 3 of 4 duplicated gene pairs shared similar expression patterns, suggesting that these duplicated genes might retain some essential functions during subsequent evolution.

CONCLUSIONS

The present study provided the first systematic analysis for the phylogenetic classification, motif and gene structure, expansion pattern, and expression profile of the bZIP family in quinoa. Our results would lay an important foundation for functional and evolutionary analysis of CqbZIPs, and provide promising candidate genes for further investigation in tissue specificity and their functional involvement in quinoa's resistance to salt stress.

Pervasive duplication, biased molecular evolution and comprehensive functional analysis of the PP2C family in Glycine max

BACKGROUND

Soybean (Glycine max) is an important oil provider and ecosystem participant. The protein phosphatase 2C (PP2C) plays important roles in key biological processes. Molecular evolution and functional analysis of the PP2C family in soybean are yet to be reported.

RESULTS

The present study identified 134 GmPP2Cs with 10 subfamilies in soybean. Duplication events were prominent in the GmPP2C family, and all duplicated gene pairs were involved in the segmental duplication events. The legume-common duplication event and soybean-specific tetraploid have primarily led to expanding GmPP2C members in soybean. Sub-functionalization was the main evolutionary fate of duplicated GmPP2C members. Meanwhile, massive genes were lost in the GmPP2C family, especially from the F subfamily. Compared with other genes, the evolutionary rates were slower in the GmPP2C family. The PP2C members from the H subfamily resembled their ancestral genes. In addition, some GmPP2Cs were identified as the putative key regulator that could control plant growth and development.

CONCLUSIONS

A total of 134 GmPP2Cs were identified in soybean, and their expansion, molecular evolution and putative functions were comprehensively analyzed. Our findings provided the detailed information on the evolutionary history of the GmPP2C family, and the candidate genes can be used in soybean breeding.

Molecular evolution and lineage-specific expansion of the PP2C family in Zea mays

97 ZmPP2Cs were clustered into 10 subfamilies with biased subfamily evolution and lineage-specific expansion. Segmental duplication after the divergence of maize and sorghum might have led to primary expansion of ZmPP2Cs. The protein phosphatase 2C (PP2C) enzymes control many stress responses and developmental processes in plants. In Zea mays, a comprehensive understanding of the evolution and expansion of the PP2C family is still lacking. In the current study, 97 ZmPP2Cs were identified and clustered into 10 subfamilies. Through the analysis of the PP2C family in monocots, the ZmPP2C subfamilies displayed biased subfamily molecular evolution and lineage-specific expansion, as evidenced by their differing numbers of member genes, expansion and evolutionary rates, conserved subdomains, chromosomal distributions, expression levels, responsive-regulatory elements and regulatory networks. Moreover, while segmental duplication events have caused the primary expansion of the ZmPP2Cs, the majority of their diversification occurred following the additional whole-genome duplication that took place after the divergence of maize and sorghum (Sorghum bicolor). After this event, the PP2C subfamilies showed asymmetric evolutionary rates, with the D, F₂ and H subfamily likely the most closely to resemble its ancestral subfamily's genes. These findings could provide novel insights into the molecular evolution and expansion of the PP2C family in maize, and lay the foundation for the functional analysis of these enzymes in maize and related monocots.

Asymmetric Evolution and Expansion of the NAC Transcription Factor in Polyploidized Cotton

Polyploidy in Gossypium hirsutum conferred different properties from its diploid ancestors under the regulation of transcription factors. The NAC transcription factor is a plant-specific family that can be related to plant growth and development. So far, little is known about the NAC family in cotton. This study identified 495 NAC genes in three cotton species and investigated the evolution and expansion of different genome-derived NAC genes in cotton. We revealed 15 distinct NAC subfamilies in cotton. Different subfamilies had different gene proportions, expansion rate, gene loss rate, and orthologous exchange rate. Paleohexaploidization (35%) and cotton-specific decaploidy (32%) might have primarily led to the expansion of the NAC family in cotton. Half of duplication events in G. hirsutum were inherited from its diploid ancestor, and others might have occurred after interspecific hybridization. In addition, NAC genes in the At and Dt subgenomes displayed asymmetric molecular evolution, as evidenced by their different gene loss rates, orthologous exchange, evolutionary rates, and expression levels. The dominant duplication event was different during the cotton evolutionary history. Different genome-derived NACs might have interacted with each other, which ultimately resulted in morphogenetic evolution. This study delineated the expansion and evolutionary history of the NAC family in cotton and illustrated the different fates of NAC genes during polyploidization.

Evolutionary Analysis of the LAFL Genes Involved in the Land Plant Seed Maturation Program

Seeds are one of the most significant innovations in the land plant lineage, critical to the diversification and adaptation of plants to terrestrial environments. From perspective of seed evo-devo, the most crucial developmental stage in this innovation is seed maturation, which includes accumulation of storage reserves, acquisition of desiccation tolerance, and induction of dormancy. Based on previous studies of seed development in the model plant Arabidopsis thaliana, seed maturation is mainly controlled by the LAFL regulatory network, which includes LEAFY COTYLEDON1 (LEC1) and LEC1-LIKE (L1L) of the NF-YB gene family, and ABSCISIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEC2 (LEAFY COTYLEDON2) of the B3-AFL gene family. In the present study, molecular evolution of these LAFL genes was analyzed, using representative species from across the major plant lineages. Additionally, to elucidate the molecular mechanisms of the seed maturation program, co-expression pattern analyses of LAFL genes were conducted across vascular plants. The results show that the origin of AFL gene family dates back to a common ancestor of bryophytes and vascular plants, while LEC1-type genes are only found in vascular plants. LAFL genes of vascular plants likely specify their co-expression in two different developmental phrases, spore and seed maturation, respectively, and expression patterns vary slightly across the major vascular plants lineages. All the information presented in this study will provide insights into the origin and diversification of seed plants.

Identification of Peach NAP Transcription Factor Genes and Characterization of their Expression in Vegetative and Reproductive Organs during Development and Senescence

The NAP (NAC-like, activated by AP3/P1) transcription factor belongs to a subfamily of the NAC transcription factor family, and is believed to have an important role in regulating plant growth and development. However, there is very little information about this subfamily in Rosaceous plants. We identified seven NAP genes in the peach genome. PpNAP2 was categorized in the NAP I group, and contained a conserved transcription activation region. The other PpNAP genes belonged to the NAP II group. The expression patterns of the PpNAP genes differed in various organs and developmental stages. PpNAP1 and PpNAP2 were highly expressed in mature and senescing flowers, but not in leaves, fruits, and flower buds. PpNAP3 and PpNAP5 were only expressed in leaves. The PpNAP4 expression level was high in mature and senescing fruits, while PpNAP6 and PpNAP7 expression was up-regulated in mature and senescent leaves and flowers. During the fruit development period, the PpNAP4 and PpNAP6 expression levels rapidly increased during the S1 and S4 stages, which suggests these genes are involved in the first exponential growth phase and fruit ripening. During the fruit ripening and softening period, the PpNAP1, PpNAP4, and PpNAP6 expression levels were high during the early storage period, which was accompanied by a rapid increase in ethylene production. PpNAP1, PpNAP4, and PpNAP6 expression slowly increased during the middle or late storage periods, and peaked at the end of the storage period. Additionally, abscisic acid (ABA)-treated fruits were softer and produced more ethylene than the controls. Furthermore, the PpNAP1, PpNAP4, and PpNAP6 expression levels were higher in ABA-treated fruits. These results suggest that PpNAP1, PpNAP4, and PpNAP6 are responsive to ABA and may regulate peach fruit ripening.

Light response and potential interacting proteins of a grape flavonoid 3'-hydroxylase gene promoter

Flavonoid 3'-hydroxylase (F3'H), a member of cytochrome P450 protein family, introduces B-ring hydroxyl group in the 3' position of the flavonoid. In this study, the cDNA sequence of a F3'H gene (VviF3'H), which contains an open reading frame of 1530 bp encoding a polypeptide of 509 amino acids, was cloned and characterized from Vitis vinifera L. cv. Cabernet Sauvignon. VviF3'H showed high homology to known F3'H genes, especially F3'Hs from the V. vinifera reference genome (Pinot Noir) and lotus. Expression profiling analysis using real-time PCR revealed that VviF3'H was ubiquitously expressed in all tested tissues including berries, leaves, flowers, roots, stems and tendrils, suggesting its important physiological role in plant growth and development. Moreover, the transcript level of VviF3'H gene in grape berries was relatively higher at early developmental stages and gradually decreased during véraison, and then increased in the mature phase. In addition, the promoter of VviF3'H was isolated by using TAIL-PCR. Yeast one-hybrid screening of the Cabernet Sauvignon cDNA library and subsequent in vivo/vitro validations revealed the interaction between VviF3'H promoter and several transcription factors, including members of HD-Zip, NAC, MYB and EIN families. A transcriptional regulation mechanism of VviF3'H expression is proposed for the first time.