Plants uptake and assimilate nitrogen from the soil in the form of nitrate, ammonium ions, and available amino acids from organic sources. Plant nitrate and ammonium transporters are responsible for nitrate and ammonium translocation from the soil into the roots. The unique structure of these transporters determines the specificity of each transporter, and structural analyses reveal the mechanisms by which these transporters function. Following absorption, the nitrogen metabolism pathway incorporates the nitrogen into organic compounds via glutamine synthetase and glutamate synthase that convert ammonium ions into glutamine and glutamate. Different isoforms of glutamine synthetase and glutamate synthase exist, enabling plants to fine-tune nitrogen metabolism based on environmental cues. Under stressful conditions, nitric oxide has been found to enhance plant survival under drought stress. Furthermore, the interaction between salinity stress and nitrogen availability in plants has been studied, with nitric oxide identified as a potential mediator of responses to salt stress. Conversely, excessive use of nitrate fertilizers can lead to health and environmental issues. Therefore, alternative strategies, such as establishing nitrogen fixation in plants through diazotrophic microbiota, have been explored to reduce reliance on synthetic fertilizers. Ultimately, genomics can identify new genes related to nitrogen fixation, which could be harnessed to improve plant productivity.

Plant uptake and assimilation of essential nitrogen compounds from the soil are mainly in the form of nitrate and ammonium ions. Plant nitrate transporters (NRTs) play a crucial role in nitrate uptake from the soil into the roots. NRT structural analysis reveals the mechanisms by which these transporters function. Similarly, plant ammonium transporters (AMTs) mediate the uptake of ammonium ions, and their structural analysis has provided valuable information on their mechanisms. After nitrogen uptake by plant roots, the nitrogen metabolism pathway involves the incorporation of nitrogen into organic compounds. Glutamine synthetase (GS) and glutamate synthase (GoGAT) are the master players in this pathway. They work together to convert ammonium ions into glutamine and glutamate, respectively. Different isoforms of GS and GoGAT exist, enabling plants to fine-tune nitrogen metabolism based on environmental cues. Under severe abiotic stress conditions, nitric oxide (NO) has been found to enhance plant survival under drought. Furthermore, the interaction between salinity stress and nitrogen availability in plants has been studied, with NO identified as a potential mediator of responses to salt stress. On the other hand, excessive use of nitrate fertilizers can lead to health and environmental issues. Therefore, alternative strategies, such as establishing nitrogen fixation in plants through diazotrophic microbiota, have been explored to reduce reliance on synthetic fertilizers. Ultimately, genomics can identify new genes related to nitrogen fixation, which could be harnessed to improve plant productivity. By deciphering the genetic basis of nitrogen-fixing traits, researchers aim to develop crops that efficiently utilize nitrogen from the environment.

Citrus nematode (Tylenchulus semipenetrans) is one of the dominant plant-parasitic nematodes in citrus-growing regions, resulting in an average yield loss between 10 and 30%. Tylenchulus semipenetrans is a sedentary semi-endoparasitic nematode that infects the roots of citrus trees, causing stunted growth, reduced fruit yield, and poor fruit quality; collectively this pathology and thus the disease caused is referred to as the slow decline of citrus. Despite its huge importance, the citrus nematode is regarded as a neglected parasite, and most research focuses on biological control and integrated pest management. Advancements in understanding the molecular mechanisms of other plant-parasitic nematodes, such as sedentary endoparasites with biological similarities to citrus nematodes, can be leveraged to gain deeper insights into the molecular mechanisms of citrus nematodes. In this review, we examine the biology, and integrated pest management of citrus nematodes, and explore future research directions toward understanding the role of genomics, gene-editing tools, and the molecular mechanisms of host-seeking and effectors used by other plant-parasitic nematodes to cause infection, which can serve as a foundation for future work in citrus nematode management.

This study utilized the Fourier-based method to analyze the morphology of over 4000 leaves from more than 190 accessions selected from the Givaudan Citrus Variety Collection at the University of California Riverside, one of the world’s most diverse collections of citrus and closely related genera. Our analysis revealed significant variations in leaf morphology among the major citrus species groups, and hybrid varieties produced through breeding exhibited intermediate leaf morphology compared to their parental citrus species. We found a positive correlation between leaf area in native citrus species and temperature in lower tropical latitudes, while negative/positive associations between aspect ratio and temperature/rainfall were also observed, respectively. These results suggest that citrus leaves may have evolved into larger but thinner leaves to increase their photosynthetic capacity per unit area while maintaining water balance by reducing water loss through transpiration. Our analysis also indicates that the existing biodiversity observed in citrus species can be attributed to their migrations across the foothills of the Himalayas, southward to the islands of Indonesia, and northward to the islands of Japan. Our study supports the hypothesis that citrus species have adapted to warm areas lacking extreme daily and nightly temperatures, where a large number of species of origin are found. Overall, this study presents a promising approach to investigate the morphological variation in citrus leaves, which could potentially aid in the selection and breeding of citrus cultivars with superior physiological traits and deepen our understanding of citrus diversity.

Background: Genetic and epigenetic perturbation of cis-regulatory sequences can shift patterns of gene expression and result in novel phenotypes. Phased genome assemblies now enable the local dissection of linkages between cis-regulatory sequences, including their epigenetic state, and allele-specific gene expression to further characterize gene regulation and resulting phenotypes in heterozygous genomes. Results: We assembled a locally phased genome for a mandarin hybrid named ‘Fairchild’ to explore the molecular signatures of allele-specific gene expression. With local genome phasing, genes with allele-specific expression were paired with haplotype-specific chromatin states, including levels of chromatin accessibility, histone modifications, and DNA methylation. We found that 30% of variation in allele-specific expression could be attributed to haplotype associated factors, with allelic levels of chromatin accessibility and three histone modifications in gene bodies having the most influence. Structural variants in promoter regions were also associated with allele-specific expression, including specific enrichments of hAT and MULE-MuDR DNA transposon sequences. Integration of haplotype-resolved genetic and epigenetic landscapes with high-throughput phenotypic analysis of fruit traits in a panel of 154 accessions with mandarin and pummelo ancestry revealed that trait-associated variants were enriched in regions of open chromatin. Mining of trait-associated variants uncovered a Gypsy retrotransposon insertion in a gene that regulates potassium transport and may contribute to the reduction in fruit size that is observed in mandarins. Conclusions: ​​Using a locally phased assembly of a heterozygous cultivar of citrus, we dissected the interplay between genetic variants and molecular phenotypes to reveal cis-regulatory sequences with potential functional effects on phenotypes relevant for genetic improvement.

Interspecific hybridization is a common and effective strategy for producing disease resilient citrus cultivars, including those with tolerance to Huanglongbing (HLB) disease. Several HLB-tolerant cultivars have been developed through hybridization of mandarins (Citrus reticulata) with their wild relative Poncirus trifoliata. One such cultivar, ‘US-897’, exhibits robust tolerance to the bacteria causing HLB disease, Candidatus Liberibacter asiaticus (CLas). To explore the genetic architecture of the early transcriptional response to Candidatus Liberibacter asiaticus (CLas) infection in ‘US-897’, we performed transcriptomic analysis of the hybrid and its parents, ‘Cleopatra’ (C. reticulata) and ‘Flying Dragon’ (P. trifoliata). A haplotype-resolved genome for ‘US-897’ was generated using PacBio HiFi sequencing reads to support quantification of the expression of both the Citrus and Poncirus alleles. By profiling gene expression in this parent-offspring trio, we were able to determine the mode of inheritance for genes differentially expressed between parents (‘Cleopatra’ and ‘Flying Dragon’) and their interspecific hybrid (‘US-897’), with the majority genes exhibiting non-additive patterns of gene expression inheritance. Additionally, analysis of allele-specific expression in the hybrid ‘US-897’ revealed the contribution of cis- versus trans-acting regulatory variants on genes with additive and non-additive modes of inheritance. A strong correlation between differential expression between parents and allele-specific expression in ‘US-897’ suggests that cis-regulatory variation is a significant source of expression divergence between species. Finally, genes responsive to infection with CLas were identified to explore how gene regulation associated with tolerance to HLB was rewired between Citrus and its relative Poncirus.