Population Diversity of 'Candidatus Liberibacter asiaticus' and Diaphorina citri in Sichuan: A Case Study for Huanglongbing Monitoring and Interception

The complete genome sequence of "Candidatus Liberibacter asiaticus" strain 9PA and the characterization of field strains in the Brazilian citriculture

"Candidatus Liberibacter asiaticus" (CLas) is associated with citrus huanglongbing, a severe disease with global importance that affects citrus production in Brazil. This study reports the first complete genome of a Brazilian strain of CLas. The genomic structure comparison of strain 9PA with those of 13 complete CLas genomes revealed 9,091 mismatches and 992 gaps/insertions, highlighting eight locally colinear blocks, among which six are in the prophage region. Phylogenetic analysis categorized 13 CLas genomes into two clusters with 9PA clustered with strains from China and the United States. Whole-genomic comparison identified diverse hypervariable genomic regions (HGRs). Three HGRs in the chromosomal region and three in the prophage region were selected and investigated by polymerase chain reaction. HGRs assessed from 68 samples, from medium- to high-huanglongbing incidence areas in Sao Paulo state, were grouped into haplotypes A to P. Haplotype A, which includes strain 9PA, is the second most prevalent, representing 19.1% of the samples. Haplotype B, the most common, accounts for 42.6%. Together with haplotype C, these make up 72% of the evaluated samples. The 9PA strain has prophage P-9PA-1, both integrated and circularized, and P-9PA-3, only found in a circularized form. Prophages show high identity with SC1 (83%) and P-JXGC-3 (98%). Co-occurrence of both type 1 and 3 prophages was observed in field samples. The approach employed provides insights into the Brazilian CLas population, providing markers for population studies and highlighting the prevalence of type 1 and 3 prophages in the population.

IMPORTANCE

CLas is a destructive pathogen responsible for causing the severe citrus disease known as huanglongbing. Our study presents the first fully sequenced Brazilian strain of CLas, designated as 9PA, and includes an analysis of two prophages occurring in this strain. The main objective of our research was to compare the genome features of this Brazilian strain with other fully sequenced genomes and to identify its hypervariable genetic regions. These regions were subsequently used to assess genomic variability within both the chromosomal and prophage regions in Brazilian isolates of CLas. Our findings offer valuable insights into the diversified adaptation of CLas.

Genetic Signatures of Contrasted Outbreak Histories of "Candidatus Liberibacter asiaticus", the Bacterium That Causes Citrus Huanglongbing, in Three Outermost Regions of the European Union

In an era of trade globalization and climate change, crop pathogens and pests are a genuine threat to food security. The detailed characterization of emerging pathogen populations is a prerequisite for managing invasive species pathways and designing sustainable disease control strategies. Huanglongbing is the disease that causes the most damage to citrus, a crop that ranks #1 worldwide in terms of fruit production. Huanglongbing can be caused by three species of the phloem-limited alpha-proteobacterium, "Candidatus Liberibacter," which are transmitted by psyllids. Two of these bacteria are of highest concern, "Ca. Liberibacter asiaticus" and "Ca. Liberibacter africanus," and have distinct thermal optima. These pathogens are unculturable, which complicates their high-throughput genetic characterization. In the present study, we used several genotyping techniques and an extensive sample collection to characterize Ca. Liberibacter populations associated with the emergence of huanglongbing in three French outermost regions of the European Union (Guadeloupe, Martinique and Réunion). The outbreaks were primarily caused by "Ca. Liberibacter asiaticus," as "Ca. Liberibacter africanus" was only found at a single location in Réunion. We emphasize the low diversity and high genetic relatedness between samples from Guadeloupe and Martinique, which suggests the putative movement of the pathogen between the two islands and/or the independent introduction of closely related strains. These samples were markedly different from the samples from Réunion, where the higher genetic diversity revealed by tandem-repeat markers suggests that the disease was probably overlooked for years before being officially identified in 2015. We show that "Ca. Liberibacter asiaticus" occurs from sea level to an altitude of 950 m above sea level and lacks spatial structure. This suggests the pathogen's medium- to long-distance movement. We also suggest that backyard trees acted as relays for disease spread. We discuss the implications of population biology data for surveillance and management of this threatful disease.

Potential habitat suitability of Candidatus Liberibacter asiaticus and genetic diversity of its prophages across China

Huanglongbing (HLB) is a severe citrus disease in China caused by Candidatus Liberibacter asiaticus (CLas). Since its initial identification, the pathogen has spread to 10 mainland provinces in China and caused devastating loss. Three distinct prophage types have been identified in CLas; however, their distribution and diversity in China remain inadequately understood. In this study, we collected 500 CLas samples from 10 provinces in China, employing three specific genomic loci to identify prophage types. Subsequently, Sanger sequencing was employed to analyze the genetic diversity of prophage within populations of CLas in China. In addition, the MaxEnt model optimized by the ENMeval software package, was used to predict the habitat suitability of populations of CLas and assess the potential impact of future climate change on its distribution in China. Our analysis revealed that type 2 prophage is the most prevalent, accounting for 55% in China. Among the 10 provinces tested, CLas populations in Yunnan and Sichuan demonstrated higher genetic diversity. Further analysis reveals that CLas populations harboring type 1 prophage remain relatively stable, whereas those carrying type 2 and type 3 prophages undergo population expansion. Furthermore, our predictive models indicate that the presently suitable habitat for CLas populations is concentrated in the southern and certain central regions of China, with an anticipated expansion under future climate change conditions. Presently, the center of populations of CLas characterized by favorable living conditions is situated in Zunyi City, Guizhou Province. Nevertheless, a projected trend indicates a shift toward the northeast, particularly targeting Tongren City in the foreseeable future.

IMPORTANCE

This study offers significant insights into the distribution and genetic diversity of three types of prophages associated with Candidatus Liberibacter asiaticus (CLas) in China. Our predictions underscore the implications of climate change on the future distribution of CLas. These findings contribute to a better understanding of Huanglongbing management strategies and can facilitate the development of effective measures to control the spread of this devastating disease within the citrus industry.

A Calcium-Dependent Protein Kinase Regulates the Defense Response in Citrus sinensis

Citrus Huanglongbing (HLB), which is caused by 'Candidatus Liberibacter asiaticus' (CLas), is one of the most destructive citrus diseases worldwide, and defense-related Citrus sinensis gene resources remain largely unexplored. Calcium signaling plays an important role in diverse biological processes. In plants, a few calcium-dependent protein kinases (CDPKs/CPKs) have been shown to contribute to defense against pathogenic microbes. The genome of C. sinensis encodes dozens of CPKs. In this study, the role of C. sinensis calcium-dependent protein kinases (CsCPKs) in C. sinensis defense was investigated. Silencing of CsCPK6 compromised the induction of defense-related genes in C. sinensis. Expression of a constitutively active form of CsCPK6 (CsCPK6CA) triggered the activation of defense-related genes in C. sinensis. Complementation of CsCPK6 rescued the defense-related gene induction in an Arabidopsis thaliana cpk4/11 mutant, indicating that CsCPK6 carries CPK activity and is capable of functioning as a CPK in Arabidopsis. Moreover, an effector derived from CLas inhibits defense induced by the expression of CsCPK6CA and autophosphorylation of CsCPK6, which suggests the involvement of CsCPK6 and calcium signaling in defense. These results support a positive role for CsCPK6 in C. sinensis defense against CLas, and the autoinhibitory regulation of CsCPK6 provides a potential genome-editing target for improving C. sinensis defense. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Detection of Candidatus Liberibacter asiaticus and five viruses in individual Asian citrus psyllid in China

Introduction

Asian citrus psyllid (ACP, Diaphorina citri) is an important transmission vector of "Candidatus Liberibacter asiaticus" (CLas), the causal agent of Huanglongbing (HLB), the most destructive citrus disease in the world. As there are currently no HLB-resistant rootstocks or varieties, the control of ACP is an important way to prevent HLB. Some viruses of insect vectors can be used as genetically engineered materials to control insect vectors.

Methods

To gain knowledge on viruses in ACP in China, the prevalence of five RNA and DNA viruses was successfully determined by optimizing reverse transcription polymerase chain reaction (RT-PCR) in individual adult ACPs. The five ACP-associated viruses were identified as follows: diaphorina citri bunyavirus 2, which was newly identified by high-throughput sequencing in our lab, diaphorina citri reovirus (DcRV), diaphorina citri picorna-like virus (DcPLV), diaphorina citri bunyavirus (DcBV), and diaphorina citri densovirus-like virus (DcDV).

Results

DcPLV was the most prevalent and widespread ACP-associated virus, followed by DcBV, and it was detected in more than 50% of all samples tested. DcPLV was also demonstrated to propagate vertically and found more in salivary glands among different tissues. Approximately 60% of all adult insect samples were co-infected with more than one insect pathogen, including the five ACP-associated viruses and CLas.

Discussion

This is the first time these viruses, including the newly identified ACP-associated virus, have been detected in individual adult ACPs from natural populations in China's five major citrus-producing provinces. These results provide valuable information about the prevalence of ACP-associated viruses in China, some of which have the potential to be used as biocontrol agents. In addition, analysis of the change in prevalence of pathogens in a single insect vector is the basis for understanding the interactions between CLas, ACP, and insect viruses.

First report on the presence of huanglongbing vectors (Diaphorina citri and Trioza erytreae) in Ghana

As significant threats to global citrus production, Diaphorina citri (Kuwayama; Hemiptera: Psyllidae) and Trioza erytreae (Del Guercio; Hemiptera: Triozidae) have caused considerable losses to citrus trees globally. Diaphorina citri vectors "Candidatus Liberibacter asiaticus" and "Ca. L. americanus", whereas T. erytreae transmits "Ca. L. africanus" and "Ca. L. asiaticus", the pathogens responsible for citrus greening disease or Huanglongbing (HLB). Though HLB is a destructive disease of citrus wherever it occurs, information on the occurrence and geographical distribution of its vectors in Africa is limited. In recent surveys to determine if HLB vectors are present in Ghana, we observed eggs, nymphs, and adults of insects suspected to be D. citri and T. erytreae. Using morphological traits and DNA analyses, the identity of the suspected insects was confirmed to be D. citri and T. erytreae. Individuals of D. citri and T. erytreae were examined using qPCR for CLaf, CLam, and CLas, but none of them tested positive for any of the Liberibacter species. Herein we report, for the first time, the presence of D. citri and T. erytreae in Ghana (West Africa). We discuss the implications of this new threat to the citrus industry to formulate appropriate management strategies.

Current Epidemic Situation and Control Status of Citrus Huanglongbing in Guangdong China: The Space–Time Pattern Analysis of Specific Orchards

Huanglongbing (HLB) is the most harmful bacterial disease in citrus production in the world, and has been seriously ravaging the citrus groves of South China since the 1930s. The surveillance of the epidemiological characteristics of HLB is of utmost priority for citrus production in this region. In order to explore the effects of disease control measures, analyses on the space–time statistical features of the HLB epidemic, from 2019 to 2021, within six orchards in the Guangdong province are presented. Overall, the number of citrus plants in the orchards usually slightly decreased year by year. The reduction was mainly related to the level of plant susceptibility, which is correlated with citrus varieties. The maximum disease severity (incidence and race increment) was correlated with the awareness of this disease and the management intensity applied by the manager. A higher disease index was found in the conventional management orchards than in the comprehensive prevention and control orchards. Proper insect-protective screen houses can effectively prevent the epidemic of HLB, without affecting the fruit quality, and can also aid with higher yields. A high correlation was found between the geometry and topography of orchards and the HLB epidemic due to the wind direction from May to September and the Asia citrus psyllid activity characteristics. For flat orchards, the incidence of HLB in the north and entrance areas was higher than that in the southwest. In the mountain area, the incidence of the windward side in the south was higher than that of the leeward side in the north. Diseased trees tended to have an edge effect in the grove, whereas the trees of the same disease scale were found clustered in their distribution. These results allow a better understanding of HLB epidemiology and provide guidance for the early warning of HLB in new groves in areas that are severely affected by this disease. Furthermore, they also provide a scientific basis for the comprehensive prevention and control of HLB in old groves.