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Huanglongbing (HLB) is a severe citrus disease worldwide. Wild Australian limes like Citrus australasica, C. inodora, and C. glauca possess beneficial HLB resistance traits. Individual trees of the three taxa were extensively used in a breeding program for over a decade to introgress resistance traits into commercial-quality citrus germplasm. We generated high-quality, phased, de novo genome assemblies of the three Australian limes using PacBio long-read sequencing. The genome assembly sizes of the primary and alternate haplotypes were determined for C. australasica (337 Mb/335 Mb), C. inodora (304 Mb/299 Mb), and C. glauca (376 Mb/379 Mb). The nine chromosome-scale scaffolds included 86–91% of the genome sequences generated. The integrity and completeness of the assembled genomes were estimated to be at 97.2–98.8%. Gene annotation studies identified 25,461 genes in C. australasica, 27,665 in C. inodora, and 30,067 in C. glauca. Genes belonging to 118 orthogroups were specific to Australian lime genomes compared to other citrus genomes analyzed. Significantly fewer canonical resistance (R) genes were found in C. inodora and C. glauca (319 and 449, respectively) compared to C. australasica (576), C. clementina (579), and C. sinensis (651). Similar patterns were observed for other gene families associated with potential HLB resistance, including Phloem protein 2 (PP2) and Callose synthase (CalS) genes predicted in the Australian lime genomes. The genomic information on Australian limes developed in the present study will help understand the genetic basis of HLB resistance. [ABSTRACT FROM AUTHOR]

Citrus is affected by many diseases, and hence, the movement of citrus propagative materials is highly regulated in the USA. Currently used regulatory pathogen detection methods include biological and laboratory-based technologies, which are time-consuming, expensive, and have many limitations. There is an urgent need to develop alternate, rapid, economical, and reliable testing methods for safe germplasm exchange. Citrus huanglongbing (HLB) has devastated citrus industries leading to an increased need for germplasm exchanges between citrus growing regions for evaluating many potentially valuable hybrids for both HLB resistance and multilocational performance. In the present study, Next-Generation Sequencing (NGS) methods were used to sequence the transcriptomes of 21 test samples, including 15 well-characterized pathogen-positive plants. A workflow was designed in the CLC Genomics Workbench software, v 21.0.5 for bioinformatics analysis of the sequence data for the detection of pathogens. NGS was rapid and found to be a valuable technique for the detection of viral and bacterial pathogens, and for the discovery of new citrus viruses, complementary to the existing array of biological and laboratory assays. Using NGS methods, we detected beet western yellows virus, a newly reported citrus virus, and a variant of the citrus yellow vein-associated virus associated with the "fatal yellows" disease. [ABSTRACT FROM AUTHOR]

Simple Summary: Citrus cultivation is affected in many parts of the world because of a devastating disease, huanglongbing (HLB) or citrus greening. In Florida, nearly all commercial citrus is compromised due to HLB, and the disease has spread to other citrus-growing regions of the United States, California and Texas. In California, testing Asian citrus psyllids (ACPs) for the HLB pathogen has been an essential part of integrated pest management. ACP and HLB surveys are essential for disease management in areas where HLB is not widespread. We developed improved ACP traps that can be deployed in the field along with the standard yellow sticky traps. The reusable traps were designed with Rhinoceros computer software and a 3D printer. These traps can be deployed for several months and provide a dynamic sampling mechanism for an improved disease survey strategy. In the present study, ACPs from the 3D-printed traps are collected in a preservative and appear suitable for HLB testing. The evaluation of traps in Florida and California under laboratory, greenhouse, and field conditions indicates that the 3D-printed traps can capture ACPs with about the same efficiency as the sticky traps. They are easy to handle and provide an important field tool for HLB management. Citrus huanglongbing (HLB) is a severe problem for citrus cultivation. The disease management programs benefit from improved field tools suitable for surveying the ACP vector (Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae)) and the associated pathogen. In the present study, we utilize three-dimensional (3D) printers and design tools to develop traps that can capture and preserve ACPs. Three novel, 3D-printed traps were designed and evaluated: stem trap, and cylinder traps 1 and 2. The traps and yellow sticky cards were deployed weekly for 8 months in 2 non-commercial citrus groves in Florida; in California, the traps were evaluated for 12 months in field cages and 4 citrus groves. The stem traps captured lower numbers of ACPs at all experimental sites compared to the cylinder traps. Capture rates in the cylinder traps were comparable to the sticky trap, making the device a viable tool for monitoring field ACPs. The two main advantages of using the reusable 3D traps over standard methods of ACP and HLB surveys include dynamic sampling that can be conducted year-round and the capture of ACPs that can be preserved and tested. Improved trapping may facilitate quick management decisions and mitigate HLB. [ABSTRACT FROM AUTHOR]

Summary: Huanglongbing (HLB) is the most devastating citrus disease in the world. Almost all commercial citrus varieties are susceptible to the causal bacterium, Candidatus Liberibacter asiaticus (CLas), which is transmitted by the Asian citrus psyllid (ACP). Currently, there are no effective management strategies to control HLB. HLB‐tolerant traits have been reported in some citrus relatives and citrus hybrids, which offer a direct pathway for discovering natural defence regulators to combat HLB. Through comparative analysis of small RNA profiles and target gene expression between an HLB‐tolerant citrus hybrid (Poncirus trifoliata × Citrus reticulata) and a susceptible citrus variety, we identified a panel of candidate defence regulators for HLB‐tolerance. These regulators display similar expression patterns in another HLB‐tolerant citrus relative, with a distinct genetic and geographic background, the Sydney hybrid (Microcitrus virgata). Because the functional validation of candidate regulators in tree crops is always challenging, we developed a novel rapid functional screening method, using a C. Liberibacter solanacearum (CLso)/potato psyllid/Nicotiana benthamiana interaction system to mimic the natural transmission and infection circuit of the HLB complex. When combined with efficient virus‐induced gene silencing in N. benthamiana, this innovative and cost‐effective screening method allows for rapid identification and functional characterization of regulators involved in plant immune responses against HLB, such as the positive regulator BRCA1‐Associated Protein, and the negative regulator Vascular Associated Death Protein. [ABSTRACT FROM AUTHOR]

Genetic traits in Poncirus trifoliata (Rutaceae) are known to confer resistance to colonization by the Asian citrus psyllid, but field surveys indicated these traits were not expressed in any of 24 simple hybrids between P. trifoliata and sweet orange. No resistance to colonization by the psyllid was observed in 14 other types of P. trifoliata hybrids. Three citrumelo hybrids appeared to be resistant in 1 survey, but in another survey, none of 6 citrumelos exhibited resistance. Interestingly, colonization was somewhat reduced on a hybrid with P. trifoliata in the pedigree of both parents, suggesting the possibility that traits suppressing oviposition may be recovered through similar crosses. [ABSTRACT FROM AUTHOR]

‘ Candidatus Liberibacter asiaticus’ (Las), associated with citrus huanglongbing (HLB or citrus greening) is spread by Diaphorina citri Kuwayama, the Asian citrus psyllid. Psyllids can be tested to assess the prevalence of Las in a population and for early detection of HLB in new areas being invaded by the psyllid. In some cases, large numbers of psyllids may need to be tested, thus there is a need for rapid and inexpensive field detection methodology. We report here on the development of a field detection kit for testing psyllids for Las using loop-mediated amplification technology (LAMP). Six samples with pools of 1–10 psyllids plus a positive and negative control can be tested at a time in about 30 min; 10 min for crude extraction and 20 min for target DNA amplification. The LAMP assays are conducted in a Smart-DART™ detection unit which is operated from an Android device. The LAMP detection method for Las is about 100 times more sensitive than the traditional real time PCR method. In addition to field testing of psyllids for Las, the methodology was validated as effective for identifying Las in plant DNA extractions. In California, where the psyllid has only recently invaded, participation of a large number of growers and extension workers in field detection may facilitate rapid containment efforts should Las be found. In areas where the disease epidemic is already in the initial stages, large scale testing can be helpful for effective disease management. The LAMP technology lends itself well in such situations. [ABSTRACT FROM AUTHOR]

Citrus huanglongbing (HLB) disease associated with the 'Candidatus Liberibacter asiaticus' (CLas) bacterium has caused significant financial damage to many citrus industries. Large-scale pathogen surveys are routinely conducted in California to detect CLas early in the disease cycle by lab-based qPCR assays. We have developed an improved reference gene for the sensitive detection of CLas from plants in diagnostic duplex qPCR and analytical digital droplet PCR (ddPCR) assays. The mitochondrial cytochrome oxidase gene (COX), widely used as a reference, is not ideal because its high copy number can inhibit amplification of small quantities of target genes. In ddPCRs, oversaturation of droplets complicates data normalization and quantification. The variable copy numbers of COX gene in metabolically active young tissue, greenhouse plants, and citrus relatives suggest the need for a non-variable, nuclear, low copy, universal reference gene for analysis of HLB hosts. The single-copy nuclear gene, malate dehydrogenase (MDH), developed here as a reference gene, is amenable to data normalization, suitable for duplex qPCR and ddPCR assays. The sequence of MDH fragment selected is conserved in most HLB hosts in the taxonomic group Aurantioideae. This study emphasizes the need to develop standard guidelines for reference genes in DNA-based PCR assays. [ABSTRACT FROM AUTHOR]