Diaci v3.0: chromosome-level assembly, de novo transcriptome, and manual annotation of Diaphorina citri, insect vector of Huanglongbing.

Background: Diaphorina citri is an insect vector of "Candidatus Liberibacter asiaticus" (CLas), the gram-negative bacterial pathogen associated with citrus greening disease. Control measures rely on pesticides with negative impacts on the environment, natural ecosystems, and human and animal health. In contrast, gene-targeting methods have the potential to specifically target the vector species and/or reduce pathogen transmission.

Annotation of putative circadian rhythm-associated genes in (Hemiptera: Liviidae).

The circadian rhythm involves multiple genes that generate an internal molecular clock, allowing organisms to anticipate environmental conditions produced by the Earth's rotation on its axis. Here, we present the results of the manual curation of 27 genes that are associated with circadian rhythm in the genome of the Asian citrus psyllid. This insect is the vector for the bacterial pathogen Liberibacter asiaticus (Las), the causal agent of citrus greening disease (Huanglongbing).

Manual curation and phylogenetic analysis of chitinase family genes in the Asian citrus psyllid, .

Chitinases are enzymes that digest the polysaccharide polymer chitin. During insect development, breakdown of chitin is an essential step in molting of the exoskeleton. Knockdown of chitinases required for molting is lethal to insects, making chitinase genes an interesting target for RNAi-based pest control methods.

Ubiquitin-proteasome pathway annotation in can reveal potential targets for RNAi-based pest management.

Ubiquitination is an ATP-dependent process that targets proteins for degradation by the proteasome. Here, we annotated 15 genes from the ubiquitin-proteasome pathway in the Asian citrus psyllid, . This psyllid vector has come to prominence in the last decade owing to its role in the transmission of the devastating bacterial pathogen, Liberibacter asiaticus (Las).

Genomic identification, annotation, and comparative analysis of Vacuolar-type ATP synthase subunits in .

The hemipteran insect , or Asian citrus psyllid, is a vector for Liberibacter asiaticus (Las), the bacterium causing citrus greening disease, or Huanglongbing (HLB). Millions of citrus trees have been destroyed, and every grove in Florida, USA, has been directly affected by this disease. In eukaryotes, vacuolar-type ATP synthase (V-ATPase) is an abundant heterodimeric enzyme that serves the cell with essential compartment acidification through the active processes that transport protons across the membrane.

Annotation of Hox cluster and Hox cofactor genes in the Asian citrus psyllid, , reveals novel features.

Hox genes and their cofactors are essential developmental genes specifying regional identity in animals. Hox genes have a conserved arrangement in clusters in the same order in which they specify identity along the anterior-posterior axis. A few insect species have breaks in the cluster, but these are exceptions.

Annotation of glycolysis, gluconeogenesis, and trehaloneogenesis pathways provide insight into carbohydrate metabolism in the Asian citrus psyllid.

Citrus greening disease is caused by the pathogen Liberibacter asiaticus and transmitted by the Asian citrus psyllid, . No curative treatment or significant prevention mechanism exists for this disease, which causes economic losses from reduced citrus production. A high-quality genome of is being manually annotated to provide accurate gene models to identify novel control targets and increase understanding of this pest.

Annotation of segmentation pathway genes in the Asian citrus psyllid, .

Insects have a segmented body plan that is established during embryogenesis when the anterior-posterior (A-P) axis is divided into repeated units by a cascade of gene expression. The cascade is initiated by protein gradients created by translation of maternally provided mRNAs, localized at the anterior and posterior poles of the embryo. Combinations of these proteins activate specific gap genes to divide the embryo into distinct regions along the anterior-posterior axis.

characterization of chitin deacetylase genes in the genome.

Chitin deacetylases (CDAs) are one of the least understood components of insect chitin metabolism. The partial deacetylation of chitin polymers appears to be important for the proper formation of higher order chitin structures, such as long fibers and bundles, which contribute to the integrity of the insect exoskeleton and other structures. Some CDAs may also be involved in bacterial defense.

Annotation of chitin biosynthesis genes in , the Asian citrus psyllid.

The polysaccharide chitin is critical for the formation of many insect structures, including the exoskeleton, and is required for normal development. Here we report the annotation of three genes from the chitin synthesis pathway in the Asian citrus psyllid, (Hemiptera: Liviidae), the vector of Huanglongbing (citrus greening disease). Most insects have two chitin synthase (CHS) genes but, like other hemipterans, has only one.

Utilizing a chromosomal-length genome assembly to annotate the Wnt signaling pathway in the Asian citrus psyllid, .

The Asian citrus psyllid, , is an insect vector that transmits Liberibacter asiaticus, the causal agent of the Huanglongbing (HLB), or citrus greening disease. This disease has devastated Florida's citrus industry, and threatens California's industry as well as other citrus producing regions around the world. To find novel solutions to the disease, a better understanding of the vector is needed.

Annotation of genes in , the vector for Huanglongbing disease.

Huanglongbing (HLB), also known as citrus greening disease, is caused by the bacterium Liberibacter asiaticus (Las). It is a serious threat to global citrus production. This bacterium is transmitted by the Asian citrus psyllid, (Hemiptera).

Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding.

Solanum pimpinellifolium (SP) is the wild progenitor of cultivated tomato. Because of its remarkable stress tolerance and intense flavor, SP has been used as an important germplasm donor in modern tomato breeding. Here, we present a high-quality chromosome-scale genome sequence of SP LA2093.

Draft Genome Sequence Resource of the Citrus Stem-End Rot Fungal Pathogen CITRA15.

is a fungal pathogen associated with perennial tropical fruit plants worldwide. In citrus, causes stem-end rot (Diplodia stem-end rot), a damaging postharvest disease that is aggravated when trees are also infected with the citrus greening bacteria ' Liberibacter asiaticus'. Due to the latent infection of during the preharvest stage, it becomes difficult to control the disease by chemical or physical treatment.

A quick guide for student-driven community genome annotation.

High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental validation over the course of many years. The majority of gene models present in biological databases today have been identified in draft genome assemblies using automated annotation pipelines that are frequently based on orthologs from distantly related model organisms and usually have minor or major errors. Manual curation is time consuming and often requires substantial expertise, but is instrumental in improving gene model structure and identification.

Fern genomes elucidate land plant evolution and cyanobacterial symbioses.

Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns-one at the base of 'core leptosporangiates' and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer.

Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community.

https://citrusgreening.org/.

The MYB36 transcription factor orchestrates Casparian strip formation.

The endodermis in roots acts as a selectivity filter for nutrient and water transport essential for growth and development. This selectivity is enabled by the formation of lignin-based Casparian strips. Casparian strip formation is initiated by the localization of the Casparian strip domain proteins (CASPs) in the plasma membrane, at the site where the Casparian strip will form.

Dirigent domain-containing protein is part of the machinery required for formation of the lignin-based Casparian strip in the root.

The endodermis acts as a "second skin" in plant roots by providing the cellular control necessary for the selective entry of water and solutes into the vascular system. To enable such control, Casparian strips span the cell wall of adjacent endodermal cells to form a tight junction that blocks extracellular diffusion across the endodermis. This junction is composed of lignin that is polymerized by oxidative coupling of monolignols through the action of a NADPH oxidase and peroxidases.

Root suberin forms an extracellular barrier that affects water relations and mineral nutrition in Arabidopsis.

Though central to our understanding of how roots perform their vital function of scavenging water and solutes from the soil, no direct genetic evidence currently exists to support the foundational model that suberin acts to form a chemical barrier limiting the extracellular, or apoplastic, transport of water and solutes in plant roots. Using the newly characterized enhanced suberin1 (esb1) mutant, we established a connection in Arabidopsis thaliana between suberin in the root and both water movement through the plant and solute accumulation in the shoot. Esb1 mutants, characterized by increased root suberin, were found to have reduced day time transpiration rates and increased water-use efficiency during their vegetative growth period.