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1. Genome Sequence and Assembly of 18 Fusarium Isolates from Florida Citrus under High Huanglongbing Disease Pressure and California Citrus under Low Huanglongbing Disease Pressure

   https://doi.org/10.1128/mra.00101-23  

   Kurbessoian, Tania ; Heimlich-Villalta, Gretchen ; Ginnan, Nichole ; Vieira, Flavia Campos ; Rolshausen, Philippe E. ; Roper, M. Caroline ; Stajich, Jason E. ( May 2023 , Microbiology Resource Announcements)

   Rokas, Antonis (Ed.)

   ABSTRACT The genomes of eighteen Fusarium isolates cultured from diseased and healthy citrus trees were sequenced, assembled, and annotated. Isolate species identification was confirmed using single marker (TEF1-alpha) phylogenetic assessment. Studies of the traits and genotypes of plant-associated isolates are important to understanding the fungal contribution to phytobiomes of citrus. 

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2. Citrus miraculin‐like protein hijacks a viral movement‐related p33 protein and induces cellular oxidative stress in defence against Citrus tristeza virus

   https://doi.org/10.1111/pbi.13523  

   Sun, Yong‐Duo ; Zhang, Lei ; Folimonova, Svetlana Y. ( December 2020 , Plant Biotechnology Journal)

   To defend against pathogens, plants have developed a complex immune system, which recognizes the pathogen effectors and mounts defence responses. In this study, the p33 protein ofCitrus tristeza virus(CTV), a viral membrane‐associated effector, was used as a molecular bait to explore virus interactions with host immunity. We discovered thatCitrus macrophyllamiraculin‐like protein 2 (CmMLP2), a member of the soybean Kunitz‐type trypsin inhibitor family, targets the viral p33 protein. The expression ofCmMLP2was up‐regulated by p33 in the citrus phloem‐associated cells. Knock‐down of theMLP2expression in citrus plants resulted in a higher virus accumulation, while the overexpression ofCmMLP2reduced the infectivity of CTV in the plant hosts. Further investigation revealed that, on the one hand, binding of CmMLP2 interrupts the cellular distribution of p33 whose proper function is necessary for the effective virus movement throughout the host. On the other hand, the ability of CmMLP2 to reorganize the endomembrane system, amalgamating the endoplasmic reticulum and the Golgi apparatus, induces cellular stress and accumulation of the reactive oxygen species, which inhibits the replication of CTV. Altogether, our data suggest that CmMLP2 employs a two‐way strategy in defence against CTV infection.

    

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3. A chromosome-level phased genome enabling allele-level studies in sweet orange: a case study on citrus Huanglongbing tolerance

   https://doi.org/10.1093/hr/uhac247  

   Wu, Bo ; Yu, Qibin ; Deng, Zhanao ; Duan, Yongping ; Luo, Feng ; Gmitter Jr, Frederick ( January 2023 , Horticulture Research)

   Abstract Sweet orange originated from the introgressive hybridizations of pummelo and mandarin resulting in a highly heterozygous genome. How alleles from the two species cooperate in shaping sweet orange phenotypes under distinct circumstances is unknown. Here, we assembled a chromosome-level phased diploid Valencia sweet orange (DVS) genome with over 99.999% base accuracy and 99.2% gene annotation BUSCO completeness. DVS enables allele-level studies for sweet orange and other hybrids between pummelo and mandarin. We first configured an allele-aware transcriptomic profiling pipeline and applied it to 740 sweet orange transcriptomes. On average, 32.5% of genes have a significantly biased allelic expression in the transcriptomes. Different cultivars, transgenic lineages, tissues, development stages, and disease status all impacted allelic expressions and resulted in diversified allelic expression patterns in sweet orange, but particularly citrus Huanglongbing (HLB) shifted the allelic expression of hundreds of genes in leaves and calyx abscission zones. In addition, we detected allelic structural mutations in an HLB-tolerant mutant (T19) and a more sensitive mutant (T78) through long-read sequencing. The irradiation-induced structural mutations mostly involved double-strand breaks, while most spontaneous structural mutations were transposon insertions. In the mutants, most genes with significant allelic expression ratio alterations (≥1.5-fold) were directly affected by those structural mutations. In T19, alleles located at a translocated segment terminal were upregulated, including CsDnaJ, CsHSP17.4B, and CsCEBPZ. Their upregulation is inferred to keep phloem protein homeostasis under the stress from HLB and enable subsequent stress responses observed in T19. DVS will advance allelic level studies in citrus. 

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4. Impact of Drying on Meso- and Nanoscale Structures of Citrus Fiber: A Study by SFG, ATR-IR, XRD, and DLS

   https://doi.org/10.1021/acs.iecr.9b06194  

   Makarem, Mohamadamin ; Kim, Hyojung ; Emami, Parinaz ; Melendez, Jesus ; Steinbach, Adam ; Lipkie, Tristan ; Deleris, Isabelle ; Desmet, Christina ; Wallecan, Jöel ; Kim, Seong H. ( January 2020 , Industrial & Engineering Chemistry Research)
5. Complete Nucleotide Sequence, Genome Organization, and Comparative Genomic Analyses of Citrus Yellow-Vein Associated Virus (CYVaV)

   https://doi.org/10.3389/fmicb.2021.683130  

   Kwon, Sun-Jung ; Bodaghi, Sohrab ; Dang, Tyler ; Gadhave, Kiran R. ; Ho, Thien ; Osman, Fatima ; Al Rwahnih, Maher ; Tzanetakis, Ioannis E. ; Simon, Anne E. ; Vidalakis, Georgios ( June 2021 , Frontiers in Microbiology)

   null (Ed.)

   Citrus yellow-vein disease (CYVD) was first reported in California in 1957. We now report that CYVD is associated with a virus-like agent, provisionally named citrus yellow-vein associated virus (CYVaV). The CYVaV RNA genome has 2,692 nucleotides and codes for two discernable open reading frames (ORFs). ORF1 encodes a protein of 190 amino acid (aa) whereas ORF2 is presumably generated by a −1 ribosomal frameshifting event just upstream of the ORF1 termination signal. The frameshift product (717 aa) encodes the RNA-dependent RNA polymerase (RdRp). Phylogenetic analyses suggest that CYVaV is closely related to unclassified virus-like RNAs in the family Tombusviridae . Bio-indexing and RNA-seq experiments indicate that CYVaV can induce yellow vein symptoms independently of known citrus viruses or viroids. 

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