Chrysanthemum morifolium is an important floral crop that is cultivated worldwide. However, due to a lack of genomic resources, very little information is available concerning the molecular ...mechanisms of flower development in chrysanthemum.
The transcriptomes of chrysanthemum vegetative buds, floral buds and buds were sequenced using Illumina paired-end sequencing technology. A total of 15.4 Gb of reads were assembled into 91,367 unigenes with an average length of 739 bp. A total of 43,137 unigenes showed similarity to known proteins in the Swissprot or NCBI non-redundant protein databases. Additionally, 25,424, 24,321 and 13,704 unigenes were assigned to 56 gene ontology (GO) categories, 25 EuKaryotic Orthologous Groups (KOG) categories, and 285 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. A total of 1,876 differentially expressed genes (DEGs) (1,516 up-regulated, 360 down-regulated) were identified between vegetative buds and floral buds, and 3,300 DEGs (1,277 up-regulated, 1,706 down-regulated) were identified between floral buds and buds. Many genes encoding important transcription factors (e.g., AP2, MYB, MYC, WRKY, NAC and CRT) as well as proteins involved in carbohydrate metabolism, protein kinase activity, plant hormone signal transduction, and the defense responses, among others, were considerably up-regulated in floral buds. Genes involved in the photoperiod pathway and flower organ determination were also identified. These genes represent important candidate genes for molecular cloning and functional analysis to study flowering regulation in chrysanthemum.
This comparative transcriptome analysis revealed significant differences in gene expression and signaling pathway components between the vegetative buds, floral buds and buds of Chrysanthemum morifolium. A wide range of genes was implicated in regulating the phase transition from vegetative to reproductive growth. These results should aid researchers in the study of flower-time regulation, breeding and molecular biology in chrysanthemum.
Huanglongbing (HLB) is an extremely destructive and lethal disease of citrus worldwide, presumably caused by phloem-limited bacteria,
Liberibacter asiaticus (
Las). The widespread invasiveness of the ...HLB pathogen and lack of natural HLB-resistant citrus cultivars have underscored the need for identifying tolerant citrus genotypes to support the current citrus industry's survival and potentially to lead to future natural HLB resistance. In this study, transverse sections of leaf lamina and midribs were examined with light and epifluorescence microscopy to determine anatomical characteristics that underlie HLB-tolerant mechanisms operating among "Bearss" lemon, "LB8-9" Sugar Belle
mandarin, and its sibling trees compared with HLB-sensitive "Valencia" sweet orange. The common anatomical aberrations observed in all
Las-infected varieties are as follows: phloem necrosis, hypertrophic phloem parenchyma cells, phloem plugging with abundant callose depositions, phloem collapse with cell wall distortion and thickening, excessive starch accumulation, and sometimes even cambium degeneration. Anatomical distribution of starch accumulation even extended to tracheid elements. Although there were physical, morphological, and pathological similarities in the examined foliage, internal structural preservation in "Bearss" lemon and "LB8-9" Sugar Belle
mandarin was superior compared with HLB-sensitive "Valencia" sweet orange and siblings of "LB8-9" Sugar Belle
mandarin. Intriguingly, there was substantial phloem regeneration in the tolerant types that may compensate for the dysfunctional phloem, in comparison with the sensitive selections. The lower levels of phloem disruption, together with greater phloem regeneration, are two key elements that contribute to HLB tolerance in diverse citrus cultivars.
The family of aquaporins (AQPs), or major intrinsic proteins (MIPs), includes integral membrane proteins that function as transmembrane channels for water and other small molecules of physiological ...significance. MIPs are classified into five subfamilies in higher plants, including plasma membrane (PIPs), tonoplast (TIPs), NOD26-like (NIPs), small basic (SIPs) and unclassified X (XIPs) intrinsic proteins. This study reports a genome-wide survey of MIP encoding genes in sweet orange (Citrus sinensis L. Osb.), the most widely cultivated Citrus spp. A total of 34 different genes encoding C. sinensis MIPs (CsMIPs) were identified and assigned into five subfamilies (CsPIPs, CsTIPs, CsNIPs, CsSIPs and CsXIPs) based on sequence analysis and also on their phylogenetic relationships with clearly classified MIPs of Arabidopsis thaliana. Analysis of key amino acid residues allowed the assessment of the substrate specificity of each CsMIP. Gene structure analysis revealed that the CsMIPs possess an exon-intron organization that is highly conserved within each subfamily. CsMIP loci were precisely mapped on every sweet orange chromosome, indicating a wide distribution of the gene family in the sweet orange genome. Investigation of their expression patterns in different tissues and upon drought and salt stress treatments, as well as with 'Candidatus Liberibacter asiaticus' infection, revealed a tissue-specific and coordinated regulation of the different CsMIP isoforms, consistent with the organization of the stress-responsive cis-acting regulatory elements observed in their promoter regions. A special role in regulating the flow of water and nutrients is proposed for CsTIPs and CsXIPs during drought stress, and for most CsMIPs during salt stress and the development of HLB disease. These results provide a valuable reference for further exploration of the CsMIPs functions and applications to the genetic improvement of both abiotic and biotic stress tolerance in citrus.
Galactinol synthase (GolS) catalyzes the first and rate-limiting step in the synthesis of raffinose family of oligosaccharides (RFOs), which serve as storage and transport sugars, signal transducers, ...compatible solutes and antioxidants in higher plants. The present work aimed to assess the potential functions of citrus GolS in mechanisms of stress response and tolerance. By homology searches, eight
GolS
genes were found in the genomes of
Citrus sinensis
and
C
.
clementina
. Phylogenetic analysis showed that there is a
GolS
ortholog in
C
.
clementina
for each
C
.
sinensis GolS
, which have evolved differently from those of
Arabidopsis thaliana
. Transcriptional analysis indicated that most
C
.
sinensis GolS
(
CsGolS
) genes show a low-level tissue-specific and stress-inducible expression in response to drought and salt stress treatments, as well as to ‘
Candidatus
Liberibacter asiaticus’ infection.
CsGolS6
overexpression resulted in improved tobacco tolerance to drought and salt stresses, contributing to an increased mesophyll cell expansion, photosynthesis and plant growth. Primary metabolite profiling revealed no significant changes in endogenous galactinol, but different extents of reduction of raffinose in the transgenic plants. On the other hand, a significant increase in the levels of metabolites with antioxidant properties, such as ascorbate, dehydroascorbate, alfa-tocopherol and spermidine, was observed in the transgenic plants. These results bring evidence that
CsGolS6
is a potential candidate for improving stress tolerance in citrus and other plants.
Late embryogenesis abundant (LEA) proteins play important roles in plant desiccation tolerance. In this study, 30
LEA
genes were identified from Chinese plum (
Prunus mume
) through genome-wide ...analysis. The
PmLEA
genes are distributed on all Chinese plum chromosomes except chromosome 3. Twelve (40 %) and five
PmLEA
genes are arranged in tandem and segmental duplications, respectively. The
PmLEA
genes could be divided into eight groups (LEA_1, LEA_2, LEA_3, LEA_4, LEA_5, PvLEA18, dehydrin and seed maturation protein). Ten gene conversion events were observed and most of them (70 %) were identified in dehydrin group. Most
PmLEA
genes were highly expressed in flower (22/30) and up-regulated by ABA treatment (19/30).
RNA splicing is an important biological process associated with cancer initiation and progression. However, the contribution of alternative splicing to pancreatic cancer (PDAC) development is not ...well understood. Here, we identify an enrichment of RNA binding proteins (RBPs) involved in splicing regulation linked to PDAC progression from a forward genetic screen using Sleeping Beauty insertional mutagenesis in a mouse model of pancreatic cancer. We demonstrate downregulation of RBFOX2, an RBP of the FOX family, promotes pancreatic cancer progression and liver metastasis. Specifically, we show RBFOX2 regulates exon splicing events in transcripts encoding proteins involved in cytoskeletal remodeling programs. These exons are differentially spliced in PDAC patients, with enhanced exon skipping in the classical subtype for several RBFOX2 targets. RBFOX2 mediated splicing of ABI1, encoding the Abelson-interactor 1 adapter protein, controls the abundance and localization of ABI1 protein isoforms in pancreatic cancer cells and promotes the relocalization of ABI1 from the cytoplasm to the periphery of migrating cells. Using splice-switching antisense oligonucleotides (AONs) we demonstrate the ABI1 ∆Ex9 isoform enhances cell migration. Together, our data identify a role for RBFOX2 in promoting PDAC progression through alternative splicing regulation.
Huanglongbing (HLB), or citrus greening, is the most devastating disease in citrus worldwide. Commercial citrus varieties including sweet orange (
) are highly susceptible to HLB, and trifoliate ...orange (
, a close
relative) is widely considered resistant or highly tolerant to HLB. In this study, an intergeneric F
population of sweet orange and trifoliate orange was genotyped by Genotyping-by-Sequencing, and high-density SNP-based genetic maps were constructed separately for trifoliate orange and sweet orange. The two genetic maps exhibited high synteny and high coverage of the citrus genome. Progenies of the F
population and their parents were planted in a replicated field trial, exposed to intense HLB pressure for 3 years, and then evaluated for susceptibility to HLB over 2 years. The F
population exhibited a wide range in severity of HLB foliar symptom and canopy damage. Genome-wide QTL analysis based on the phenotypic data of foliar symptom and canopy damage in 2 years identified three clusters of repeatable QTLs in trifoliate orange linkage groups LG-t6, LG-t8 and LG-t9. Co-localization of QTLs for two traits was observed within all three regions. Additionally, one cluster of QTLs in sweet orange (linkage group LG-s7) was also detected. The majority of the identified QTLs each explained 18-30% of the phenotypic variation, indicating their major role in determining HLB responses. These results show, for the first time, a quantitative genetic nature yet the presence of major loci for the HLB tolerance in trifoliate orange. The results suggest that sweet orange also contains useful genetic factor(s) for improving HLB tolerance in commercial citrus varieties. Findings from this study should be very valuable and timely to researchers worldwide as they are hastily searching for genetic solutions to the devastating HLB crisis through breeding, genetic engineering, or genome editing.
Despite significant advances in the development and refinement of immunotherapies administered to combat cancer over the past decades, a number of barriers continue to limit their efficacy. One ...significant clinical barrier is the inability to mount initial immune responses towards the tumor. As dendritic cells are central initiators of immune responses in the body, the elucidation of mechanisms that can be therapeutically leveraged to enhance their functions to drive anti-tumor immune responses is urgently needed. Here, we report that the dietary sugar L-fucose can be used to enhance the immunostimulatory activity of dendritic cells (DCs). L-fucose polarizes immature myeloid cells towards specific DC subsets, specifically cDC1 and moDC subsets.
, L-fucose treatment enhances antigen uptake and processing of DCs. Furthermore, our data suggests that L-fucose-treated DCs increase stimulation of T cell populations. Consistent with our functional assays, single-cell RNA sequencing of intratumoral DCs from melanoma- and breast tumor-bearing mice confirmed transcriptional regulation and antigen processing as pathways that are significantly altered by dietary L-fucose. Together, this study provides the first evidence of the ability of L-fucose to bolster DC functionality and provides rational to further investigate how L-fucose can be used to leverage DC function in order to enhance current immunotherapy.
BackgroundThe immunogenic nature of melanoma has been exploited for the development of adoptive transfer of ex-vivo expanded tumor infiltrating lymphocytes (TIL). This adoptive cell transfer therapy ...has overall response rates of around 50%. Multiple factors may determine the quality of the TIL product including components of the tumor microenvironment. B-cells are frequently found in melanoma metastasis, and display signs of antigen experience. Recently, B-cell tumor infiltration has been associated with improved clinical responses to immune checkpoint inhibitors,1 2 but their role in TIL therapy remains unexplored. Considering the potential role of B cells, we aim to develop strategies to enhance the quality of TIL products through B-cell stimulation during ex-vivo TIL expansion.MethodsWe stimulated melanoma infiltrating B-cells using human recombinant CD40L on the first day of ex-vivo TIL expansion. Thirteen samples were expanded from melanoma tumor single cell suspensions, in high dose IL-2 alone (standard protocol), or in high dose IL-2 plus CD40L. After up to four weeks of expansion, the TIL phenotype was analyzed by flow cytometry.ResultsThe expansion success rate from the frozen tumor digests was 69% (95% CI: 38.6–90.9%) in the CD40L treatment condition compared to 23% with the standard protocol. Also, TILs cultured in the presence of CD40L expanded to higher numbers than with the standard protocol (P = 0.02). Interestingly, most of the samples expanded with CD40L had a significant increase in the percentage of CD4+ T cells (P = 0.03), but not to the detriment of the absolute number of CD8+ T cells. Treatment with CD40L increased the percentage of effector memory-like T cells (P = 0.03) and of CD39- CD69- T cells (P < 0.05), which were recently associated with response to TIL therapy.3 ConclusionsThis preliminary work demonstrates that the stimulation with CD40L at the initiation of TIL culture leads to enhanced TIL expansion and an increase in CD4+ T cells with an effector memory-like and stem-like phenotype. Our group and others have previously described cases of patients who had tumor regression after receiving TIL therapy that were predominantly CD4+ T cells, suggesting that expansion of the CD4+ TIL repertoire may enhance TIL therapy.4 AcknowledgementsThis work has been supported in part by the Flow Cytometry, Genomics and Biostatistics and Bioinformatics Core Facilities at Moffitt Cancer Center, an NCI designated Comprehensive Cancer Center (P30-CA076292). We acknowledge Moffitt’s Melanoma Center of Excellence for the financial support.ReferencesCabrita R, Lauss M, Sanna A. Tertiary lymphoid structures improve immunotherapy and survival in melanoma. Nature 2020;577:561–565.Petitprez F, de Reynies A, Keung EZ. B cells are associated with survival and immunotherapy response in sarcoma. Nature 2020;577:556–560.Krishna S, Lowery FJ, Copeland AR. Stem-like CD8 T cells mediate response of adoptive cell immunotherapy against human cancer. Science 2020;370:1328–1334.Friedman KM, Prieto PA, Devillier LE. Tumor-specific CD4+ melanoma tumor-infiltrating lymphocytes. J Immunother 2012;35:400–408.Ethics ApprovalThe study was approved by Advarra IRB, approval number MCC20559.
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