(A) Schematic of the experiment (B) The proportion of infected larvae that gave rise to adult flies with visible capsules. An outbred population of D. melanogaster (source, blue square) was used to …
Encapsulation rate during selection for parasitoid resistance.
(A) Summary of the comparisons shown in the other panels. (B) The change in gene expression following infection in populations maintained without parasitoid infection (x axis) compared to the …
Log2 fold change in gene expression following selection and/or infection with parasitoid wasp L.boulardi.
atilla and PPO3 expression normalized by the housekeeping gene RpL32 in populations evolved under no parasitism (blue) or high parasitism (orange). Hemocyte samples for RNA extraction were collected …
Gene expression in circulating hemocytes measured by qPCR.
Two-dimensional UMAP projections and cell state classification. (A) All 19,344 cells combined. PLASM: plasmatocytes; MET: metabolic plasmatocyte cluster; AMP: antimicrobial peptide plasmatocyte …
(A) Relative level of expression of described plasmatocyte and cell cycle genes and (B) Relative level of expression most significant marker genes for the plasmatocyte and crystal cell clusters. The …
A reference-based label transfer was used to predict cell cluster identity in the query data set. The scale bar indicates the proportion of cells in query clusters (y axis) that are predicted to …
HP: high parasitism, NP: No parasitism, I: Infection and NI: no infection. Numbers following HP or NP correspond to replicate.
(A) Clustering 8,596 cells from replicate one, (B) clustering 10,784 cells from replicate three and (C) clustering 6,296 cells where 787 cells were randomly subsampled without replacement in each of …
Only cells expressing >250 features and <2500 features and cells that were either He+ or Srp+ were kept. Cells expressing high levels of sperm-cell, muscle, or fat body marker genes were identified …
(A) Distribution of gene expression levels of described lamellocyte marker genes, for clusters identified from round three clustering. (B) Relative level of expression of described plasmatocyte and …
(A) Trajectory of lamellocyte differentiation. Plasmatocyte progenitors and lamellocytes were subclustered, the trajectories inferred from multi-dimensional principle components analysis, and the …
Changes in cell state following infection and adaptation to high rates of parasitism.
(A) Proportions of cells in G1, G2M, and S phase in the plasmatocyte progenitor and lamellocyte clusters. (B) Trajectory of lamellocyte differentiation inferred following cell cycle correction and …
(A) The proportion hemocytes that were morphologically identified as lamellocytes and (B) the concentration of total circulating hemocytes in no infection conditions (light colours) and 48 hr post …
Changes in circulating and lymph gland hemocytes following infection and adaptation to high parasitism rates.
Proportion of lamellocytes (A) and concentration of total circulating hemocytes (B) in population evolved with no parasitism (blue bars) and with high parasitism (orange bars). Samples were …
Hemocytes were stained for nuclei (A, hoechst 33342), Actin (A’, Phalloidin- Alexa594) and atilla (A’’, L1 antibody + Alexa488). Composite images were created for phallodin and hoechst staining to …
(a) Anterior lobe of a lymph gland from a larva from No Parasitism selection regime. Immature lamellocytes are stained with Myspheroid (Mys, green, with arrow). Mature lamellocytes are double …
Total number of hemocytes (A), lamellocytes (B) and lamellocyte proportions (C) in larvae 12-, 24-, 36-, and 48-hr post infection (dark colours) and corresponding controls with no infection (light …
Hemocyte concentrations during development of 3rd instar larvae.
Points represent the mean of four biological replicas for each triplicate line from populations evolved with no parasitism (blue) and high parasitism (orange) selection regimes. Bar heights …
Hemocyte concentrations (circulating and circulating + sessile).
Number of sessile crystal cells in dorsal side of the A7 abdominal segment of larvae in male and female larvae. Dots represent the average number of crystal cells calculated from 10 larvae of each …
Sessile crystal cell numbers.
Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
---|---|---|---|---|
Software, algorithm | GitHub | https://github.com/ | RRID:SCR_002630 | |
Software, algorithm | LSD | Schwalb et al., 2020 | https://cran.r-project.org/web/packages/ LSD/index.html | |
Software, algorithm | MAST | Finak et al., 2015; https://doi.org/10.1186/s13059-015-0844-5 | ||
Software, algorithm | tidymodels | Kuhn and Wickham, 2020; https://www.tidymodels.org/. | https://www.tidymodels.org/ | |
Software, algorithm | ranger | doi:10.18637/jss.v077.i01 | RRID:SCR_017344 | https://cran.r-project.org/web/packages/ranger/index.html Version 0.12.1 |
Software, algorithm | R | http://www.r-project.org/ | RRID:SCR_001905 | Versions 3.6 and 4 |
Software, algorithm | EBI database | doi: 10.1093/nar/gkz268. | RRID:SCR_004727 | |
Software, algorithm | Sequence Read Archive | http://www.ncbi.nlm.nih.gov/sra | RRID:SCR_004891 | |
Software, algorithm | pheatmap | https://www.rdocumentation.org/packages/pheatmap/versions/0.2/topics/pheatmap | RRID:SCR_016418 | |
Software, algorithm | ArrayExpress | http://www.ebi.ac.uk/arrayexpress/ | RRID:SCR_002964 | |
Software, algorithm | Gene Expression Omnibus | https://www.ncbi.nlm.nih.gov/geo/ | RRID:SCR_005012 | |
Software, algorithm | REViGO | doi: 10.1371/journal.pone.0021800. | RRID:SCR_005825 | |
Software, algorithm | gridExtra | Auguie, 2017; https://CRAN.R-project.org/package=gridExtra | https://cran.r-project.org/web/packages/gridExtra/index.html | |
Software, algorithm | cowplot | cran | RRID:SCR_018081 | https://cran.r-project.org/web/packages/cowplot/index.html version 1.0.0 |
Software, algorithm | tidyverse | cran | RRID:SCR_019186 | https://CRAN.R-project.org/package=tidyverse version 1.3.0 |
Software, algorithm | limma | doi: 10.1093/nar/gkv007. | RRID:SCR_010943 | Version 3.44.3 |
Software, algorithm | Slingshot | doi: 10.1186/s12864-018-4772-0. | RRID:SCR_017012 | Version 1.6.1 |
Software, algorithm | KEGG | doi: 10.1093/nar/gkj102. | RRID:SCR_012773 | |
Software, algorithm | Reactome | doi: 10.1093/nar/gkv1351. | RRID:SCR_003485 | |
Software, algorithm | Cell Ranger | https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome | RRID:SCR_017344 | Version 2.1.1 |
Software, algorithm | Seurat | doi:10.1016/j.cell.2019.05.031 | RRID:SCR_007322 | Version 3.1.1 |
Software, algorithm | Flymine | doi:10.1186/gb-2007-8-7-r129 | RRID:SCR_002694 | v51 2020 December |
Strain, strain background (Drosophila melanogaster) | CAMOP3 | This paper | CAMOP3 | Outbred population of D. melanogaster |
Antibody | anti-Atilla (mouse monoclonal) | doi: 10.1556/ABiol.58.2007.Suppl.8 | L1 | 1 in 100 |
Antibody | anti-alphaPS4 (rabbit polyclonal) | doi: 10.1038/nature05650 | 1 in 200 | |
Antibody | anti-Mys (mouse monoclonal) | Developmental Studies Hybridoma Bank | RRID:AB_528310C; Cat#:F.6G11c | 1 in 100 |
Sequence-based reagent | PPO3_qPCR_2_Fw | This paper | qPCR primers | GATGTGGACCGGCCTAACAA |
Sequence-based reagent | PPO3_qPCR_2_Rev | This paper | qPCR primers | GATGCCCTTAGCGTCATCCA |
Sequence-based reagent | atilla_qPCR2_Fw | This paper | qPCR primers | ACCCACCAAATATGCTGAAACA |
Sequence-based reagent | atilla_qPCR2_Rv | This paper | qPCR primers | TTGATGGCCGATGCACTGT |
Sequence-based reagent | RpL32_qPCR_F-d | https://doi.org/10.1371/journal.ppat.1004728 | qPCR primers | TGCTAAGCTGTCGCACAAATGG |
Sequence-based reagent | RpL_qPCR_R-h | https://doi.org/10.1371/journal.ppat.1004728 | qPCR primers | TGCGCTTGTTCGATCCGTAAC |
Other | Phalloidin staining | Invitrogen | RRID:AB_2315633; Cat. #: A12381 | 1 in 2000 |
Other | Mineral oil | Sigma-Aldrich | Cat#: M5904 |
Gene ontology enrichment for 173 genes that had >50% change in transcript levels after infection or selection.
Enriched gene ontology categories and pathways for non-lamellocyte clusters.
10x v2 library sequencing metrics.
Lamellocyte lineage classification with and without cell cycle correction.
List of marker genes for predicting lamellocyte differentiation.
Enriched gene ontology categories and pathways for lamellocytes.
Genes detected in scRNA-seq dataset.
Cluster markers identified from round one of clustering.
Cluster markers identified from round two of clustering.
Hemocyte classification with and without cell cycle correction.
Hemocyte classification using 2000 highly variable genes or all 7716 detected genes.
Cluster markers identified from round one of subclustering.
Marker genes for non-lamellocyte clusters.