Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita

  1. Karl R Wotton  Is a corresponding author
  2. Eva Jiménez-Guri
  3. Anton Crombach
  4. Hilde Janssens
  5. Anna Alcaine-Colet
  6. Steffen Lemke
  7. Urs Schmidt-Ott
  8. Johannes Jaeger  Is a corresponding author
  1. Centre for Genomic Regulation, Spain
  2. Universitat Pompeu Fabra, Spain
  3. Universitat de Barcelona, Spain
  4. University of Chicago, United States
12 figures, 2 tables and 4 additional files

Figures

The evolution of the dipteran gap gene network.

A simplified phylogenetic tree of the order Diptera indicates the relative position of M. abdita with regard to other species of flies, midges, and mosquitoes in which gap genes have been studied in …

https://doi.org/10.7554/eLife.04785.003
Data acquisition and processing of wild-type and RNAi knock-down embryos.

As an example, we show kni mRNA expression in wild-type and hb RNAi-treated embryos. (A) Data acquisition: wild-type or RNAi-treated embryos were stained by single or double in situ hybridisation …

https://doi.org/10.7554/eLife.04785.004
Trunk gap gene expression in M. abdita.

(A) Wild-type mRNA expression patterns for trunk gap genes hunchback (hb), Krüppel (Kr), giant (gt), and knirps (kni) are shown in M. abdita embryos at selected time points (cleavage cycle 12, C12; …

https://doi.org/10.7554/eLife.04785.006
Gap domain boundary positioning is dependent on Bicoid levels in M. abdita.

hb expression (purple) is shown in wild-type (A) and in bcd RNAi-treated embryos (BD). The position of the posterior boundary of the anterior hb domain moves anteriorly as Bcd levels are reduced by …

https://doi.org/10.7554/eLife.04785.008
Absence of maternal cad delays posterior patterning in D. melanogaster.

The expression of gt (AC) and hb (DF) is shown in wild-type embryos (A, D) and in cad germ-line clones (cad GLC) lacking only maternal cad (B, E; purple stain: gt or kni, red stain: even-skipped). …

https://doi.org/10.7554/eLife.04785.009
RNAi knock-down of complementary gap genes (alternating cushions).

Columns show the expression of hb (AC; yellow), kni (DF; red), gt (GI; blue), and Kr (JL; green) in wild-type embryos (top row; A, D, G, J), in RNAi-treated embryos as indicated (middle row; B, E

https://doi.org/10.7554/eLife.04785.011
RNAi knock-down of overlapping gap genes (shift mechanisms and others).

Columns show the expression of gt (AC, M, N; blue), kni (DF, O, P; red), Kr (GI, Q, R; green), and hb (JL, S, T; yellow) in wild-type embryos (top row; A, D, G, J), in RNAi-treated embryos as …

https://doi.org/10.7554/eLife.04785.012
Knock-down of the terminal gap genes.

Columns show the expression of hb (A1A7; yellow), Kr (B1B7; green), kni (C1C7; red), gt (D1D7; blue) in wild-type embryos (top row; A1, B1, C1, D1), in RNAi-treated embryos as indicated (rows 2, …

https://doi.org/10.7554/eLife.04785.013
Comparison of posterior boundary positions and gene network structure between M. abdita and D. melanogaster.

(A) This graph shows the position of the posterior boundaries of anterior gt (blue) and hb (yellow), central Kr (green), abdominal kni (red), and posterior gt (blue) and hb (yellow). Initial …

https://doi.org/10.7554/eLife.04785.014
Expression data—maternal co-ordinate and terminal gap genes.

Time series of mRNA expression patterns of the maternal genes bcd and cad, as well as the terminal gap genes hkb and tll are shown for D. melanogaster (left) and M. abdita (right). Expression …

https://doi.org/10.7554/eLife.04785.015
Expression data—trunk gap genes.

Time series of mRNA expression patterns of trunk gap genes hb, gt, Kr, and kni are shown for D. melanogaster (left) and M. abdita (right). Expression patterns are visualised by colorimetric …

https://doi.org/10.7554/eLife.04785.016
Cuticle phenotypes resulting from RNAi knock-down of gt, kni, and Kr in M. abdita.

(A) A wild-type cuticle is shown for comparison to severe phenotypes in gt (B), kni (C), and Kr (D) RNAi-treated embryos. We tentatively assign segment identity to persisting abdominal segments …

https://doi.org/10.7554/eLife.04785.017

Tables

Table 1

mRNA expression datasets for M. abdita. and D. melanogaster

https://doi.org/10.7554/eLife.04785.005
Domainant hbant gtKrknipost gtpost hb
BoundaryPAPAPAPAPAP
C114----------
-----------
C12222287444-2-
4--11-11---
C13811117714141125-
318896161411-1-
T1865981010737-
151414107151311105-
T2777771919748-
138106519168981
T3191413881212151018-
1611159517151417116
T441113109141413134-
711121041817913107
T5588871111984-
121617161118171414108
T6410107788101043
914141715151514121114
T72771313886622
58811115586109
T889866667588
8121266667698
  1. This table shows the number of embryos used to calculate median positions for each expression boundary at each point in time (M. abdita: white rows; D. melanogaster: grey rows). Ant: anterior, Post: posterior domain. A indicates anterior, P posterior boundary of a domain. Time classification as defined in Wotton et al. (2014) for M. abdita and in Surkova et al. (2008b) for D. melanogaster: C11–13 correspond to cleavage cycles 11 to 13; T1–8 represent time classes subdividing C14A. Our M. abdita expression dataset consists of a total of 367 embryos (91 stained for hb, 83 for Kr, 87 for gt, and 106 for kni). An additional 115 embryos make up the dataset for maternal co-ordinate and terminal gap genes shown in Supplementary file 1. The D. melanogaster gap gene dataset has been published previously (Crombach et al., 2012a). It is included here for comparison.

Table 2

Overview of the RNAi dataset for M. abdita

https://doi.org/10.7554/eLife.04785.010
hb
RNAi
gt
RNAi
Kr
RNAi
kni
RNAi
tll
RNAi
hkb
RNAi
tll:hkb
RNAi
hbn/a17/28 (60%)21/41 (51%)35/52 (67%)12/29 (41%)21/22 (95%)15/15 (100%)
gt28/35 (80%)n/a13/20 (65%)24/30 (80%)24/30 (80%)10/10 (100%)35/36 (97%)
Kr24/53 (46%)7/17 (41%)n/a26/40 (65%)7/18 (38%)10/10 (100%)12/21 (57%)
kni9/14 (64%)11/25 (44%)3/21 (14%)n/a6/44 (14%)4/10 (40%)16/16 (100%)
Total10270821221215288
  1. A total of 637 RNAi-treated embryos were used for the analysis. This table shows the number of embryos that were stained for each of the trunk gap genes (rows), in each RNAi-treated background (columns), and the number of embryos that showed a knock-down phenotype (see also percentages). The total number of embryos used for each knock-down experiment is shown in the bottom row. A more detailed breakdown of embryos per cleavage cycle and time class, including detailed plots of boundary positions, is provided in Supplementary file 4.

Additional files

Supplementary file 1

Maternal co-ordinate and terminal gap gene mRNA expression dataset for M. abdita. This file contains a table with numbers of embryos in our dataset for maternal co-ordinate and terminal gap gene mRNA expression in M. abdita.

https://doi.org/10.7554/eLife.04785.018
Supplementary file 2

Boundary positions/shifts and domain widths/overlaps contain tables with numerical comparisons of expression data between M. abdita and D. melanogaster. (A) Comparison of expression data between M. abdita and D. melanogaster: gap domain boundary positions. (B) Comparison of expression data between M. abdita and D. melanogaster: gap domain widths. (C) Comparison of expression data between M. abdita and D. melanogaster: gap domain boundary shifts. (D) Comparison of expression data between M. abdita and D. melanogaster: gap domain overlaps.

https://doi.org/10.7554/eLife.04785.019
Supplementary file 3

Megaselia segmentation gene expression.

https://doi.org/10.7554/eLife.04785.020
Supplementary file 4

RNAi dataset.

https://doi.org/10.7554/eLife.04785.021

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