Table 1 Number of HGTC in significantly up- and downregulated gene subsets in response to biotic (pathogen exposure) and abiotic (desiccation) stress

From: Bdelloid rotifers deploy horizontally acquired biosynthetic genes against a fungal pathogen

Testa

Species

Contrast

DE subsetb

HGTCc in:

Odds ratio (95% CI)

P-valued

DE0

DE1

Pathogen

A. ricciae

T7

Up

6041 / 57461 (11%)

196 / 709 (28%)

3.3 (2.7–3.8)

2.1e–36

   

Down

68 / 253 (27%)

3.1 (2.3–4.2)

3.1e–13

  

T24

Up

5738 / 56035 (10%)

372 / 1590 (23%)

2.7 (2.4–3.0)

5.8e–50

   

Down

195 / 798 (24%)

2.8 (2.4–3.3)

4.9e–30

 

A. vaga

T7

Up

7918 / 65732 (12%)

145 / 452 (32%)

3.4 (2.8–4.2)

6.1e–29

   

Down

26 / 89 (29%)

3.0 (1.8–4.8)

1.2e–5

  

T24

Up

7629 / 64506 (12%)

285 / 1093 (26%)

2.6 (2.3–3.0)

3.2e–37

   

Down

175 / 674 (26%)

2.6 (2.1–3.0)

1.8e–23

Desiccation

A. vaga

Entering

Up

7975 / 65354 (12%)

77 / 558 (14%)

1.2 (0.9–1.5)

0.24

   

Down

37 / 362 (10%)

0.8 (0.6–1.2)

0.29

  

Recovering

Up

7553 / 63144 (12%)

266 / 1807 (14%)

1.3 (1.1–1.5)

5.6e–4

   

Down

270 / 1322 (20%)

1.9 (1.6–2.2)

5.9e–18

  1. aTest: ‘Pathogen’, treatment groups represent animals exposed to live pathogen spores, versus controls exposed to inactivated spores, at 7 h (T7) and 24 h (T24) post-inoculation; ‘Desiccation’, treatment groups represent animals either taken from wet dishes (hydrated controls), or equivalent dishes left without lids for 2-4 days until only a thin water film remained (entering into desiccation), or animals left for a further 4 days to enter full desiccation for 7 days, then harvested 1 h after rehydration51.
  2. bDE subset: ‘Up’, genes that are significantly upregulated in the treatment group; ‘Down’, genes that are significantly downregulated in the treatment group. Significance is defined as genes with absolute fold change in expression > 4 and FDR < 1e–3.
  3. cThe number of HGTC in different subsets as follows: ‘DE0’, genes with no significant change in expression (either up or down); ‘DE1’, genes significantly up- or downregulated, depending on the defined subset. Fraction denominators show the total number of genes in each subset.
  4. dP-value for Fisher’s exact test (two sided) for an association between classifications; null hypothesis: true odds ratio is equal to 1.
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