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Table 1 The phylogenetic distribution of HGT genes. The number and percentage of foreign genes unique to species, sister species pairs, the genus Rotaria and shared between Rotaria and Adineta, based on two ortholog assignment methods: 1) reciprocal BLAST and 2) Markov clusters. The unbracketed numbers show presence/absence in transcriptomes. The bracketed numbers are adjusted for false negative rates estimated from BLAST matches to the R. magnacalcarata genome (see Methods)

From: Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats

Ortholog method

Species

Unique to species

Sister species

Rotaria

Rotaria + Adineta

Total

  

Number

Percentage (%)

Number

Percentage (%)

Number

Percentage (%)

Number

Percentage (%)

 

Method 1: Reciprocal BLAST

mag

76 (53)

13.1 (6.7)

27 (37)

4.6 (4.7)

154 (351)

26.5 (43.9)

324 (356)

55.8 (44.7)

581 (798)

soc

127 (94)

22.1 (12.3)

27 (37)

4.7 (4.9)

128 (309)

22.3 (40.5)

293 (322)

51 (42.3)

575 (763)

sor

350 (263)

29.6 (18.8)

222 (308)

18.8 (22)

129 (294)

10.9 (21)

483 (531)

40.8 (38.1)

1,184 (1,396)

tar

497 (364)

37 (23.3)

222 (308)

16.5 (19.7)

155 (374)

11.5 (23.9)

469 (516)

34.9 (33)

1,343 (1,561)

Method 2: Markov clusters

mag

67 (46)

6.1 (3.5)

53 (53)

4.8 (4)

305 (489)

27.9 (37)

668 (735)

61.1 (55.6)

1,093 (1,322)

soc

126 (90)

11.8 (7.2)

53 (53)

5 (4.2)

271 (422)

25.4 (34)

617 (679)

57.8 (54.6)

1,067 (1,244)

sor

280 (201)

17.3 (11.3)

248 (247)

15.3 (13.9)

263 (421)

16.3 (23.7)

827 (910)

51.1 (51.1)

1,618 (1,779)

tar

303 (211)

17.9 (11.3)

248 (247)

14.6 (13.3)

321 (500)

18.9 (26.9)

823 (905)

48.6 (48.6)

1,695 (1,863)