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Table 4 Full-breadth-coverage consensus sequences generated from transcriptomes determined using UNESP ‘Rhodnius robustus’ colonies

From: Transcriptome-based molecular systematics: Rhodnius montenegrensis (Triatominae) and its position within the Rhodnius prolixus–Rhodnius robustus cryptic–species complex

Transcriptome

Colony at UNESP

Locus

Query

Depth-coverage

Identity

Divergencea

Group [refs.]

NCBI SRA

Sequence

Species

Mean

Minimum

< 10 readsb (%)

Percent

Distance

SE

UNESP [12, 13]

SRX1996483

Rhodnius robustus ‘CTA 85’

cytb

EF011721.1

R. prolixus

13,238.94

7978

–

99.85

0.00152

0.00145

EF011716.1

R. prolixus

13,235.83

8029

–

99.85

0.00152

0.00144

AF421339.1

R. prolixus

11,680.80

29

–

99.70

0.00308

0.00211

EF011724.1

R. robustus IIc

6.18

2

90.2

99.85

0.00152

0.00144

ITS2d

MK411270

R. prolixus

21.37

2

42.2

100.00

0.00000

0.00000

MK411269

R. prolixus

20.03

2

36.9

100.00

0.00000

0.00000

MK411271

R. prolixus

19.84

1

25.1

100.00

0.00000

0.00000

MK411272

R. prolixus

17.30

2

53.7

100.00

0.00000

0.00000

D2-28S

JQ897670.1e

R. neglectus

2131.15

8

1.0

99.34

0.00702

0.00407

AF435862.1

R. prolixus

2002.57

315

–

100.00

0.00000

0.00000

AF435860.1

R. prolixus

1996.21

313

–

100.00

0.00000

0.00000

AF435861.1

R. robustus I

1978.62

316

–

100.00

0.00000

0.00000

SRX1996484

Rhodnius robustus ‘CTA 85’

cytb

EF011721.1

R. prolixus

15,319.04

9426

–

99.85

0.00152

0.00145

EF011716.1

R. prolixus

15,185.29

9224

–

99.85

0.00152

0.00144

AF421339.1

R. prolixus

13,564.95

29

–

99.70

0.00306

0.00207

JX273156.1

R. neglectus c

8.63

1

53.5

99.40

0.00621

0.00314

D2-28S

JQ897670.1e

R. neglectus

1319.28

6

5.7

99.68

0.00334

0.00257

AF435861.1

R. robustus I

1266.95

169

–

100.00

0.00000

0.00000

AF435862.1

R. prolixus

1259.78

173

–

100.00

0.00000

0.00000

AF435860.1

R. prolixus

1238.28

188

–

100.00

0.00000

0.00000

CNRS [21]

ERX1387159

Rhodnius robustus ‘Peru’

cytb

EF011721.1

R. prolixus

245.46

102

–

100.00

0.00000

0.00000

AF421339.1

R. prolixus

233.66

1

2.7

100.00

0.00000

0.00000

EF011716.1

R. prolixus

219.03

60

–

99.85

0.00152

0.00144

AF421341.1

R. robustus II

43.65

6

10.9

100.00

0.00000

0.00000

ITS2d

MK411271

R. prolixus

78.31

21

–

100.00

0.00000

0.00000

MK411272

R. prolixus

66.01

20

–

100.00

0.00000

0.00000

MK411270

R. prolixus

64.70

18

–

100.00

0.00000

0.00000

MK411269

R. prolixus

60.10

15

–

99.87

0.00139

0.00130

D2-28S

AF435861.1

R. robustus I

896.28

28

–

100.00

0.00000

0.00000

AF435860.1

R. prolixus

891.44

34

–

100.00

0.00000

0.00000

AF435862.1

R. prolixus

879.61

37

–

100.00

0.00000

0.00000

AF435857.1

R. robustus III

735.23

2

2.1

99.84

0.00159

0.00154

JQ897670.1e

R. neglectus

710.08

3

6.9

99.84

0.00165

0.00187

ERX1387160

Rhodnius robustus ‘Peru’

cytb

EF011721.1

R. prolixus

222.43

136

–

100.00

0.00000

0.00000

AF421339.1

R. prolixus

205.40

1

3.2

100.00

0.00000

0.00000

EF011716.1

R. prolixus

197.09

60

–

99.85

0.00152

0.00144

AF421341.1

R. robustus II

186.42

19

–

100.00

0.00000

0.00000

ITS2d

MK411271

R. prolixus

28.28

9

2.1

100.00

0.00000

0.00000

MK411269

R. prolixus

24.03

7

6.9

100.00

0.00000

0.00000

MK411272

R. prolixus

23.66

5

14.4

100.00

0.00000

0.00000

MK411270

R. prolixus

22.48

5

8.6

100.00

0.00000

0.00000

D2-28S

AF435860.1

R. prolixus

57.74

3

1.6

100.00

0.00000

0.00000

AF435861.1

R. robustus I

54.91

3

0.5

100.00

0.00000

0.00000

AF435859.1

R. robustus IV

33.38

1

34.3

100.00

0.00000

0.00000

  1. Notes: Depth-coverage (reads/position) and sequence identity (percent of identical bases) and divergence (model-based genetic distance estimates) of query vs consensus sequences are presented for three loci and four transcriptomes determined by two research groups
  2. aFrom the best-fit models of nucleotide substitution: Tamura three-parameter with γ-distributed rates for cytb (γ = 0.20) and D2-28S (γ = 0.05), and Tamura three-parameter for ITS2; standard errors (SE) computed after 1000 bootstrap pseudo-replicates
  3. bPercent of positions at which depth-coverage was < 10 reads (Additional file 6: Figure S4)
  4. cConsensus sequences with mean depth-coverage < 10 reads/position (Additional file 1: Table S1, Additional file 6: Figure S4) that were excluded from phylogenetic analyses
  5. dSee details in Additional file 1: Table S2
  6. eJQ897670.1 is from a bug identified as Rhodnius neglectus from ‘Orellana, Ecuador’ (see [31]), where neither R. neglectus nor R. prolixus occur (R. robustus II and R. barretti do); this is most likely a case of misidentification or mislabeling of the specimen
  7. Abbreviations: UNESP, Universidade Estadual Paulista ‘Júlio de Mesquita Filho’, Brazil; CNRS, Centre National de la Recherche Scientifique, France; NCBI, National Center for Biotechnology Information, USA; SRA, transcriptome access code at NCBI’s Sequence Read Archive; cytb, mitochondrial cytochrome b gene; ITS2, second internal transcribed spacer of the nuclear ribosomal DNA; D2-28S, D2 variable region of the nuclear ribosomal DNA
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