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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 prolixusRhodnius 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