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Table 3 Full-breadth-coverage consensus sequences generated from transcriptomes determined using UNESP Rhodnius montenegrensis colonies

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

Transcriptome Locus Query Depth-coverage Identity Divergencea
NCBI SRA Sequence Species Mean Minimum < 10 readsb (%) Percent Distance SE
SRX1996481 cytb EF011724.1 Rhodnius robustus II 13,831.35 1996 99.85 0.00152 0.00144
AF421341.1 R. robustus II 5745.50 48 99.55 0.00463 0.00252
EF071583.1 R. robustus II 4646.05 67 99.70 0.00306 0.00205
EF011720.1 R. robustus II 4061.95 25 99.85 0.00152 0.00140
KR072682.1 R. montenegrensis 3298.10 12 100.00 0.00000 0.00000
ITS2c MK411275 R. robustus II 24.41 3 1.6 99.59 0.00411 0.00231
D2-28S AF435857.1 R. robustus III 631.85 18 100.00 0.00000 0.00000
AF435858.1 R. robustus II 334.82 2 1.3 100.00 0.00000 0.00000
AF435859.1 R. robustus IV 199.84 1 33.0 99.68 0.00316 0.00220
SRX1996482 cytb EF011724.1 R. robustus II 11,834.29 1689 99.85 0.00152 0.00144
AF421341.1 R. robustus II 4834.87 32 99.55 0.00463 0.00252
EF071583.1 R. robustus II 3450.87 47 99.70 0.00306 0.00205
EF011720.1 R. robustus II 3203.49 13 100.00 0.00000 0.00000
KR072682.1 R. montenegrensis 2311.50 6 0.3 100.00 0.00000 0.00000
ITS2c MK411274 R. robustus II 20.29 1 29.6 99.32 0.00686 0.00290
D2-28S AF435857.1 R. robustus III 714.15 20 100.00 0.00000 0.00000
AF435859.1 R. robustus IV 211.15 1 31.3 99.68 0.00316 0.00205
  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 two transcriptomes determined by UNESP researchers [12, 13]
  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. cSee details in Additional file 1: Table S2
  5. Abbreviations: UNESP, Universidade Estadual Paulista ‘Júlio de Mesquita Filho’, Brazil; 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