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

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

Transcriptome	Locus	Query		Depth-coverage			Identity	Divergence^a
NCBI SRA	Locus	Sequence	Species	Mean	Minimum	< 10 reads^b (%)	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
	ITS2^c	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
	ITS2^c	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
	D2-28S	AF435859.1	R. robustus IV	211.15	1	31.3	99.68	0.00316	0.00205

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]
^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
^bPercent of positions at which depth-coverage was < 10 reads (Additional file 6: Figure S4)
^cSee details in Additional file 1: Table S2
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

ISSN: 1756-3305