1% of the sites showed variation (110/906; Epacadostat Table 3). In fact, strong and significant differentiation (Fct = 0.69*, explaining 69% of the total variation in the sample, Table S1 in Additional file 1) was observed between groups of alleles, with each group being mostly associated to a genetic group within the B. tabaci complex

or the other Aleyrodidae species tested (T. vaporariorum or B. afer). Table 4 Haplotype distribution among the three sequenced genes of Arsenophonus (fbaA, ftsK, yaeT). Haplotype (B. tabaci genetic group) Profile Number Frequency (%)   fbaA ftsK yaeT     DATO11(Ms) 6 8 11 59 38.82 BLAPE1 (Q2) 1 5 9 22 14.47 B4-16 (Q3) 4 4 5 19 12.50 co_p1_2 (Tv/Ms) 5 7 10 22 14.47 B1-34 (ASL) 1 2 1 5 3.29 B2-32 (ASL/AnSL) 3 3 2 5 3.29 BLAPE11 (Q2) 1 6 9 4 2.63 B1-21 (ASL) 1 1 1 3 1.97 B1-45 (ASL/AnSL) 2 3 2 3 1.97 B2-37 (ASL) 1 2 4 1 0.66 B1-42 (ASL) 1 3 1 1 0.66 B1-47 (ASL/AnSL) 2 2 2 1 0.66 BE8-23 (ASL/AnSL) 3 3 8 1 0.66 O2-22 (Q3) 4 4 2 1 0.66 PiHarF55 (Ms) 6 8 12 1 0.66 SE616 (Ms) 6 8 14 1 0.66 DIAU8 (Ms) 7 8 11 1 0.66 SaaubF53 8 9 13 1 0.66 Tanza_4.1 (Tv/Ms) 9 7 10 1 0.66 n haplotypes 9 9 11 152 100 Number of individuals per haplotype and frequencies are indicated. The name of each haplotype is the name

of one of its representatives. GDC-0994 chemical structure The genetic groups of B. tabaci associated with the haplotype are indicated in parentheses. For the ftsK locus, we observed indels of two types: a 2-bp insertion found exclusively in the Arsenophonus hosted by the Q2 genetic MycoClean Mycoplasma Removal Kit group and a 1-bp deletion found in some ASL and Q2 individuals. These two indels resulted in hypothetical truncated ftsK proteins potentially encoding 866 or 884 amino acids, respectively (predicted ftsK has 1030 amino acids in Arsenophonus nasoniae [Genbank: CBA73190.1]; (Table S2 in Additional file 1). Among the 152 individuals used in this

study, a total of 19 haplotypes of Arsenophonus were identified, which is low compared to the theoretical 891 allelic combinations (9 x 9 x 11, 9 alleles for both ftsK and fbaA, and 11 for yaeT; Table 4). Recombination analysis Using the RDP3 package, recombination events were tested for each gene separately and for the concatenated data set using all sequences studied (see Figure 2). No recombination events were detected for any of the gene portions analyzed separately, suggesting that there is no intragene recombination. For the concatenated data set sequences, among the seven algorithms tested, four (GENECONV, Bootscan, Maximum Chi Square, and Chimaera) showed two significant recombination events (Table S3 in Additional file 1). Recombination events were detected in individuals B1-47 and B1-42 (ASL genetic group) for the whole region of the ftsK gene (positions 366 to 617 in the concatenated alignment). Figure 2 Arsenophonus phylogeny constructed using maximum-likelihood (ML) analyses based on the concatenated sequences of three genes: fbaA , ftsK and yaeT .