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Authors’ original file for figure 1

Additional file of Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita

Additional file of Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencing

Authors’ original file for figure 3

Authors’ original file for figure 2

Additional file 4: Representativeness of genome features using the equiprobability model. Representativeness of genome features using the equiprobability model in the case of Apis mellifera (A) and Danio rerio (B) for each of the six considered two-way tables chromosome × chromosomic region, chromosome × length of sequences, chromosome × microsatellite motifs, chromosomic region × length of sequences, chromosomic region × microsatellite motifs and length of sequences × microsatellite motifs. "Stat" refers to the overall χ2 statistic for the test of independence between the two variables defining the table. For each cell of the table: a red dot corresponds to an observed number significantly higher than expected under the hypothesis of independence between the two variables defining the table; a blue dot corresponds to an observed number significantly lower than expected under the hypothesis of independence between the two variables defining the table; absence of circle means a non-significant deviation. The size of the dot is inversely-proportional to the P-value, the scaling being made to the six considered tables so that the comparison of sizes between tables is meaningful. For cell tests, Benjamini-Hochberg20 correction for multiple tests was performed. (PDF 4 MB)

Authors’ original file for figure 4

Authors’ original file for figure 1

Authors’ original file for figure 2

Additional file of Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita

Additional file of Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita

Authors’ original file for figure 3

Additional file 2: Representativeness of genome distribution after digestion with Rsa I. Representativeness of genome distribution after digestion with Rsa I in the case of Apis mellifera (A) and Danio rerio (B) for each of the six considered two-way tables: chromosome × chromosomic region, chromosome × length of sequences, chromosome × microsatellite motifs, chromosomic region × length of sequences, chromosomic region × microsatellite motifs and length of sequences × microsatellite motifs. "Stat" refers to the overall χ2 statistic for the test of independence between the two variables defining the table. For each cell of the table: a red dot corresponds to an observed number significantly higher than expected under the hypothesis of independence between the two variables defining the table, a blue dot corresponds to an observed number significantly lower than expected under the hypothesis of independence between the two variables defining the table; absence of dot means a non-significant deviation. The size of the dot is inversely-proportional to the P-value. The scaling is computed for the six considered tables so comparison of significance between tables is meaningful. For cell tests, Benjamini-Hochberg20 correction for multiple tests was performed. (PDF 3 MB)

Additional file 3: Comparison of genome features using the equiprobability model Comparison of genome features using the equiprobability model in the case of Apis mellifera (A) and Danio rerio (B) for each of the four considered one-way tables: chromosome, chromosomic region, length of sequences and microsatellite motifs. For each table is figured in red the 95% confidence interval of the expected number of microsatellites under the equiprobability hypothesis, in black are figured observed numbers (genome distribution after digestion in silico with Rsa I). (PDF 2 MB)

Authors’ original file for figure 2

Additional file 3: Breakdown of error rate variation using all available variables. For each plate, we used a logistic model to decipher the role of each selected variable in explaining the variation of error rate (see materials and methods). The figure is broken down by error type: a) insertions, b) deletions, c) mismatches and d) ambiguous base calls. We tested the deviance from the complete model by breaking down the model into the sum of three terms: the first exclusive to the single effect of the variable considered (in black), the second exclusive effect of the rest of the variables without the variable of interest (in gray) and the last expressing the sum of the effects of interactions between the variable considered and the other variables (in white). The contribution of each term (the proportion) for a considered variable can be viewed on the y-axis. Additional file 3 displays the results for plates #2 and #3 (results from the plate #1 are presented as Figure 2). (PDF 117 KB)

Additional file 2: Distribution of errors along the reference sequences. The blue line represents the proportion of sequences generated (y-axis) according to the sequence position (x-axis), using data obtained from the analysis of reference 5 reference sequences (excluding reference #3, which is displayed in Figure 1). The error rate for each type of error (insertions, deletions, mismatches and ambiguous base calls) is presented as a function of the sequence position (x-axis) and specific position on the y-axis. The position and length of homopolymers for each base is given on the x-axis to facilitate interpretation (green: A, red: T, black: G, blue: C). (PDF 265 KB)

Authors’ original file for figure 1

Additional file of Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing

Additional file 1: Number of sequences to correct erroneous positions. 1a: this file illustrates the number of sequences necessary to obtain a majority of correct sequences. The x-axis shows the error rate and the y-axis shows the number of sequences needed, according to three possible probabilities: 0.001 0.01 and 0.05. 1b the x-axis shows the error rate for a given position (ranging from 0 to 0.5); the y-axis shows the cumulative proportion of erroneous sequences sampled (ranging from 0 to 0.5) in the total sample. Sample size varies from 10 to 100, 500 and 1,000 sequences. For a given error rate and a cumulative proportion of erroneous sequences in the sample of size N, the probability of observing this combination is indicated in color: green: 1 to 0.95, blue: 0.95 to 0.8, yellow: 0.8 to 0.6, orange: 0.6 to 0.5, red: 0.5 to 0.4, gray: 0.4 to 0.2 and white: below 0.2. For example, if the error rate is 0.2, the probability of observing a cumulative proportion of erroneous sequences in the sample of between 0 and 0.2 ranges between 0.4 and 0.5 (red envelope). In this case, the probability of there being 20% erroneous sequences in the sample is between 0.4 and 0.5. If we consider the same error rate (0.2) with 40% erroneous sequences, then the probability ranges from 0.8 to 0.95 (blue envelope). If N increases, the variance of the probability envelopes decreases. (PDF 5 MB)

Additional file 4: Spatial localization of error rate variation. For each error type and the sequence length, the x-axis represents the spatial localization of 454 reads as x-coordinates and the y-axis represents the y-coordinates on the PT plate. The results presented in this additional data file 4 correspond to plates #2 and #3. The strips represent the regions. We display separately the four types of error (insertions, deletions, mismatches and ambiguous base calls) and the length of the generated sequences. Colors represent the ranges of error rates from 0 to 1 (or the length of the sequences from 0 to 500), using a sliding window (see materials and methods). (PDF 550 KB)

Pseudococcus meridionalis Prado sp. n. (Fig. 4) Diagnosis. P. meridionalis belongs to the Pseudococcus maritimus complex, characterized by the presence of discoidal pores near the eyes (Gimpel & Miller, 1996) and is very similar to P. maritimus and P. v ib u r n i. One of the most important diagnosis characteristics of P. maritimus, the presence of a marginal OR between cerarii 15 and 16, is absent from P. meridionalis. Other important characteristics of P. meridionalis include OC present in ventromarginal areas of thorax, translucent pores present on hind tibia and femur, and discoidal pores near eyes not located on sclerotized rim. External appearance. P. meridionalis shows four long caudal tails; the length of the wax tail of cerarius 2 reaches less than half the length of the wax tail of the anal cerarius. Body color is dark gray. A compact ovisac is produced containing orange color eggs. Mounted material. (data in brackets for paratypes) Adult female. Holotype elongated oval, length 2.09 mm (1.6���3.1), width 1.19 mm (0.80���1.75). Anal lobes well developed. Longest anal lobe seta 80 mm (78.2���119.5), approximately twice greatest width of anal ring (n = 23). Antennae each 480 ��� 468 ��m long, with eight segments. Average lengths of each segment as follows: I 65.0 mm (53.7���85.4); II 62.2 mm (51.2 ���78.0); III 61.0 mm (51.2 ��� 75.0); IV 45.0 mm (31.7���56.1); V 55.0 mm (46.3���63.4); VI 40.2 mm (36.6���51.2); VII 47.5 mm (41.5���51.2); VIII 105.0 mm (95.1���109.8). Legs well developed; hind trochanter + femur 345���350 mm (300���400); hind tibia + tarsus 405 ��� 390 mm (345���460); ratio of length of hind tibia + tarsus to hind trochanter + femur 1.17 ��� 1.11: 1 (1.01���1.22: 1). Ratio of length of hind tibia to tarsus 2.5 ��� 2.5: 1 (2.0��� 2.9: 1). Translucent pores: 40 ��� 39 (16���60) present on hind femur and 48 ��� 45 (26���52) on hind tibia; absent from hind coxa and trochanter. Hind tibia with 22 ��� 21 (21���38) setae. Longest seta on hind trochanter 97.6���107.3 (80���131) mm long. Labium 150 mm long (117���183). Circulus 1.6 times as wide as long, 162 mm wide (158���176). Longest anal-ring seta 125 mm long (117���173). Cerarii numbering 17 pairs. Each anal lobe cerarius lightly sclerotized, with three setae of different sizes, long, medium and short. Cerarii 1���11 each mainly with 2 conical setae per cerarius (rarely 3 in ce 2 and 6); ce 12 with 3 (rarely 2); ce 13 and 14 with 2; ce 15 with 3; ce 16 with 4 (3 or 4); and ce 17 with 3 (sometimes 4). All cerarii with auxiliary setae, more numerous in anal cerarius with 5 (4���7), ce 2 with 4 (3���7) and ce 17 with 4 (2���5). Dorsal surface with flagellate setae of mostly one size, only somewhat longer on segment VIII; with 5 dorsomedial setae on segment VIII (3���9), longest of 22 mm long (14.6���24.4). Multilocular pores absent. Trilocular pores scattered throughout. Each oral rim tubular duct (OR) usually with 0 to 3 associated discoidal pores and 0 or 1 seta, present on submargin close to ce 2 to 9 and 11, between ce 13 and 14, and close to ce 17 (ce 17 rarely with 2 OR on paratypes); absent near ce 10 on holotype but sometimes present on paratypes; absent near ce12, 15 and 16. In addition, abdomen with 6 OR located in the medial line (3���9) and 9 in the submedial lines (9���21); also present on thorax as submarginal (as mentioned above in association with cerarii), 2 in the medial line (1���6) and 9 in submedial line (3���13). Few dorsal OC, located in margin. Discoidal pores of one size scattered over dorsum approximately same size as on venter. Discoidal pores present near eyes 1 or 2 (0���4). Ventral surface with normal flagellate setae, longest on abdominal segment VII each 57 mm long (43���63); 3 cisvulvar setae on each side (2���3), 40 mm long (30���43). Longest interantennal seta 98 mm long (66���98). Multilocular pores present on abdominal segments IV���VIII but not extending laterally to margin; pores restricted to an anterior band on segment VII and around vulva but present as both an anterior and a posterior band on VI and V but more dispersed on the V anterior band; on IV they are dispersed; absent from head and thorax on holotype but occasionally present on paratypes. Trilocular pores scattered throughout the body. One size OC in the holotype, some paratypes show 2 sizes with the second type being somewhat longer and narrower, located in the medial and submedial part of abdomen; associated with multilocular pores on posterior band of abdominal segments IV���VII, also present submarginally on head and thorax; numerous between ce 1 and 7, much less frequent between ce 8 and 11; then with 5���7 (3���17) OC between ce 10 and 11; 4���9 (7���27) close to ce 12; 9���12 (7���13) near ce 13; 7���8 (6���28) between ce 14 and 15; none near ce 16; 7���8 (6���16) on each side of head. OR each with 1 (0���2) discoidal pore and 1 (0���1) setae associated with rim; with 1 submarginal between ce 8 and 9, also 1 submarginal duct at level of cerarii ce 10 and 12 (2���3), and 1 submedial between ce 9 and 10; thus a total of 4 OR between anterior spiracle and abdominal segment 2 on each side of abdomen on holotype but varying from 2 to 9 on paratypes. Posterior spiracle greatest length 68.3���70.7 mm long (60.9���80.5). Type material. HOLOTYPE: adult female on one slide, Chile, La Serena, 10.V. 2002, on pomegranate (Punica granatum), Col. M. Zambrano (depositary Museo Nacional de Historia Natural, Chile, MNNC). PARA- TYPES: Four adult females on four slides, same data as holotype; 29 specimens on 24 slides, Chile, Calera de Tango, Santiago, 18.III. 2002 and 30.IV. 2002, on Pyrus pyrifolia; 12 specimens on 10 slides, Chile, Huelqu��n, Santiago, 17.IV. 2002, on Pyrus pyrifolia; one specimen on one slide, Chile, San Bernardo, SAG fruit inspection, on Pyrus communis; eight specimens on eight slides, Chile, Buin, March 2010, on Vitis vinifera. Paratypes deposited in MNNC, USNM; MNHN and ANSES. Non-type material. The specimens identified previously as Pseudococcus sp. 1 preserved at Servicio Agr��cola y Ganadero (SAG, Chile), and at Instituto de Investigaciones Agropecuarias (INIA, Chile) were also identified as P. meridionalis. Hosts and distribution. This species has been collected in Chile from Antofagasta Region (23 �� 11`23 ``S, 68 ��00`13 ``W) to Los Angeles (37 �� 27`48 ``S, 72 �� 19`36 ``W) on blueberries, nectarine, peach, pear, Japanese pear, persimmon, plum, cherimoya, pomegranate and grapevine. Etymology. The species name ��� meridionalis ��� refers to the location of this species at the southern part of South America, Chile., Published as part of Correa, Margarita, Aguirre, Carlos, Germain, Jean-Fran��ois, Hinrichsen, Patricio, Zaviezo, Tania, Malausa, Thibaut & Prado, Ernesto, 2011, A new species of Pseudococcus (Hemiptera: Pseudococcidae) belonging to the " Pseudococcus maritimus " complex from Chile: molecular and morphological description, pp. 46-54 in Zootaxa 2926 on pages 51-53, DOI: 10.5281/zenodo.205308, {"references":["Gimpel, W. F. Jr. & Miller, D. R. (1996) Systematic analysis of the mealybugs in the Pseudococcus maritimus complex (Homoptera: Pseudococcidae). Contributions on Entomology, International 2 (1), 1 - 162."]}