Figure 1.
Strategy to obtain non-model organism transcriptomics resources.
NGS: Next-generation sequencing; ESTs: Expressed Sequence Tags; aCGH: array-based Comparative Genomic Hybridization; GE: Gene Expression; GO: Gene Ontology; EC: Enzyme Commission numbers. * adapted from http://extension.missouri.edu/explorepdf/agguides/pests/g07402.pdf.
Table 1.
C. riparius sample list summary.
Table 2.
C. riparius transcriptome sequencing and assembly statistics.
Figure 2.
Array-based comparative genomic hybridization (aCGH) experiment.
(A) Box- and-whisker plot summarizing the obtained log2 signal intensity distributions for the four indicated probes collections, with the light grey boxes representing the C. riparius aCGH signal and the dark grey the aCGH A. gambiae signal. (B) MA-plot of the aCGH data. The dots with the different shades of grey represent the entire probe-library (with a GC-content below 50%). The three defined signal-intensity parameters are indicated by the dashed blue line and the captions I, II, III. The three categories containing the selected probes are indicated by different shades of grey and the letters A, B and C. The red dots are the negative control probes and the green dots the positive control (A. gambiae EST) probes.
Figure 3.
Array-based gene expression (aGE) experiment.
(A) Schematic representation of the two mRNA linear amplification protocols. The coloured bar represents the mRNA with the 3′ polyA tail indicated by the stretch of A’s. The arrows represent the amplified cDNA products obtained for the regular procedure and the modified procedure, with the length of the arrows indicating the length of the synthesized cDNA’s. (B) MA-plot of the aGE data. The light grey dots represent all aCGH selected probes. The three coloured regions are expected to contain probes targeting transcripts at the 3′ side (blue), probes targeting the middle of the transcripts (red) and probes targeting the 5′side as well as probes with no target transcripts (green). (C) Density plot where the relative position of the three probe populations on the isotigs is demonstrated. The colours of the lines correspond to the colours used in panels A and B. The black line represents a random selection of probes that covers, as expected, the isotigs evenly over the entire length.
Figure 4.
Taxonomic distribution of the best blastx hits matching C. riparius transcripts.
Distribution of the best blastx hits that were matched to the isotigs (black) and the singletons (light grey) according to their taxonomic origin. (A) All transcripts (isotigs n = 16,824; singletons n = 24,129) that were matched to a BLASTX hit. (B) Transcripts (isotigs n = 16,537; singletons n = 4,7539) that were matched to a BLASTX hit and that are targeted by the final aGE microarray.
Figure 5.
Gene Ontology (GO) terms obtained for C. riparius transcripts.
The data represents the distribution of the annotated isotigs (black) and the annotated singletons (light grey) over the various level-2 GO terms. Each bar represent the number of annotated transcripts associated with the specified level-2 GO term as a percentage of the total number of annotated transcripts belonging to the higher-ranked GO category, i.e. cellular component (isotigs n = 8,380; singletons n = 9,277), molecular function (isotigs n = 10,663; singletons n = 11,359) and biological process (isotigs n = 6,249; singletons n = 7,343).
Table 3.
C. riparius transcriptome annotation summery.