primer design for sdic  (PrimerDesign Inc)

Journal: Molecular Biology and Evolution

Article Title: Understanding the Early Evolutionary Stages of a Tandem Drosophila melanogaster -Specific Gene Family: A Structural and Functional Population Study

doi: 10.1093/molbev/msaa109

Figure Lengend Snippet: Annotation of the Sdic region across seven populations of the DSPR panel. The most reliable organization of the region at 19C1 on the X chromosome in the ISO-1 is provided as a reference ( Clifton et al. 2017 ). The region is depicted from centromere (Cen) to telomere (Tel), including the flanking genes sw and AnxB10 (gray-filled arrows). Population names are color-coded based on the broad continental region where they were collected: green, Africa; red, Americas; and blue, Eurasia. The number of annotated Sdic copies in reference-quality genome assemblies ( Chakraborty et al. 2018 , ) is indicated in parentheses next to the name of the population. Sdic copies in the ISO-1 strain are named as reported ( Clifton et al. 2017 ). In the rest of populations, the copy identifiers are roman numerals according to their relative order from sw to AnxB10 . Sdic copies are color-coded, and a lower character ( a–m ) added to their identifier, both indicating the associated paratype. Three TE insertions (solid boxes) are shown, indicating both their size in kb and the location in relation to the gene structure (e, exon). One TE insertion is located within intronic sequence (A5_I), a common occurrence ( Chakraborty et al. 2018 ). In the other two cases, A7_III and B3_IV, the TE disrupts coding and 3′-UTR sequence, respectively. In the first case, the TE has possibly no functional consequence as a premature STOP codon resides upstream of the TE insertion; the apostrophe indicates an ancestral coding exon, which now situates outside of the predicted open reading frame.

Article Snippet: Primer design for Sdic took into consideration sequence differences with sw and AnxB10 to confidently survey solely Sdic expression, as well as perfect sequence conservation across copies and strains to prevent any copy or population bias.

Techniques: Sequencing, Functional Assay

Journal: Molecular Biology and Evolution

Article Title: Understanding the Early Evolutionary Stages of a Tandem Drosophila melanogaster -Specific Gene Family: A Structural and Functional Population Study

doi: 10.1093/molbev/msaa109

Figure Lengend Snippet: Global expression of the Sdic multigene family in whole-body males using qRT–PCR. ( A ) Sdic primers are shown relative to the Sdic transcriptional unit. See figure 3 A for details about the relationship of different parts of this transcriptional unit with the structure of the parental genes. Primers were designed upon examining the sequence of all the copies across all the strains of geographically diverse origin, plus ISO-1, making sure that there was no mismatch or gap. The upstream primer was designed spanning the intron between exons 1 and 2 of Sdic , with only 5 nt within exon 2, to prevent amplification of sw . ( B ) Fold change in expression of ten strains, including ISO-1 (value of 1 on the y axis), which was used as calibrator. Green, w 1118 and its synthetic derivatives carrying the duplication of the Sdic region (2T and 4M). Blue, strains of different geographical origin plus OR-R. Error bars, SEM. ( C ) Linear regression between CN and log2-fold change in expression for the two subsets of strains examined. Each dot represents the values obtained for each biological replicate included in the analysis. Determination coefficients ( r 2 ) and their corresponding P values are shown.

Article Snippet: Primer design for Sdic took into consideration sequence differences with sw and AnxB10 to confidently survey solely Sdic expression, as well as perfect sequence conservation across copies and strains to prevent any copy or population bias.

Techniques: Expressing, Quantitative RT-PCR, Sequencing, Amplification