Additional file 2 of Identification and characterization of four Drosophila suzukii cellularization genes and their promoters
Creators: name: Yan, Ying
name: Jaffri, Syeda A.
name: Schwirz, Jonas
name: Stein, Carl
name: Schetelig, Marc F.
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Figure S1. Drosophila suzukii NULLO protein alignment. DsNULLO is aligned with orthologs from Drosophila biarmipes [DbNULLO] (GenBank: XP_016948821.1), Drosophila hydei [DhNULLO] (GenBank: XP_023161247.1), Drosophila kikkawai [DkNULLO] (GenBank: XP_017022675.1), Drosophila melanogaster [DmNULLO] (GenBank: NP_511067.3), Drosophila miranda [DmirNULLO] (GenBank: XP_017156218.1), Drosophila navojoa [DnNULLO] (GenBank: XP_017964581.1), Drosophila obscura [DoNULLO] (GenBank: XP_022210380.1), Drosophila rhopaloa [DrNULLO] (GenBank: XP_016982709.1), Drosophila serrata [DserNULLO] (GenBank: XP_020805612.1) and Drosophila willistoni [DwNULLO] (GenBank: XP_002071148.1). Identical amino acids are shaded black and conservative changes are indicated in gray. All proteins contain a consensus site for N-terminal myristoylation (M) followed by a positively charged cluster (P). The remainder of the protein contains five conserved regions of amino acids (A–E) separated by short non-conserved regions. Figure S2. Drosophila suzukii SERENDIPITY-α (SRY-α) protein alignment. DsSRY-α is aligned with orthologs from Drosophila grimshawi [DgSRY-α] (GenBank: XP_001995347.1), Drosophila hydei [DhSRY-α] (GenBank: XP_023168708.1), Drosophila melanogaster [DmSRY-α] (GenBank: NP_524580.1) and Drosophila virilis [DvSRY-α] (GenBank: XP_002056142.1). The putative transmembrane domain is underlined and the region of similarity with proteins of the ERM family is boxed. Figure S3. Drosophila suzukii BOTTLENECK (BNK) protein alignment. DsBNK is aligned with orthologs from Drosophila grimshawi [DgBNK] (GenBank: EDV90810.1), Drosophila hydei [DhBNK] (GenBank: XP_023168586), Drosophila kikkawai [DkBNK] (GenBank: XP_017034088.1), Drosophila melanogaster [DmBNK] (GenBank: NP_524604.2), Drosophila miranda [DmirBNK] (GenBank: XP_017140437.1), Drosophila obscura [DoBNK] (GenBank: XP_022213695.1), Drosophila virilis [DvirBNK] (GenBank: XP_002055918.1) and Drosophila willistoni [DwBNK] (GenBank: XP_002072000.1). Highly conserved regions are marked with red lines. Figure S4. Drosophila suzukii SLOW-AS-MOLASSES (SLAM) protein alignment. DsSLAM is aligned with orthologs from Drosophila grimshawi [DgSLAM] (GenBank: XP_001988112.1), Drosophila pseudoobscura [DpSLAM] (GenBank: XP_001355861.2), Drosophila melanogaster [DmSLAM] (GenBank: NP_001285668.1), and Drosophila busckii [DbuSLAM] (GenBank: ALC38995.1). Highly conserved regions are marked with red lines. Figure S5. Reverse-transcriptase (RT)-PCR to evaluate the reference (a) and cellularization (b) genes through the development of Drosophila suzukii. Primer sequences for reference genes TATA binding protein (TBP), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), arginine kinase (AK), a-Tubulin (α-Tub) and Histone H3 (His3) (Zhai et al., 2014; Li and Handler, 2017), as well as for four cellularization genes can be found in “Additional file 1”. Embryos collected at different time points after egg laying (in hours), larvae (first, second and third instar), pupae (2 days after prepupae), adult female and male (1 and 5 days old). Additional 0–0.5 h samples were used for cellularization genes. The PCR product sizes are 140 bp for AK, 130 bp for GAPDH, 189 bp for α-Tub, 129 bp for His3, and 182 bp for TBP, 161 bp for sry-a, 155 bp for nullo, 159 bp for bnk, and 149 bp for slam. M is the molecular weight ladder. Figure S6. Alignment of the Ds_sry-α and Dm_sry-α 5′ flanking sequences. The upstream flanking sequence from Ds_sry-α (165 bp, before it reaches the upstream gene DS10_00012896, the ortholog of D. melanogaster janus A) and Dm_sry-α (167 bp) together with the 5′-UTR (annotated in green) are compared. The 5′ flanking sequences of Ds_sry-α and Dm_sry-α contain three and four conserved motifs that confer blastoderm-specific expression, respectively. Both 5′ flanking sequences contain two TAGteam motifs (annotated in yellow), and a TATA box (TATATAAA) 23 bp upstream of the putative transcription start site. The Ds_sry-α 5′ flanking sequence was fused to DsRed-NLS in V205 to act as a gene promoter for the in vitro test. Figure S7. Alignment of the Ds_nullo and Dm_nullo 5′ flanking sequences. The upstream flanking sequence from Ds_nullo (1876 bp) and Dm_nullo (1753 bp) together with the 5′-UTR (annotated in green) are compared. The 5′ flanking sequences of Ds_nullo sequence contains one TAGteam motif (annotated in yellow), whereas that of Dm_nullo contains none. The TATA box (TATATAT) is 24 bp upstream of the putative transcription start site. The Ds_nullo 5′ flanking sequence was fused to DsRed-NLS in V206 to act as a gene promoter for the in vitro test. Figure S8. Alignment of the Ds_bnk and Dm_bnk 5′ flanking sequences. The upstream flanking sequence from Ds_bnk (1581 bp) and Dm_bnk (1523 bp) together with the 5′ UTR (annotated in green) are compared. The 5′ flanking sequences of Ds_bnk and Dm_bnk contain three and four TAGteam motifs (annotated in yellow), respectively, and the TATA box (TATATAAA) is 25 bp upstream of the putative transcription start site. The Ds_bnk 5′ flanking sequence was fused to DsRed-NLS in V208 to act as a gene promoter for the in vitro test. Figure S9. Alignment of the Ds_slam and Dm_slam 5′ flanking sequences. The upstream flanking sequence from Ds_slam (822 bp) and Dm_slam (887 bp) together with the 5′ UTRs (annotated in green) are compared. Neither the Ds_slam nor Dm_slam 5′ flanking sequences contain TAGteam motifs or a TATA box. The Ds_slam 5′ flanking sequence was fused to DsRed-NLS in V207 to act as a gene promoter for the in vitro test.