Additional file 1 of Neofunctionalization driven by positive selection led to the retention of the loqs2 gene encoding an Aedes specific dsRNA binding protein
Creators: name: Estevez-Castro, Carlos F.
name: Rodrigues, Murillo F.
name: Babarit, Antinéa
name: Ferreira, Flávia V.
name: de Andrade, Elisa G.
name: Marois, Eric
name: Cogni, Rodrigo
name: Aguiar, Eric R. G. R.
name: Marques, João T.
name: Olmo, Roenick P.
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Fig. S1. (Related to Fig. 1). Non-collapsed phylogenetic tree from Fig. 1A and read mapping of RNA-seq and whole-genome-seq data from different Aedini species aligned to the Ae. aegypti and Ae. albopictus reference genomes. A Terminals correspond to the VEuPathDB accession numbers. The dsRBP orthology groups are indicated by black bars and the protein lengths of the Ae. Aegypti orthologs are indicated in parentheses. Tree was rooted at the midpoint for visualization purposes. Node values correspond to the percentages of 1000 ultra-fast bootstrap iterations. Branch lengths represent substitutions per site. B loqs and loqs2 exons are colored in purple and blue respectively. Black boxes represent the read mapping along loqs and loqs2 gene sequences. Lines represent intronic regions of both gene sequences and reads. *indicates species where whole genome sequencing were analyzed. Fig. S2. (Related to Fig. 2). Non-collapsed phylogenetic tree from Fig. 2B. Terminals correspond to the VEuPathDB accession numbers. Each orthology group’s dsRBDs are numbered and indicated by black bars. The tree was rooted at the midpoint for visualization purposes. Node values correspond to the percentages of 1000 ultra-fast bootstrap iterations. Branch lengths represent substitutions per site. Fig. S3. (Related to Fig. 2). Cladogram built from the Loqs-D1-Loqs2 subtree from Fig. 2B and exon–intron organization of the loqs and loqs2 genes in Ae. aegypti and Ae. albopictus. A The cladogram was built with equal branch lengths. The clade containing the Loqs2 dsRBDs is colored in grey. B The exon–intron structure of the loqs and loqs2 genes is indicated by boxes (exons) and continuous lines (introns). dsRBD regions are indicated in blue boxes. Exons are represented by boxes and introns by grey continuous lines. C Zoomed-in view of the amino-acid sequences from the exon–intron-exon boundaries within the dsRBD domains of loqs and loqs2. Fig. S4. (Related to Fig. 3). dsRBDs from Loqs2 present high conservation among the residues important for folding and dsRNA binding. Translated amino acid alignment from the codon-based alignment used to build phylogenetic framework reported in Fig. 3B. The top row displays the consensus residues for dsRBD folding and dsRNA binding, as previously reported  [39]. Conserved residues along the alignment are highlighted in pale green boxes. The specific residues necessary for dsRNA binding are highlighted in dark green. Secondary structure elements of the dsRBDs are showed at the bottom of the alignment. Sites with significant evidence of purifying or diversifying selection, as detected by FEL analysis, are indicated by blue or red boxes, respectively. Fig. S5. (Related to Fig. 5). A Expression levels of loqs2 in transgenic or wild-type sibling larvae quantified by RT-qPCR. B sRNA abundance (18 to 35 nt) from wild-type and transgenic larvae (related to Fig. 5D). C-D Heatmaps showing the abundances of sRNAs mapped to the miRNAs and siRNA clusters references among the wild-type and transgenic larvae (related to Fig. 5E-F). Abundances are reported as reads per million mapped (RPM) and bar colors represent the nucleotide base distribution. Only normalized abundances &gt; 50 RPM are reported. Normalized mapped sRNA abundances were used for hierarchical clustering. Names of the siRNA clusters are given by the genome version, followed by the chromosome and initial genomic position of the cluster. Fig. S6. (Related to Fig. 5). sRNA abundance (18 to 35 nt) from wild-type and transgenic larvae that mapped to a de novo generated piRNA cluster reference, and expression of transposable element (TE) families among L2 and L4 wild-type and transgenic larvae. A bar colors represent the nucleotide base distribution. B Heatmap shows the abundances of sRNAs mapped to the de novo predicted piRNA clusters. Normalized mapped sRNA abundances were used for hierarchical clustering. In A and B, abundances are reported as reads per million mapped (RPM). C The heatmap shows the normalized expression of TE families as log2 counts per million (Log2CPM). TE family expression between conditions and TE families was used for hierarchical clustering. Fig. S7. (Related to Fig. 5). Ectopic expression of loqs2 in larval stages lead to major metabolic shutdown. GSEA analysis plot showing extended gene sets prior to redundancy removal relative to Fig. 5G.