Panel A: A diagram showing the homology-assisted gene annotation of the Saccoglossus kowalevskii AMPAR gene. It includes scaffold 1273 with manually annotated exons as blue arrows, previously automatically annotated exons as red and orange arrows, and amino acid sequence homology with other AMPARs. Panel B: An amino sequence alignment of key pore-forming and ligand-binding segments of Symsagittifera roscoffensis AMPAR-like 17384.1 and other genes. Panel C: A bar graph showing RNA transcript prevalence data from a previous Lingula anatina genomic study, with fragments per kilobase of transcript per million mapped reads on the y-axis and different embryonic stages and adult tissues on the x-axis. Panel D: A diagram showing the adjacent location of Lingula anatina AMPAR genes in indicated scaffolds from genome GCF_001039355.2.
AMPAR gene expression, gene loci, and gene annotation AMPAR gene expression, gene loci, and gene annotation. (A) Scaffold 1273 from S. kowalevskii genome version 3 http://bioinfo.szn.it/genoma-repo/Skowalewski/OIST/Saccoglossus_kowalevskii_v3.fasta.tbz2 (similar to genome version 2/GCF_000003605.2, scaffold 2021/NW_003107109.1 at NCBI GenBank [Simakov et al., 2015]), base pair numbering at left of black lines, with our manually annotated exons shown as blue arrows. Also shown are previous, automatically annotated exons (red and orange arrows) corresponding to NCBI entries XP_006811838.1 and XP_006811839.1 from NW_003107109.1. Translations above and below highlight selected differences between manual and automatic predictions; amino acid sequence alignments (below) of these segments illustrate how we also used homology with fellow hemichordate AMPAR (S. californicum) and rat AMPAR to identify likely exons (secondary structure from published Rat-GluA2 PDB:3KG2 [Sobolevsky et al., 2009]). Updated NCBI/GenBank entry XP_085353805.1 is 97% identical to our prediction (99% excluding signal peptide). (B) Amino acid sequence alignment of key pore-forming and ligand-binding segments of S. roscoffensis AMPAR-like 17384.1 and other genes. (C) RNA transcript prevalence data from a previous L. anatina genomic study (Luo et al., 2018). SHANK is a postsynaptic protein included to show a gene with higher expression than AMPA genes. (D) Adjacent location of L. anatina AMPAR genes in indicated scaffolds from genome GCF_001039355.2 (NCBI GenBank) (Luo et al., 2018).