Fig 1.
Putative horizontally transferred genes in the genome of A. queenslandica.
(A) The number of candidate HGTs detected by Alien Index (AI45), Blast, EvolMAP, and the nucleotide pipeline (NT). (B) Comparison of compositional traits of putatively transferred genes and host genes. Scatterplots show primary codon usage plotted against the GC content of protein coding genes (GC%), the size of the genome contig on which the gene is located, and the average expression in sponge larvae and adult tissues (reads per kilobase per million, rpkm). Candidate HGTs, blue; potential contaminants, dark grey; spherulin, yellow; other sponge genes, light grey. (C) The number of putative horizontally transferred genes in A. queenslandica with homology to sequences in the demosponges, H. amboinensis and E. muelleri. (D) Boxplots showing the exon number distribution for horizontally transferred genes with homologs in the indicated sponge lineages.
Fig 2.
Classification of putative horizontally transferred genes based on number of supporting methods and host-like features.
AI45, Blast, EvolMAP, and the nucleotide pipeline (NT) detect candidate HGTs with distinct characteristics, suggesting that these methods have different sensitivities for identification of young versus old HGTs or for discriminating against contaminating prokaryotic sequences. Only candidate HGTs that passed the additional criteria for location on larger contigs and expression in sponge tissues were included in this analysis (numbers in parentheses). Sizes of the circles represent the number of genes under each classification.
Fig 3.
Functions represented in putative horizontally transferred genes in the A. queenslandica genome.
(A) Number of putative horizontally transferred genes containing the indicated PFAM protein domains. (B) Gene ontology analysis for putative horizontally transferred genes in A. queenslandica. Enrichment p-values for selected functions of putative horizontally transferred genes are shown.
Fig 4.
Examples of candidate horizontally transferred genes in the A. queenslandica genome.
Unrooted phylogenetic trees depicting the relationship of (A) spherulin, (B) 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), (C) phosphatidylserine decarboxylase (PSD), and (D) M35 metallopeptidase sequences from A. queenslandica (red) to sequences in other sponges (orange), prokaryotes (blue), fungi or opisthokonts (green), and other metazoans (black). Trees were generated using MrBayes with posterior probabilities depicted on selected branches. Support values on some branches and tip labels in (D) were omitted for clarity. Sequences for spherulin, HMGR, and PSD genes were obtained by Blastp searches in NCBI or Compagen [47]. Prokaryotic and fungal metallopeptidase sequences were obtained from MEROPS [49]. (E) Example of a cluster of prokaryote-like genes (red) flanked by metazoan-like genes (blue) on an A. queenslandica contig. Genes are labeled with the name of their best hit in the UniProt database; metallopeptidases are labeled M35. Genes of unknown origin are shown in grey. The figure was adapted from Ensembl. (F) Alignment of partial sequences for selected metallopeptidase genes showing the presence of introns (blue) with canonical splice sites (red) and polypyrimidine tract (underlined).