The G. cometa library was sequenced by Agencourt Bioscience Corporation (Beverly, Mass .. We performed TblastN searches against GenBank using as queries a rhizarian dataset made of all translated sequences (translations done with transeq, available at the University of Oslo Bioportal; http://www.bioportal.uio.no) for R. filosa, Quinqueloculina sp., G. cometa, and B. natans.
From the Ensembl (release 72) annotations of these three genomes we downloaded protein sequences (translations of all known or novel Ensembl genes) and cDNA sequences.
When supplied with "meaningful" RNA sequences, translation systems of this kind should be capable of generating pools of proteins a small fraction of which will be functional.
Assembly of sequences, translation of nucleotide sequences into protein sequences, and initial multiple sequence alignments were performed with the Clustal V method using MegAlign software version 1.03 (SNAStar Inc., Madison, WI).
Nucleotide sequences translation into protein sequences was performed using also BioEdit.
An alternative selective factor could be the fidelity of transcription, splicing, and in the case of exon sequences, translation.
Nucleotide sequences translation aligned using the MAFFT program [ 29] with the FFT-NS-i x1000 option in Geneious Pro 5.4.6 [ 28].
Sequences were aligned using Geneious R6 aligner and were visually inspected and corrected, if necessary, using amino acidic sequences (translation) as a guide.
The GO terms with the largest number of assigned sequences in the BP category were oxidation reduction (1,833 sequences), RNA metabolic process (1,402 sequences), catabolic process (1,259 sequences), translation (1,234 sequences) and response to stimulus (1,105 sequences).
Other genes included those involved in nucleotide metabolism (2 sequences), translation (2 sequences), energy metabolism (1 sequence), lipid metabolism (1 sequence), and metabolism of other amino acids (1 sequence).
Such a low number of differentially expressed genes suggests that differences between resistant and susceptible phenotypes are linked more to variation in gene sequences, translation, and/or variation of catalytic efficiencies than to regulatory differences.
