Both of these predicted enzymes are encoded in the Showa transcriptome at low to moderate sequence coverage.
Contigs with low to moderate sequence coverage have been identified for these two inferred enzymes in the B. braunii Showa transcriptome (Additional file 1: Table S15).
All three SSL enzymes are represented by curated contigs of moderate sequence coverage in the Showa transcriptome (Additional file 1: Table S8), with no additional SQS isozymes detectable.
Curated contig 30447 for RPE has moderate sequence coverage at 55.8 reads/kb, while reads for curated contig 32329 for TKTL are highly abundant at 436.6 reads/kb.
Contigs with low to moderate sequence coverage encoding predicted autophagy pathway proteins are present in the Showa transcriptome (Additional file 1: Table S17).
Two nonredundant curated contigs for two putative isozymes of FDPS with 72% amino acid identity were identified in the Showa transcriptome, both with moderate sequence coverage (Additional file 1: Table S7).
These pools were subsequently mapped back to their corresponding reference sequences using commonly applied alignment software and at a range of ultra-low to moderate sequencing coverage depths (0.1×, 0.5×, 1×, 2×, 4×, 8× and 16×).
Machine-assembled contigs with moderate to high sequence coverage, apparently derived from these long 3' UTRs, are abundant in the transcriptome database.
Contigs of moderate to high sequence coverage encode the presumed AccA, B and C (Additional file 1: Table S14), while contigs for AccD (carboxyl transferase β-subunit) was missing from the Showa transcriptome as expected for a plastid-encoded gene [ 98].
Thus, multiple contigs with moderate to high sequence coverage that encode putative very long chain fatty acid elongase (ELOVL5, E.C. 2.3.1.-), β-ketoacyl-CoA reductase (KAR, E.C. 1.1.1.-), 3-hydroxyacyl-CoA dehydratase (PHS1, E.C. 4.2.1.-), and enoyl-CoA reductase (TER, E.C. 1.3.1.-) enzymes have been found in the Showa transcriptome.
Machine-assembled contigs for all these deduced enzymes have been identified in the Showa transcriptome, with low (MetK, MmuM), low to moderate (MetH) and high to extremely high sequence coverage (AhcY, MetE, Additional file 1: Table S13).
