Table 2.

Non-standard genes identified as freestanding ORFs in the chloroplast genomes compared in this study.

Taxon	ORFa	Coordinatesb	Conserved domain
Mesotaenium endlicherianum	519	108900–110459	Type II intron maturase MatK (CHL00002)
Zygnema circumcarinatum	531	66206–67801	Type II intron maturase MatK (CHL00002)
Spirogyra maxima	659	72632–74611	Phage integrase family (pfam00589) and integrase core domain (pfam00665)
Netrium digitus	132	102944–103342	Phage integrase family (pfam00589)
Roya obtusa / Roya anglica	268	96776–97582	Phage integrase family (pfam00589)
Staurastrum punctulatum	108	142226–142552	Phage DNA primase, D5 N terminal like domain (pfam08706)

^aReported here are the freestanding ORFs larger than 100 codons that revealed similarity (E-value threshold of 1e-08) with recognized protein domains in BlastP searches. Each ORF is identified by the number of amino acid residues in the encoded protein. ^bGenomic coordinates of the ORFs in the GenBank accessions provided in Table 1.