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[…] nknown functions (A and , online); the corresponding Pseudendoclonium ORFs are orf307, orf325, and orf361, respectively (). In addition, we found 5′ to cox2, one free-standing LAGLIDADG ORF in G. sarcinoidea (orf193) and two in G. planctonica (orf102 and orf174) that are highly similar to the proteins encoded by group I introns in the mitochondrial atp1 and chloroplast atpA genes of Pseudendoclonium. , Intronic genes and freestanding ORFs not usually found in green plant mitochondrial genomes are not included in these values. Duplicated genes were counted only once., Number of group I (GI) and group II (GII) introns is given., Non-overlapping repeat elements were mapped on each genome with RepeatMasker using as input sequences the repeats of at least 30 bp identified with REPuter., Unlike the Ulva mtDNAs whose genes are all encoded on the same DNA strand (; ; , ), the Gloeotilopsis and Pseudendoclonium genomes have their genes distributed between the two strands. The four Ulva genomes exhibit the same gene order but are substantially rearranged compared to ulotrichalean genomes. The Gloeotilopsis mtDNAs show slight differences in gene organization: nearly 90% of their conserved genes and free-standing ORFs form four syntenic blocks () and as inferred by GRIMM analysis, only four reversals are required to convert gene order in one genome to that of the other. Our comparison of G. planctonica and G. sarcinoidea mtDNAs with their Pseudendoclonium counterpart revealed seven and eight syntenic blocks (), respectively, with 11 and 12 reversals inferred using GRIMM., Gloeotilopsis planctonica mtDNA contains ten group I introns, seven of which are present in cox1, as well as one group II intron, whereas G. sarcinoidea mtDNA contains five group I introns (). The introns uncovered so far in ulvophycean mtDNAs represent 22 distinct insertion sites, half of which have not been identified in other clades of chlorophytes (see arrows in ). Note that a number of introns were not annotated or correctly annotated in the GenBank accessions of Ulvales; numerous changes related to intron types and insertion positions were introduced in the course of this study (). All known ORF-containing group I introns in ulvophycean mitochondria encode putative LAGLIDADG h […]

Pipeline specifications

Software tools RepeatMasker, REPuter, GRIMM
Organisms Tupiella akineta