Polyadenylated transcripts containing random gene fragments are expressed in dinoflagellate mitochondria

An AT-rich cDNA isolated from a Gonyaulax library was identified as a putative mitochondrial cytochrome oxidase subunit 3 (cox3) by sequence comparisons. Transcripts hybridizing to this cox3 probe are abundant, are found in poly(A) enriched RNA fractions and have a variable length when tested by Northern blot analysis. A PCR analysis of 21 cox3 clones, designed to measure the length of 5' and 3' ends separately, indicated that the greatest variability in length was found at the 3' end. The variable length of the 3' end may be due to polyadenylation at random sites or to a reduced stringency for polyadenylation signals. Eight cox3 cDNAs were completely sequenced, and were found to differ by up to thirteen bases in the regions of overlap. Curiously, the longest cDNA contained a 350 base pair fragment of a dinoflagellate cox1 gene and a 600 bp fragment of a cytochrome b (cob) gene in the region 3' to the cox3 sequence. Gene fragments or multiple copies of the cox3 and cob sequences may be abundant in the mitochondrial genome since Southern blots, using these sequences separately as probes, show multiple restriction fragments with several enzymes.