The Dark Side of Photosymbiosis: Elaborate Repeats with TEs and Unknown ORFs in Photosymbiotic Bivalves Made Exceptionally Big Metazoan Mitogenomes

Limited truly "complete" mitogenomes have been published for marine invertebrates, with many being partial and focused on protein-coding genes. Dispelling the traditional myth of "metazoan mitogenomes being highly conserved in size and gene order", long-read technologies have revealed novel structures and complexities in animal mitogenomes. Our investigation of PacBio-assembled mitogenomes of several marine bivalve species (family Cardiidae), revealed a photosymbiotic bivalve, Fragum sueziense, possesses one of the largest circular metazoan mitogenome (92,770 bp). Additionally, mitogenomes of photosymbiotic bivalves from the genera Fragum and Tridacna ranged from 22 to 92.8 kb, surpassing the more typical sizes in non-photosymbiotic cardiids ([~]14 to 19 kb). Those expansions in mitogenomes are attributed to elaborate, species-specific repetitive sequences in the major non-coding region (NCR) which manifest an inability to assemble "complete" mitogenomes from Illumina short reads (at 150 bp) alone; divergent nature of those NCRs also hinder interspecies alignment. However, we annotated supernumerary tRNAs, transposable element fragments and open reading frames in NCRs despite their hitherto unknown functions. We postulate that NCR inflation in these photosymbiotic species may be associated with elevated reactive oxygen species in their mantle and altered immune states due to host-symbiont interactions involving photosymbionts. More complete mitogenomes are needed to uncover novel genetic elements and their functions otherwise undocumented to science. SIGNIFICANCE STATEMENTMany published animal mitogenomes does not truly span the entirety of the major non-coding region (NCR), often due to the inability of short-read sequencing to confidently cover highly repetitive sequences. In this study, long-read sequencing enabled us to access "more complete" mitogenomes for a comparative analysis focused on the nature of the NCRs between photosymbiotic and non-photosymbiotic bivalves, and the elements within them. We not only uncovered one of the largest circular metazoan mitogenomes (Fragum sueziense), but also found ample genetic elements within the conventionally "non-coding" regions, including extensive elaborate repeat patterns, transposable elements and unknown open reading frames. To our knowledge, this is the first time extensive transposable elements have been reported in animal mitogenomes. Our study revealed extreme mitogenome expansions and complexities as potential costs to bivalve-algal photosymbiosis, and provide insights into metazoan symbiosis evolution.