Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.01.13.632863

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

Tan, A. D. Y.·Li, R.·Li, J.
View original source ↗Export metadata ↓

Abstract

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.

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Tan, A. D. Y., Li, R., Li, J.. 2025-01-17. The Dark Side of Photosymbiosis: Elaborate Repeats with TEs and Unknown ORFs in Photosymbiotic Bivalves Made Exceptionally Big Metazoan Mitogenomes. https://doi.org/10.1101/2025.01.13.632863

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Genomic correlates of metastatic competence and progression in human melanoma

Genomic events and their timing that grant a primary tumour the competence to disseminate remain poorly defined. We performed sequencing of 247 stage I/II primary cutaneous melanomas (CMs) and 60 matched metastases without intervening therapy from a prospectively followed registry cohort with a median followup of 92 months, integrating copy-number, mutational, protein and spatial-transcriptomic analyses. Relapse was not distinguished by oncogenic point mutations, which were largely shared between primaries and metastases, but by somatic copy-number alterations (SCNAs) and global chromosomal instability. We defined OncoCycle, a six-gene copy-number signature (amplification of CDK4, MCL1 and CD276; biallelic loss of CDKN2A, CDKN2B and TP53BP1) that predicted relapse independently of established clinicopathological features in melanoma, and a pan-cancer analysis. In matched pairs, metastatic progression was driven by continued copy-number evolution and reduction in intra-tumoural heterogeneity, rather than by acquired point mutations, and OncoCycle alterations from primary tumours were preserved in metastasis seeding clones. Clonal reconstruction revealed both monoclonal and polyclonal metastasis seeding, and spatial transcriptomics resolved copy-number-defined metastatic subclones occupying and programming distinct immune and stromal niches. Thus, metastatic competence was primed early by focal SCNAs on a background of chromosomal instability, elaborated by continued copy-number evolution during dissemination and spatio-temporal interactions with the tumour-microenvironment.

genomics↗
bioRxiv2026

PfPHAST: Plasmodium falciparum Public Health Amplicon Sequencing Tool, a Streamlined Panel for Malaria Genomic Surveillance

Genomic tools can support malaria control policy through surveillance of Plasmodium falciparum populations, tracking antimalarial drug resistance, pfhrp2/3 deletions that compromise rapid diagnostic tests, and selection at the circumsporozoite protein (PfCSP) vaccine target, as well as through molecular correction of therapeutic efficacy studies (TES). Multiplex Amplicons for Drug, Diagnostic, Diversity, and Differentiation Haplotypes using Targeted Resequencing (MAD4HatTeR), a comprehensive amplicon sequencing panel covering up to 276 targets, supports these applications but is tailored to research rather than routine programmatic use. We developed P. falciparum Public Health Amplicon Sequencing Tool (PfPHAST), a 56-target derivative of MAD4HatTeR spanning drug resistance loci, pfhrp2/3 deletion, PfCSP genotyping, non-falciparum species identification, and 20 high-heterozygosity microhaplotype loci for TES classification. We compared PfPHAST and MAD4HatTeR using laboratory strain controls, including two-strain dilution series and a five-strain mixture, across parasite densities of 100 to 10,000 parasites/L. At matched per-target depth, PfPHAST achieved a higher quality-control pass rate than MAD4HatTeR (94.4% versus 90.0%) and distributed reads more evenly across targets. The panels showed comparable recall and precision for drug resistance codons and microhaplotypes, reaching near-complete recall above 40% within-sample allele frequency (WSAF) at all densities, with reduced sensitivity for minor alleles below 10% WSAF at low parasite density in both panels. Observed and expected WSAF correlated strongly for both panels, and both resolved a five-strain polyclonal mixture, including a 5% minor strain. By concentrating sequencing capacity on targets of greatest programmatic relevance, PfPHAST offers a scalable, lower-cost alternative to comprehensive research panels without sacrificing performance on shared targets, complementing MAD4HatTeR for routine molecular malaria surveillance.

genomics↗
bioRxiv2026

Structural variation in repeat elements is widespread in normal human tissues and in tumorigenesis

Somatic mosaicism contributes to genomic variation, yet postzygotic structural variants remain under-characterized. We performed long- and short-read WGS from multiple individuals (n=47 normal tissues; n=168 samples) and identified mosaic structural variants in all individuals and germ layers, impacting a median 285.2 kb/genome. Nearly half of breakpoints were independently validated, with tissue distributions reflecting both early and late developmental origins. Most mosaic variants were repeat-mediated and 8.3% overlapped functional elements, an enrichment compared to germline variants. To extend these analyses in samples where long-read sequencing is infeasible, we measured repeat alterations from short-read sequencing, recapitulating mosaic tissue-specific differences. We characterized tumor- and tissue- specific variation in repeats across 15 cancer types and found tumor-related repeat variation to be similar in scale to that of normal mosaic variation. Tracking repeat changes in cell-free DNA provided a noninvasive approach for tumor monitoring. Our analyses revealed widespread repeat-driven structural variation in health and disease.

genomics↗