bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.02.01.635949

Complete mitochondrial genome assembly of two searobin species (genus Prionotus) and their phylogenetic relationships (Triglidae: Prionotinae)

Marin, A.·Alfaro, R.·Zelada-Mazmela, E.
View original source ↗Export metadata ↓

Abstract

Species from the genera Bellator and Prionotus, commonly known as searobins, are marine ray-finned fish that belong to the subfamily Prionotinae. These fish have evolved distinctive morphological features and specialized behaviors that enable them to walk along the seafloor while detecting buried prey. This unique adaptation makes them ideal candidates for studies in evolutionary genetics. However, their phylogenetic relationships remain poorly understood. In this study, we utilized publicly available genomic reads from the GenBank database to assemble the first complete mitochondrial genomes of three searobin species: Bellator militaris, Prionotus alatus, and P. stephanophrys. We conducted a comparative analysis of these mitochondrial genomes, including the first phylogenetic analysis of the Prionotinae based on complete mitogenomic data. The resulting circular contigs measured 16,765 base pairs for B. militaris, 16,602 base pairs for P. alatus, and 16,896 base pairs for P. stephanophrys. The three mitogenomes exhibited a typical vertebrate organization, which includes 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a putative control region. Notably, P. stephanophrys contained an additional tRNA-Leu and an extra non-coding region. A Bayesian phylogenetic analysis grouped all Bellator species into a monophyletic clade within Prionotinae, while the sister taxon Prionotus formed a separate monophyletic subclade. The findings of this research provide valuable insights into the phylogenetic relationships and evolutionary history of the genera Bellator and Prionotus. Clarifying the taxonomy of these species may also support future management and conservation efforts for these economically valuable species.

Source connections

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Marin, A., Alfaro, R., Zelada-Mazmela, E.. 2025-02-06. Complete mitochondrial genome assembly of two searobin species (genus Prionotus) and their phylogenetic relationships (Triglidae: Prionotinae). https://doi.org/10.1101/2025.02.01.635949

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

KEEP EXPLORING

Related preprints

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↗
bioRxiv2026

RNA isoform-resolved multiplexed sequencing with bioorthogonal barcoding

RNA isoform dysregulation drives disease pathogenesis and is the target of FDA-approved splice-switching therapeutics. However, multiplexed sequencing methods discard splice junction information because only 3' termini are barcoded and counted. Here, we repurpose acylation and click chemistries to conjugate bioorthogonal barcodes (bobcodes) directly onto multiple internal positions along cellular RNAs. Bobcoded RNAs from multiple samples are pooled for multiplexed cDNA synthesis, during which reverse transcriptase switches from each RNA template onto its tethered bobcode with greater than 99% accuracy in species mixing experiments. Bobcode attachment intervals set cDNA insert sizes without a library fragmentation step, and priming with poly(dT) or random hexamers selects between 3'-end counting and full-length isoform capture. A bioorthogonal barcode-sequencing (BOB-seq v0.1) drug screen identifies transcriptome-wide on- and off-target RNA splicing effects and outperforms existing multiplexing RNA sequencing methods in workflow simplicity, sample-to-sample variability, and barcoding accuracy. Bobcodes add isoform resolution to scalable multiplexed RNA sequencing.

genomics↗
bioRxiv2026

Structural polymorphism and population-variable coding capacity of HERV-K(HML-2) in human pangenomes

Approximately 8% of the human genome is derived from ancient retroviral infections. The most recently integrated of these endogenous retroviruses is the HERV-K(HML-2) clade, whose expression has been associated with cancer, amyotrophic lateral sclerosis, and embryogenesis. Studies of HERV expression, particularly HML-2, have relied predominantly on short-read sequencing. However, the high similarity among HML-2 proviruses prevents many short reads from being assigned uniquely to individual loci. We therefore compared haplotype-resolved long-read genome assemblies from 292 donors to resolve variation in proviral structure and coding capacity. Several loci previously thought to be fixed were structurally polymorphic. Tandem arrays occurred at 13 loci and contained up to six proviral copies in a single array. At 8q11.23, we identified a previously undescribed full-length provirus in one haplotype. All 583 other haplotypes carried a solo-LTR. We found that standard reference genomes failed to represent the coding capacity retained in many individuals, whose proviruses contained intact open reading frames despite disruptive mutations in the reference sequences. Short-read genotypes left 32.5% of the tested donor-variant pairs unresolved at sites associated with viral reading frames. These findings show why HML-2 expression must be interpreted in the context of the structural and coding alleles each individual carries.

genomics↗