Raw sequence data and analytical resources for: Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic

Background Phylogenetic gaps of public databases of reference sequences
are a major obstacle for comparative genomics and management of marine
resources, particularly in the Global South, where economically important
fisheries and conservation flagship species often lack closely-related
references. We applied target-enrichment to obtain complete mitochondrial
genomes of marine ichthyofauna from the Brazilian coast selected based on
economic significance, conservation status and lack of
phylogenetically-close references. These included sardines (Dorosomatidae,
Alosidae), mackerels (Scombridae) croakers (Sciaenidae), groupers
(Epinephelidae) and snappers (Lutjanidae). Results Custom baits were
designed to enrich mitochondrial DNA across a broad phylogenetic range of
fishes. Sequencing generated approximately 100k reads per sample, which
were assembled in a total of 70 complete mitochondrial genomes and include
fifty-two new additions to GenBank, including five species with no
previous mitochondrial data. Departures from the typical gene content and
order occurred in only three taxa and mostly involved tRNA gene
duplications. Start-codons for all genes, except Cytochrome C Oxidase
subunit I (COI), were consistently ATG, whilst a wide range of stop-codons
deviated from the prevailing TAA. Phylogenetic analysis confirmed assembly
accuracy and revealed signs of cryptic diversification within the Mullus
genus. Lineage delimitation methods using Sardinella aurita and S.
brasiliensis mitochondrial genomes support a single Operational Taxonomic
Unit. Conclusions Target enrichment was highly efficient, providing
complete novel mitochondrial genomes with little sequencing effort. These
sequences are deposited in public databases to enable subsequent studies
in population genetics and adaptation of Latin American fish species and
serve as a vital resource for conservation and management programs that
rely on molecular data for species and genus-level identification.