To connect human biology to fish biomedical models, we sequenced the
genome of spotted gar (Lepisosteus oculatus), whose lineage
diverged from teleosts before the teleost genome duplication (TGD). The slowly
evolving gar genome conserved in content and size many entire chromosomes from
bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the
evolution of immunity, mineralization, and development (e.g., Hox, ParaHox, and
miRNA genes). Numerous conserved non-coding elements (CNEs, often
cis-regulatory) undetectable in direct human-teleost
comparisons become apparent using gar: functional studies uncovered conserved
roles of such cryptic CNEs, facilitating annotation of sequences identified in
human genome-wide association studies. Transcriptomic analyses revealed that the
sum of expression domains and levels from duplicated teleost genes often
approximate patterns and levels of gar genes, consistent with
subfunctionalization. The gar genome provides a resource for understanding
evolution after genome duplication, the origin of vertebrate genomes, and the
function of human regulatory sequences.
Genomic resources for hundreds of species of evolutionary, agricultural, economic, and medical importance are unavailable due to the expense of well-assembled genome sequences and difficulties with multigenerational studies. Teleost fish provide many models for human disease but possess anciently duplicated genomes that sometimes obfuscate connectivity. Genomic information representing a fish lineage that diverged before the teleost genome duplication (TGD) would provide an outgroup for exploring the mechanisms of evolution after whole-genome duplication. We exploited massively parallel DNA sequencing to develop meiotic maps with thrift and speed by genotyping F1 offspring of a single female and a single male spotted gar (Lepisosteus oculatus) collected directly from nature utilizing only polymorphisms existing in these two wild individuals. Using Stacks, software that automates the calling of genotypes from polymorphisms assayed by Illumina sequencing, we constructed a map containing 8406 markers. RNA-seq on two map-cross larvae provided a reference transcriptome that identified nearly 1000 mapped protein-coding markers and allowed genome-wide analysis of conserved synteny. Results showed that the gar lineage diverged from teleosts before the TGD and its genome is organized more similarly to that of humans than teleosts. Thus, spotted gar provides a critical link between medical models in teleost fish, to which gar is biologically similar, and humans, to which gar is genomically similar. Application of our F1 dense mapping strategy to species with no prior genome information promises to facilitate comparative genomics and provide a scaffold for ordering the numerous contigs arising from next generation genome sequencing.
The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin’s importance for illuminating vertebrate biology and diversity in the genomic era.
Small (4.4 ± 1.50 g; mean ± SD) Nile tilapias Oreochromis niloticus were more tolerant of nitrite than large (90.7 ± 16.43 g) fish. The 96‐h median lethal concentration of nitrite‐N to small fish was 81 mg/L (95% confidence interval = 35–127 mg/L) compared with 8 mg/L (4–11 mg/L) for large fish. Addition of chloride to test water (as either calcium chloride or sodium chloride) protected both small and large fish from nitrite. Sodium chloride and calcium chloride appeared to be similarly effective in inhibiting nitrite toxicity.
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