NEW YORK (GenomeWeb) – An international team led by researchers at the University of Oregon has gained new insights into vertebrate evolution from sequencing the genome of the spotted gar, Lepisosteus oculatus, a member of a ray-finned lineage.
In a Nature Genetics study published today, the team described some of the evolutionary findings for tetrapods and teleosts being fished from spotted gar genome.
The researchers uncovered more than tens of thousands of predicted protein-coding genes in the draft assembly of the spotted gar draft genome, which was annotated with help from transcriptome sequences for numerous gar tissues.
Through comparisons with sequences from two dozen other vertebrates, the team examined spotted gar relationships to other vertebrates and began untangling evolutionary features found in various vertebrate groups.
"Because of gar's phylogenetic position, slow rate of sequence evolution, dense genetic map, and ease of laboratory culture, this resource provides a unique bridge between tetrapods and teleost biomedical models," senior author John Postlethwait, a neuroscience researcher at the University of Oregon, and co-authors wrote.
Humans and other tetrapods descended from the lobe-finned fish lineage, a bony vertebrate group that split from the ray-finned fish lineage some 450 million years ago after two rounds of vertebrate whole-genome duplication. On the other side of this split, the ray-finned fish went on to diversify into teleosts or bony fish, which underwent another whole-genome duplications, and the spotted gar lineage, which did not.
The teleost duplication can make it tricky to compare genomes from the ray-finned and lobe-finned lineages, the researchers explained, prompting interest in genomes from representatives such as the spotted gar that did not undergo this duplication.
To that end, the team used Illumina sequencing to tackle genomic DNA from a female spotted gar captured in Louisiana, putting together a draft genome assembly that spanned 945 million bases and was covered to an average depth of 90-fold.
It also sequenced RNA in adult gar, gar embryos, and gar larvae, using the transcript sequences to investigate gene expression and predict gene models. The group also generated transcriptome sequences for the bowfin, a presumed relative of the gar.
Along with repetitive sequences, which make up roughly one-fifth of the spotted gar genome, the researchers estimated that the gar has the coding wherewithal to produce 21,443 proteins and nearly 2,600 non-coding RNAs.
Using sequences of 243 orthologous genes, they examined phylogenetic relationships for the spotted gar and 24 other jawed vertebrates — an analysis that verified the spotted gar and bowfin position in a lineage that's well separated from the bony fish.
Compared to the teleosts, the available evidence suggested the spotted gar and bowfin have experienced relatively pokey rates of evolutionary change, the team noted, perhaps reflecting the evolutionary boost offered by the additional round of whole-genome duplication in the bony fish.
With the newly available gar genome, the researchers went on to retrace chromosomal structures, gene family patterns, microRNA repertoires, and gene regulatory features in various vertebrates, using the gar as a signpost for defining ray-finned features present prior to the teleost duplication.
In the processes, they got a glimpse at pre-teleost duplication patterns for families of genes involved in development, circadian rhythm control, and vertebrate immunity, for example.
The genome sequence, transcriptome, and additional RT-PCR data also offered hints about the roots of tooth and scale enamel formation in vertebrates — a feature that another team tackled using gene expression data on the spotted gar, a study that was published in Nature last year.