Abstract
Order Acipenseriformes contains 27 extant species distributed across the northern hemisphere, including so-called “living fossil” species of garfish and sturgeons. Previous studies have focused on their mitochondrial genetics and have rarely used nuclear genetic data, leaving questions as to their phylogenetic relationships. This study aimed to utilize a bioinformatics approach to screen for candidate single-copy nuclear genes, using transcriptomic data from sturgeon species and genomic data from the spotted gar, Lepisosteus oculatus. We utilized nested polymerase chain reaction (PCR) and degenerate primers to identify nuclear protein-coding (NPC) gene markers to determine phylogenetic relationships among the Acipenseriformes. We identified 193 nuclear single-copy genes, selected from 1850 candidate genes with at least one exon larger than 700 bp. Forty-three of these genes were used for primer design and development of 30 NPC markers, which were sequenced for at least 14 Acipenseriformes species. Twenty-seven NPC markers were found completely in 16 species. Gene trees according to Bayesian inference (BI) and maximum likelihood (ML) were calculated based on the 30 NPC markers (20,946 bp total). Both gene and species trees produced very similar topologies. A molecular clock model estimated the divergence time between sturgeon and paddlefish at 204.1 Mya, approximately 10% later than previous estimates based on cytochrome b data (184.4 Mya). The successful development and application of NPC markers provides a new perspective and insight for the phylogenetic relationships of Acipenseriformes. Furthermore, the newly developed nuclear markers may be useful in further studies on the conservation, evolution, and genomic biology of this group.
Highlights
In 2010, the International Union for Conservation of Nature (IUCN) Red List of ThreatenedSpecies concluded that “Sturgeon more critically endangered than any other group of species”.Considering IUCN Red List data, twenty-seven species of sturgeon are listed with 63 percent as Critically Endangered—the Red List’s highest category of threat
We aimed to develop a similar approach to generate new nuclear protein-coding (NPC) markers for phylogenetic analysis using a transcriptome plus reference genome strategy
We used a strategy of multi-sequence alignment of transcriptomes combined with spotted gar genomic data to develop single-copy NPC markers to construct the phylogenetics of Acipenseriformes
Summary
In 2010, the International Union for Conservation of Nature (IUCN) Red List of ThreatenedSpecies concluded that “Sturgeon more critically endangered than any other group of species”.Considering IUCN Red List data, twenty-seven species of sturgeon are listed with 63 percent as Critically Endangered—the Red List’s highest category of threat. In 2010, the International Union for Conservation of Nature (IUCN) Red List of Threatened. Species concluded that “Sturgeon more critically endangered than any other group of species”. Considering IUCN Red List data, twenty-seven species of sturgeon are listed with 63 percent as Critically Endangered—the Red List’s highest category of threat. Progress was made in recovery of North American species during the last decade, Genes 2019, 10, 38; doi:10.3390/genes10010038 www.mdpi.com/journal/genes. Genes 2019, 10, 38 the situation is dire for most Eurasian species. The latest update of the Red List assessed the status of 18 species of sturgeon from all over Europe and Asia and found that all were threatened Within the Eurasian species, some are on the brink of extinction [1]
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