High‐throughput SNP‐genotyping analysis of the relationships among Ponto‐Caspian sturgeon species

Abstract

Legally certified sturgeon fisheries require population protection and conservation methods, including DNA tests to identify the source of valuable sturgeon roe. However, the available genetic data are insufficient to distinguish between different sturgeon populations, and are even unable to distinguish between some species. We performed high-throughput single-nucleotide polymorphism (SNP)-genotyping analysis on different populations of Russian (Acipenser gueldenstaedtii), Persian (A. persicus), and Siberian (A. baerii) sturgeon species from the Caspian Sea region (Volga and Ural Rivers), the Azov Sea, and two Siberian rivers. We found that Russian sturgeons from the Volga and Ural Rivers were essentially indistinguishable, but they differed from Russian sturgeons in the Azov Sea, and from Persian and Siberian sturgeons. We identified eight SNPs that were sufficient to distinguish these sturgeon populations with 80% confidence, and allowed the development of markers to distinguish sturgeon species. Finally, on the basis of our SNP data, we propose that the A. baerii-like mitochondrial DNA found in some Russian sturgeons from the Caspian Sea arose via an introgression event during the Pleistocene glaciation.

Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations

“…A large number of SNP markers useful for conservation purposes was discovered and characterized using RAD sequencing for four tetraploid sturgeon species, A. naccarii from the Adriatic Sea (hatchery), A. gueldenstaedtii and A. persicus from the Caspian Sea and A. baerii from Siberia [ 104 ]. High-throughput SNP-genotyping analysis among Ponto-Caspian sturgeon species from the Caspian Sea region revealed that Russian sturgeons ( Acipenser gueldenstaedtii ) from the Volga and Ural Rivers were essentially indistinguishable, but they differed from the Russian sturgeons in the Azov Sea, and from Persian ( A. persicus ) and Siberian river ( A. baerii ) sturgeons [ 105 ]. A species-specific SNP pattern in the nuclear MHC II antigen gene in museum samples of a now-extinct Baltic sturgeon population allowed for the detection of both European sturgeon A. sturio and American sea sturgeon A. oxyrinchus alleles [ 106 ].…”

Re-Establishing Naturally Reproducing Sturgeon Populations in the Caspian Basin: A Wicked Problem in the Ural River

“…Progress in addressing the wicked Ural problem will require sustained and integrated efforts to answer a myriad of scientific questions at scale [169], and it stands to benefit from the availability of sophisticated and rapidly advancing technology that includes telemetric tagging systems to monitor fish movement, microsatellite and mitochondrial DNA analyses to differentiate fish populations, and sensors and other electronic devices to combat IUU fishing [142,[172][173][174][175]. Although the financial and logistical difficulties of deploying technology to study fish in the Caspian basin are well known contributors to the current shortage of information about sturgeon [106], it is encouraging to note that they are gradually coming into use [145,[176][177][178].…”

The mitochondrial gene order and CYTB gene evolution in insects

“…К настоящему времени применение NGS технологий стало рутинной процедурой, которую ис пользуют многие исследовательские группы, в том числе в России (Rastorguev et al, 2013;Nedoluzhko et al, 2016;Sokolov et al, 2016). Успех этих методов привел к экспо ненциальному росту количества отсеквенированных и аннотированных геномов (ядерных и митохондриальных), которые депонированы в различные общедоступные базы данных.…”