scholarly journals Development of a set of oligonucleotides for the identification of the Sakhalin sturgeon Acipenser mikadoi Hilgendorf, 1892 by PCR

2021 ◽  
Vol 4 ◽  
Author(s):  
Sergei Turanov
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Natural Populations ◽  
Individual Genome ◽  
Commercial Fish ◽  
Endangered Fish ◽  
Russian Territory ◽  
Sakhalin Sturgeon ◽  
D Loop ◽  
Rare And Endangered

Sturgeons (family Acipenseridae) are valuable commercial fish and aquaculture resources. The Acipenser genus includes about 20 species, 12 of which are recorded for the Russian territory. One of the rarest is the Sakhalin sturgeon A. mikadoi Hilgendorf, 1892. At present, its population size is significantly decreased and the species is close to extinction. Natural populations of the species have survived in the Tumnin River in Khabarovsk Region and the Viakhtu River in Sakhalin Region. Vihtu River in Sakhalin Region. Due to the small numbers of rare and endangered fish species, noninvasive approaches, including the use of DNA from the environment, appear to be the most suitable for monitoring their species and genetic diversity. The method is well established in this area and has been successfully tested for the monitoring of several species of rare and endangered sturgeons. This paper presents the results of the development of primers specific for the mitochondrial DNA of the species A. mikadoi. A matrix of 15 sequences of complete mitochondrial genomes from 3 sturgeon species whose ranges may overlap - A. mikadoi (KX276658), A. dauricus (KJ402277) and A. schrenckii (MH973728- MH973734, KX276660, KX276659, KF150287, KC905169, KC820796) - was generated. A. medirostris (NC_028405), which is genetically closest to the Sakhalin sturgeon, was also included in the analysis. A sliding window algorithm was applied to the sequence matrix. A graph showing the distribution of divergence values along the mitochondrial genome of sturgeon was plotted based on the results of the analysis Fig. 1. Based on matrices of individual genome fragments (16S rRNA, COI, ND1, and D-loop), a search for species-specific primers was performed in the DECIPHER program. A Primer-BLAST algorithm was run based on each pair of primers. Taxa Actinopterygii and Acipenseridae were used as references separately in different runs. In addition, primers were checked using local reference sequences of the complete mitochondrial genome of representatives of the genus Acipenser. The results of primer evaluation are summarized in the table Table 1. As a result, a combination of primer pairs developed on the basis of D-loop and COI fragments seems to be the most successful for error-free identification of Sakhalin sturgeon.

scholarly journals Complete mitochondrial genome of the Endangered fish Anabarilius liui yalongensis (Teleostei, Cyprinidae, Cultrinae)

2018 ◽  
Vol 4 (1) ◽  
pp. 21-22 ◽  
Author(s):  
Liwen Zeng ◽  
Kun Yang ◽  
Anxiang Wen ◽  
Meng Xie ◽  
Yongfang Yao ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Endangered Fish

The complete mitochondrial genome of the black star fat minnow (Rhynchocypris semotilus), an endemic and endangered fish of Korea

2015 ◽  
Vol 28 (1) ◽  
pp. 114-115 ◽  
Author(s):  
Jeong-Nam Yu ◽  
Byung-Jik Kim ◽  
Changmu Kim ◽  
Joo-Hong Yeo ◽  
Soonok Kim
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Endangered Fish

scholarly journals The phylogeny of the Anderson’s White-bellied Rat (Niviventer andersoni) based on complete mitochondrial genomes provides insight into its evolutionary history

2021 ◽  
Author(s):  
Shujing Liu ◽  
Lili Fu ◽  
Jihua Zhou ◽  
Jizhou Lv ◽  
Zhongyang Tan ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Gene Tree ◽  
Sister Group ◽  
Protein Coding ◽  
Mitogenome Sequence ◽  
D Loop ◽  
Coding Control ◽  
Rna Genes

Anderson’s White-bellied Rat, Niviventer andersoni (Thomas, 1911) (Muridae, Niviventer) is an species endemic to China. In the present study, we have sequenced the first complete mitochondrial genome of N. andersoni using next-generation sequencing. The 16,291 bp mitochondrial genome consists of 22 transfer RNA genes, 13 protein-coding genes (PCGs), two ribosomal RNA genes, and one non-coding control region (D-Loop). Phylogenetic analyses of the nucleotide sequences of all 13 PCGs, PCGs minus ND6 and the entire mitogenome sequence except for the D-loop, produce nearly identical, well-resolved topologies. Our results support that N. andersoni clustered with N. excelsior and form a sister group with N. confucianus, and they statistically reject the hypothesis from one cytochrome b (cytb) gene tree that N. confucianus is sister to N. fulvescens. Our research may be helpful to further reconsideration of clearer taxonomy and improve our understanding of mitogenomic evolution in the genus Niviventer.

scholarly journals The mitochondrial genome and phylogenetic characteristics of the Thick-billed Green-Pigeon, Treron curvirostra: the first sequence for the genus

ZooKeys ◽  
2021 ◽  
Vol 1041 ◽  
pp. 167-182
Author(s):  
Nan Xu ◽  
Jiayu Ding ◽  
Ziting Que ◽  
Wei Xu ◽  
Wentao Ye ◽  
...  
Keyword(s):  
Information System ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Base Pairs ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Close Relationship ◽  
D Loop ◽  
The Common

Members of the genus Treron (Columbidae) are widely distributed in southern Asia and the Indo-Malayan Region but their relationships are poorly understood. Better knowledge of the systematic status of this genus may help studies of historical biogeography and taxonomy. The complete mitochondrial genome of T. curvirostra was characterized, a first for the genus. It is 17,414 base pairs in length, containing two rRNAs, 22 tRNAs, 13 protein coding genes (PCGs), and one D-loop with a primary structure that is similar to that found in most members of Columbidae. Most PCGs start with the common ATG codon but are terminated by different codons. The highest value of the Ka/Ks ratio within 13 PCGs was found in ATP8 with 0.1937, suggesting that PCGs of the mitochondrial genome tend to be conservative in Columbidae. Moreover, the phylogenetic relationships within Columbidae, which was based on sequences of 13 PCGs, showed that (T. curvirostra + Hemiphaga novaeseelandiae) were clustered in one clade, suggesting a potentially close relationship between Treron and Hemiphaga. However, the monophyly of the subfamilies of Columbidae recognized by the Interagency Taxonomic Information System could not be corroborated. Hence, the position of the genus Treron in the classification of Columbidae may have to be revised.

scholarly journals Complete mitochondrial genome of Dong Tao chicken breed (Gallus gallus domesticus) of Vietnam

2020 ◽  
Vol 16 (4) ◽  
pp. 589-593
Author(s):  
Dang Ton Nguyen ◽  
Nguyen Hai Ha ◽  
Vu Phuong Nhung ◽  
Nguyen Thi Thanh Hoa ◽  
Ma Thi Huyen Thuong ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Gallus Gallus ◽  
Nucleotide Composition ◽  
Gallus Domesticus ◽  
Rrna Genes ◽  
Trna Genes ◽  
Gallus Gallus Domesticus ◽  
Chicken Breed ◽  
D Loop

The complete mitochondrial genome of Dong Tao chicken breed (Gallus gallus domesticus, Dong Tao) was obtained by PCR and sequencing. The complete mitogenome was 16,783 bp in length, with the nucleotide composition for A, T, C, G was 30.29%, 23.75%, 32.48%, and 13.48%, respectively. The mitogenome of Dong Tao chicken contained a non-coding control region (D-loop), 2 rRNA genes, 13 protein-coding genes, and 22 tRNA genes. Phylogenetic analysis revealed that breed Dong Tao chicken breed was sister-close to G. gallus breed Guangxi, and paraphyletic to G. spadiceus, S. jabouillei, and a range of Chinese indigenous, ie. breeds Rugao and Taoyuan.

scholarly journals MODERN STATUS AND PROSPECTS OF ARTIFICIAL BREEDING OF RARE, EXTINCTING FISH SPECIES FOR CONSERVATION OF BIODIVERSITY AND RESTORATION OF ABUNDANCE IN NATURAL WATER RESERVES OF THE ILE-BALKHASH BASIN

2019 ◽  
pp. 17-30
Author(s):  
Maral Aydynkyzy Zhaparova ◽  
Saule Zhangirovna Asylbekova ◽  
Damir Kayirkeldyevich Zharkenov ◽  
Kuanysh Baibulatovich Isbekov ◽  
Vyacheslav Nickolaevich Tsoy
Keyword(s):  
Fish Species ◽  
Large Scale ◽  
Irrigation System ◽  
Food Competition ◽  
Artificial Reproduction ◽  
Commercial Fish ◽  
Endangered Fish ◽  
The Status ◽  
Acipenser Nudiventris ◽  
Rare And Endangered

This article presents materials on the current state of the native ichthyofauna of the Ile-Balkhash basin, affected by large-scale acclimatization works. Four species of the ichthyofauna composition are listed in the Red Book of Kazakhstan: spike ( Acipenser nudiventris Lovetsky, 1828), Aral barbel ( Barbus brachycephalus brachycephalus Kessler, 1872), Balkhash marinka ( Schizothorax argentatus argentatus Kessler, 1874), Balkhash perch ( Perca schrenkii Kessler, 1874). Due to the ineffectiveness of fish conservation measures, including the prohibition for catching of these fish species, which are not found anywhere except in the Ile-Balkhash basin, it is necessary to impose artificial reproduction, changes in the Fishery Rules and organization of commercial rearing. The work is based on research materials of 2001-2018 conducted in Lake Balkhash, the delta and the lower reaches of the Ile and the Tokraun. The status of spike populations ( Acipenser nudiventris Lovetsky, 1828), Aral barbel ( Barbus brachycephalus brachycephalus Kessler, 1872), Balkhash marinka ( Schizothorax argentatus argentatus Kessler, 1874) and Balkhash perch ( Perca schrenkii Kessler, 1874). The main reasons preventing the maintenance of a high number of endangered species have been established: small area of natural spawning grounds, death of fry in linmeshing fishing gear, large-scale poaching (spike); deterioration of conditions for the natural reproduction, mass mortality of young fishes in the irrigation system (Aral barbel); total elimination and food competition with pike perch (Balkhash marinka, Balkhash perch). The prospects for preservation of rare and endangered fish species have been considered, recommendations for breeding and replenishing populations of species listed in the Red Book have been given: measures for artificial reproduction and prevention of juvenile death, creating favorable conditions for fattening and reducing the pressure of trophic competition. Without taking adequate measures for reducing the anthropogenic impact on natural resources, including ichthyofauna, the number of main commercial fish species will decrease, rare species of fish will die out.

scholarly journals Complete mitochondrial genome of the nesting Colombian Caribbean loggerhead turtle: first approach of tRNAs and phylogenetic analysis

2018 ◽  
Vol 23 (3) ◽  
pp. 355-381 ◽  
Author(s):  
Javier Hernández-Fernández ◽  
Katherin Otálora
Keyword(s):  
Mitochondrial Genome ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Population Decline ◽  
3D Structure ◽  
Loggerhead Turtle ◽  
Nucleotide Composition ◽  
Marine Turtle ◽  
D Loop

The loggerhead marine turtle, Caretta caretta, is a widely distributed and endangered species that is facing critical population decline, especially in Colombian Caribbean rookeries. Mitochondrial DNA sequence data are of great importance for the description, monitoring, and phylogenetic analyses of migratory turtle populations. In this study, the first full mitochondrial genome of a loggerhead turtle nesting in the Colombian Caribbean was sequenced and analyzed. This mitochondrial genome consists of 16 362 bp with a nucleotide composition of T: 25.7 %, C: 27 %, A: 35 % and G: 12 %. Sequence annotation of the assembled molecule revealed an organization and number of coding and functional units as reported for other vertebrate mitogenomes. This Colombian loggerhead turtle (Cc-AO-C) showed a novel D-Loop haplotype consisting of thirteen new variable sites, sharing 99.2 % sequence identity with the previously reported Caribbean loggerhead CC-A1 D-Loophaplotype. All 13 protein-coding genes in the Cc-AO-C mitogenome were compared and aligned with those from four other loggerhead turtles from different locations (Florida, Greece, Peru, and Hawaii). Eleven of these genes presented moderate genetic diversity levels, and genes COII and ND5 showed the highest diversity, with average numbers of pair-wise differences of 16.6 and 25, respectively. In addition, the first approach related to t-RNAs 2D and 3D structure analysis in this mitogenome was conducted, leading to observed unique features in two tRNAs (tRNATrp and tRNALeu). The marine turtle phylogeny was revisited with the newly generated data. The entire mitogenome provided phylogenetically informative data, as well as individual genes ND5, ND4, and 16S. In conclusion, this study highlights the importance of complete mitogenome data in revealing gene flow processes in natural loggerhead turtle populations, as well as in understanding the evolutionary history of marine turtles.

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