Interpopulational and intrapopulational genetic diversity of the endangered Itasenpara bitterling (Acheilognathus longipinnis) with reference to its demographic history

Yamazaki, Y.; Uehara, Kazuhiko; Ikeya, Koki; Nishio, Masaki

doi:10.1007/s10592-019-01232-x

Cited by 5 publications

(3 citation statements)

References 48 publications

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“…In this study, we measured the genetic diversity of 120 individuals from six populations using 21 microsatellite markers of R. uyekii . The measured genetic diversity was H O = 0.496–0.642, showing a moderate level of genetic diversity compared to other carp families [ 29 , 30 ]. Acheilognathinae fishes exhibit extensive genetic diversity [ 29 , 30 ].…”

Section: Discussionmentioning

confidence: 93%

“…The measured genetic diversity was H O = 0.496-0.642, showing a moderate level of genetic diversity compared to other carp families [29,30]. Acheilognathinae fishes exhibit extensive genetic diversity [29,30]. Because Rhodeus uyekii has lower genetic diversity (H O = 0.766) than Acheilognathus koreensis, it may have problems with its ability to adapt to environmental changes and its evolutionary potential.…”

Section: Genetic Diversity and Population Structure Of R Uyekiimentioning

confidence: 94%

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Genetic Diversity and Population Structure of Rhodeus uyekii in the Republic of Korea Revealed by Microsatellite Markers from Whole Genome Assembly

Kim,

Park,

Jeong

et al. 2024

IJMS

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This study is the first report to characterize the Rhodus uyekii genome and study the development of microsatellite markers and their markers applied to the genetic structure of the wild population. Genome assembly was based on PacBio HiFi and Illumina HiSeq paired-end sequencing, resulting in a draft genome assembly of R. uyekii. The draft genome was assembled into 2652 contigs. The integrity assessment of the assemblies indicates that the quality of the draft assemblies is high, with 3259 complete BUSCOs (97.2%) in the database of Verbrata. A total of 31,166 predicted protein-coding genes were annotated in the protein database. The phylogenetic tree showed that R. uyekii is a close but distinct relative of Onychostoma macrolepis. Among the 10 fish genomes, there were significant gene family expansions (8–2387) and contractions (16–2886). The average number of alleles amplified by the 21 polymorphic markers ranged from 6 to 23, and the average PIC value was 0.753, which will be useful for evolutionary and genetic analysis. Using population genetic analysis, we analyzed genetic diversity and the genetic structures of 120 individuals from 6 populations. The average number of alleles per population ranged from 7.6 to 9.9, observed heterozygosity ranged from 0.496 to 0.642, and expected heterozygosity ranged from 0.587 to 0.783. Discriminant analysis of principal components According to the analysis method, the population was divided into three populations (BS vs. DC vs. GG, GC, MS, DC). In conclusion, our study provides a useful resource for comparative genomics, phylogeny, and future population studies of R. uyekii.

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Section: Discussionmentioning

confidence: 93%

Section: Genetic Diversity and Population Structure Of R Uyekiimentioning

confidence: 94%

Genetic Diversity and Population Structure of Rhodeus uyekii in the Republic of Korea Revealed by Microsatellite Markers from Whole Genome Assembly

Kim,

Park,

Jeong

et al. 2024

IJMS

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“…Neutral molecular markers have been frequently used in genetic studies for conservation purposes, e. g., the mitochondrial genome was used for Alburnus species (Briolay et al, 1998;Ketmaier et al, 2009;Kubanç et al, 2016) and microsatellites have also been used (Longwu et al, 2013). Although the various genetic markers for estimating genetic variation have their advantages, the use of microsatellites is still beneficial because they have several advantages that researchers exploit in a wide variety of applications (Khaefi et al, 2018;Kaczmarczyk, 2019;Yamazaki et al, 2020). Microsatellite DNA markers are extensively used for the estimation of the genetic variation between different fish populations in which there are the high levels of polymorphism due to small locus size, abundant in genomes and the codominant nature of Mendelian inheritance.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and population structure of Tarek (Alburnus tarichi), an endemic species to the Lake Van basin, Turkey

Çi̇ftçi

Eroğlu

Firidin

et al. 2021

Aquat. Living Resour.

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In this study, the genetic relationships of 804 tarek (Alburnus tarichi) samples from a total of 18 populations, including the potamodromus and resident individuals from Lake Van basin in eastern Turkey, were studied by using nine microsatellite loci. A total of 93 alleles was detected, and the average number of alleles per locus was 10.3 ± 3.39. The mean estimated observed and expected heterozygosity were 0.340 ± 0.016 and 0.362 ± 0.015, respectively, which indicated a low level of polymorphism. After Bonferroni correction (P < 0.0027), the multi-locus test applied to each population revealed that 12 out of 18 populations were in Hardy-Weinberg equilibrium (HWE) (P = 0.0120–0.9981). Analysis of molecular variance (AMOVA) showed more than 76% genetic variability within individuals and 19% among populations, which was significantly higher than zero (FST = 0.19), and furthermore, a low level of genetic variation was observed among individuals within populations (4.84%: FIS = 0.06). Bayesian clustering analysis indicated that the total genetic variation grouped into 3 clusters. Additionally, the significance test results revealed that 11 of the 18 populations are threatened with extinction due to recent bottleneck events.We conclude that the tarek populations from the Lake Van basin can be classified into distinct genetic groups, based on microsatellite information. In addition, our results provide essential information for the development of a management plan that conserves the tarek's genetic diversity and achieves a sustainable fishery.

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Genetic dynamics of a 11-year ex situ managed Itasenpara bitterling population

Yamazaki

Ikeya²

2022

Conserv Genet

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Interpopulational and intrapopulational genetic diversity of the endangered Itasenpara bitterling (Acheilognathus longipinnis) with reference to its demographic history

Cited by 5 publications

References 48 publications

Genetic Diversity and Population Structure of Rhodeus uyekii in the Republic of Korea Revealed by Microsatellite Markers from Whole Genome Assembly

Genetic Diversity and Population Structure of Rhodeus uyekii in the Republic of Korea Revealed by Microsatellite Markers from Whole Genome Assembly

Genetic diversity and population structure of Tarek (Alburnus tarichi), an endemic species to the Lake Van basin, Turkey

Genetic dynamics of a 11-year ex situ managed Itasenpara bitterling population

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