Microsatellite DNA variation among samples of bronze gudgeon, Coreius heterodon, in the mainstem of the Yangtze River, China

Cheng, Fei; Li, Wei; Wu, Qingping; Hallerman, Eric M.; Xie, Shuguang

doi:10.1007/s10228-012-0329-4

Cited by 12 publications

(7 citation statements)

References 25 publications

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“…Although the complete mitochondrial genome has been reported [ 25 – 27 ], available sequences in S . sinensis were still limited compared to other Gobioninae fish species, such as Gobiocypris rarus [ 28 ], Hemibarbus maculates [ 29 ], Coreius heterodon [ 30 ], etc.…”

Section: Introductionmentioning

confidence: 99%

De novo assembly, characterization and annotation for the transcriptome of Sarcocheilichthys sinensis

et al. 2017

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The Chinese lake gudgeon Sarcocheilichthys sinensis is a small cyprinid fish with great aquaculture potential both for its edible and ornamental values. Nevertheless, available genomic and transcriptomic information for this fish is extremely deficient. In this study, a normalized cDNA library was constructed using 13 mixed tissues of an adult male S. sinensis, and was sequenced by the Illumina HiSeq2500 platform. De novo assembly was performed using 38,911,511 obtained clean reads, and a total of 147,282 unigenes with an average length of 900 bp were finally achieved. 96.2% of these unigenes were annotated in 9 public databases, and 16 segments of growth-related genes were identified for future studies. In addition, 28,493 unigenes were assigned to 61 subcategories of Gene Ontology (GO), and 10,483 unigenes were assigned to 25 categories of Cluster of Orthologous Group (COG). Moreover, 14,943 unigenes were classified into 225 pathways of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. A total of 30,666 microsatellites were detected from 17,627 unigenes with an average distribution density of 1:2405 bp. This transcriptome data set will be valuable for researches on discovery, expression and evolution on genes of interest. Meanwhile, the identified microsatellites would be useful tools for genetic and genomic studies in S. sinensis.

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Section: Introductionmentioning

confidence: 99%

De novo assembly, characterization and annotation for the transcriptome of Sarcocheilichthys sinensis

et al. 2017

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“…The upper Yangtze River is located upstream from Yichang (30°41 0 N, 111°17 0 E) and is divided into three segments, i.e., the headstream, the Jinsha segment, and the upper mainstem. It harbors a diverse fish fauna Cheng et al 2013a) and is one of the ''Global 200 Ecoregions'' of the World Wildlife Fund (Olson and Dinerstein 1998). In this river, the construction of the Three Gorges Reservoir alone was thought to threaten 20 endemic species and to cause high extinction risk for six fish species mainly due to the environmental changes occurring in the reservoir after filling (Park et al 2003), so the further ten dams that are under construction may be expected to cause even more-severe effects on fish fauna and biodiversity.…”

Section: Introductionmentioning

confidence: 99%

Potential effects of dam cascade on fish: lessons from the Yangtze River

Cheng

Castello

et al. 2015

Rev Fish Biol Fisheries

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132

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Construction of hydroelectric dams affect river ecosystems, fish diversity, and fisheries yields. However, there are no studies assessing the combined effects on fish caused by several adjacent dams and their reservoirs, as in a 'dam cascade'. This study predicts the potential effects that a cascade of ten dams currently under construction in the upper Yangtze River in China will have on local fishes, and uses such predictions to assess the effectiveness of possible fish conservation measures. We found that the dam cascade will have serious combined effects on fishes mainly due to impoundment, habitat fragmentation and blocking, flow regime modification, and hypolimnetic discharges. The impoundments will cause loss of critical habitats for 46 endemic species. The dams will fragment the populations of 134 species and will block migration routes for 35 potamodromous fishes.Corieus guichenoti will have a high risk of extinction due to the combined effects of impoundment and blocking. Modification of the flow regime will adversely affect the recruitment of 26 species that produce drifting eggs. The start of annual spawning for 13 fishes will be postponed by more than 1 month, and fish spawning and growth opportunities will be reduced due to low water temperatures associated with hypolimnetic discharges. Combined dam effects will further reduce the likelihood of successful recruitment of some endangered species, such as Acipenser dabryanus and Psephurus gladius. Three countermeasures hold promise to mitigate the nearterm effects of the dam cascade, including preservation and rehabilitation of critical habitat, restoration of a semi-natural flow regime, and stock enhancement that respects genetic integrity. These conclusions can guide the development of protection plans for fishes in the upper Yangtze River. The approach undertaken in this study-by which the known and likely effects of present and future dams were simultaneously Electronic supplementary material The online version of this article (doi:10.1007/s11160-015-9395-9) contains supplementary material, which is available to authorized users. 123Rev Fish Biol Fisheries (2015) 25:569-585 DOI 10.1007 considered in light of the biology of the specieshighlights the usefulness of ichthyology for fish conservation.

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“…Assuming a two-year age-at-maturity (based on our experience breeding the species), the 21-29 generations of S. hilarii since construction of the dams may have been too short a time for the signatures of demographic processes (population contraction or expansion) or genetic differentiation (due to selection or drift) to become apparent in molecular genetic data sets. This was the case also for bronze gudgeon Coreius heterodon populations separated by dams in the Yangtze River in China (Cheng et al, 2013).…”

Section: Within-population Genetic Variabilitymentioning

confidence: 56%

Genetic structuring of Salminus hilarii Valenciennes, 1850 (Teleostei: Characiformes) in the rio Paraná basin as revealed by microsatellite and mitochondrial DNA markers

et al. 2015

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Genetic variation of Salminus hilarii was assessed by screening microsatellite loci and mitochondrial D-loop DNA across four sampling in the upper rio Paraná basin of Brazil. Genetic diversity -measured as mean expected heterozygosity (0.904) and mean number of alleles across populations (13.7) -was reasonably high. Differentiation of microsatellite allele frequencies among populations was shown to be low but significant by AMOVA Φ ST (0.0192), and high by D EST (0.185). D-loop variation was high, with haplotypic diversity of 0.950 and nucleotide diversity of 0.011. Mitochondrial DNA-based estimates for population differentiation were high, with an overall Φ ST of 0.173. The results of tests of nuclear and mitochondrial variation yielded no unequivocal inference of historical demographic bottleneck or expansion. Genetic differentiation observed among S. hilarii populations in the rio Grande may be caused by a combination of historical differentiation and recent gene-flow disruption caused by the dams followed by reproduction of isolated spawning assemblages in mid-sized tributaries of the respective reservoirs. We present spatially more intensive sampling of S. hilarii populations across the rio Paraná basin in order to more effectively distinguish between historical and contemporary differentiation.A variabilidade genética de Salminus hilarii foi avaliada por lócus microssatélites e sequências D-Loop do DNA mitocondrial em quatro populações da região da bacia do Alto Paraná. A diversidade genética -medida pela heterozigosidade média (0,904) e número de alelos médios das populações (13,7) -foi razoavelmente alta. A diferenciação das frequências alélicas entre as populações foi baixa, mas significativa pela AMOVA Φ ST (0,0192), e alta pelo D EST (0,185). A variação mitocondrial foi alta com uma diversidade haplotípica de 0,950 e uma diversidade nucleotídica de 0,011. Estimativas de diferenciação populacional baseadas no DNA mitocondrial foram altas, com um valor global de Φ ST de 0,173. Os resultados dos testes da variação nuclear e mitocondrial demonstram nenhuma inequívoca inferência histórica de contração e expansão demográfica. A diferenciação genética observada entre as populações de S. hilarii no rio Grande pode ter sido causada pela combinação de diferenciação histórica e interrupção recente do fluxo gênico causada pela construção de barragens seguida por um isolamento reprodutivo de populações em tributários de médio porte dos respectivos reservatórios. Nós apresentamos uma amostragem mais ampla e intensiva de populações de S. hilarii ao longo da bacia do alto rio Paraná para se efetivamente distinguir se a diferenciação genética das populações encontrada é histórica ou contemporânea.

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Microsatellite DNA variation among samples of bronze gudgeon, Coreius heterodon, in the mainstem of the Yangtze River, China

Cited by 12 publications

References 25 publications

De novo assembly, characterization and annotation for the transcriptome of Sarcocheilichthys sinensis

De novo assembly, characterization and annotation for the transcriptome of Sarcocheilichthys sinensis

Potential effects of dam cascade on fish: lessons from the Yangtze River

Genetic structuring of Salminus hilarii Valenciennes, 1850 (Teleostei: Characiformes) in the rio Paraná basin as revealed by microsatellite and mitochondrial DNA markers

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