Development of a set of SNP markers for population genetics of the red gorgonian (Paramuricea clavata), an emblematic species of the Mediterranean coralligenous

AbstractThe interaction of genetic susceptibility and dietary habits in cardiovascular disease (CVD) remains undetermined. The purpose of this study was to investigate whether a Mediterranean dietary style modified the genetic risk of developing CVD in a Chinese cohort. A total of 2098 subjects with dietary information from a Chinese community cohort (CVDFACTS) were enrolled. Candidate genes, including SNP markers rs1333049 (CDKN2B, 9p21.3), rs17465637 (MIA3, 1q41) and rs501120 (CXCL12, 10q11.21), were genotyped to analyze the association with future CVD. The impact of dietary pattern was also analyzed according to adherence to the diet using the Mediterranean Diet Score (MDS). After an average follow-up of 7.8 years, only the C risk allele of rs1333049 at chromosome 9p21.3 was associated with a higher risk of MI with either an additive [HR = 1.78, 95% CI:1.23–2.5] or a recessive model [HR = 2.40, 95% CI: 1.42–4.04], and the CC genotype had a higher risk of developing MI (p = 0.009, log-rank test). There was no significant difference in the association of the lipid profile with future CV outcomes among the MDS tertiles. However, the high MI risk of the CC genotype in individuals consuming a less healthy diet (MDS1) (HR: 6.39, 95% CI: 1.74–23.43) significantly decreased to 2.38 (95% CI: 0.57–10.04) in individuals consuming a healthier diet (MDS3), indicating that a healthier dietary pattern (higher MDS) modified the risk of developing MI in carriers of variants in CDKN2B. In conclusion, genetic variants of CDKN2B at 9p21 were significantly associated with future MI risk in a Chinese cohort, and the genetic risk of MI could be modified by a healthier diet.

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Population Genetics of VNTR Markers (TPO and 3’APOB Loci) in the Mediterranean Area (Albania, Greece and Italy)

Advances in Forensic Haemogenetics ◽

10.1007/978-3-642-78782-9_133 ◽

1994 ◽

pp. 487-489 ◽

Cited By ~ 2

Author(s):

G. De Benedictis ◽

G. Rose ◽

E. Falcone ◽

O. Semino ◽

M. De Luca ◽

...

Keyword(s):

Population Genetics ◽

Mediterranean Area ◽

The Mediterranean

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SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics

Malaria Journal ◽

10.1186/s12936-020-03440-0 ◽

2020 ◽

Vol 19 (1) ◽

Author(s):

Abebe A. Fola ◽

Eline Kattenberg ◽

Zahra Razook ◽

Dulcie Lautu-Gumal ◽

Stuart Lee ◽

...

Keyword(s):

Population Genetics ◽

Population Structure ◽

Microsatellite Markers ◽

Plasmodium Vivax ◽

Malaria Transmission ◽

Snp Markers ◽

North Coast ◽

High Quality ◽

Catchment Areas ◽

The Impact

Abstract Background Genomic surveillance of malaria parasite populations has the potential to inform control strategies and to monitor the impact of interventions. Barcodes comprising large numbers of single nucleotide polymorphism (SNP) markers are accurate and efficient genotyping tools, however may need to be tailored to specific malaria transmission settings, since ‘universal’ barcodes can lack resolution at the local scale. A SNP barcode was developed that captures the diversity and structure of Plasmodium vivax populations of Papua New Guinea (PNG) for research and surveillance. Methods Using 20 high-quality P. vivax genome sequences from PNG, a total of 178 evenly spaced neutral SNPs were selected for development of an amplicon sequencing assay combining a series of multiplex PCRs and sequencing on the Illumina MiSeq platform. For initial testing, 20 SNPs were amplified in a small number of mono- and polyclonal P. vivax infections. The full barcode was then validated by genotyping and population genetic analyses of 94 P. vivax isolates collected between 2012 and 2014 from four distinct catchment areas on the highly endemic north coast of PNG. Diversity and population structure determined from the SNP barcode data was then benchmarked against that of ten microsatellite markers used in previous population genetics studies. Results From a total of 28,934,460 reads generated from the MiSeq Illumina run, 87% mapped to the PvSalI reference genome with deep coverage (median = 563, range 56–7586) per locus across genotyped samples. Of 178 SNPs assayed, 146 produced high-quality genotypes (minimum coverage = 56X) in more than 85% of P. vivax isolates. No amplification bias was introduced due to either polyclonal infection or whole genome amplification (WGA) of samples before genotyping. Compared to the microsatellite panels, the SNP barcode revealed greater variability in genetic diversity between populations and geographical population structure. The SNP barcode also enabled assignment of genotypes according to their geographic origins with a significant association between genetic distance and geographic distance at the sub-provincial level. Conclusions High-throughput SNP barcoding can be used to map variation of malaria transmission dynamics at sub-national resolution. The low cost per sample and genotyping strategy makes the transfer of this technology to field settings highly feasible.

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Genome-wide analysis clarifies the population genetic structure of wild Gilthead Sea Bream (Sparus aurata)

10.1101/2020.07.06.189241 ◽

2020 ◽

Author(s):

Francesco Maroso ◽

Konstantinos Gkagkavouzis ◽

Sabina De Innocentiis ◽

Jasmien Hillen ◽

Fernanda do Prado ◽

...

Keyword(s):

Genetic Structure ◽

Sparus Aurata ◽

Snp Markers ◽

Gilthead Sea Bream ◽

Sea Bream ◽

Commercial Fishing ◽

North East ◽

The North ◽

In The Wild ◽

The Mediterranean

AbstractGilthead sea bream is an important target for both recreational and commercial fishing in Europe, where it is also one of the most important cultured fish. Its distribution range goes from the Mediterranean to the African and European coasts of the North-East Atlantic. So far, the genetic structure of this species in the wild has been studied with microsatellite DNA, but the pattern of differentiation could not be fully clarified. In this study, almost 1000 wild sea bream from 23 locations in the Mediterranean Sea and Atlantic ocean where genotyped at 1159 SNP markers, of which 18 potentially under selection. Neutral markers suggested the presence of a weak subdivision into three genetic clusters: Atlantic, West and East Mediterranean. This last group could be further subdivided into an Ionian/Adriatic and an Aegean group using outlier markers. Seascape analysis suggested that this differentiation was mainly due to difference in salinity, and this was also supported by preliminary genomic functional analysis. These results are of fundamental importance for the development of proper management of this species in the wild and are a first step toward the study of the potential genetic impact of the sea bream aquaculture industry.

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Population collapse of habitat-forming species in the Mediterranean: a long-term study of gorgonian populations affected by recurrent marine heatwaves

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2021.2384 ◽

2021 ◽

Vol 288 (1965) ◽

Author(s):

D. Gómez-Gras ◽

C. Linares ◽

A. López-Sanz ◽

R. Amate ◽

J. B. Ledoux ◽

...

Keyword(s):

Marine Protected Area ◽

Size Structure ◽

Term Study ◽

Temperate Reefs ◽

Long Term Study ◽

Recovery Capacity ◽

Paramuricea Clavata ◽

The Mediterranean ◽

Density And Biomass

Understanding the resilience of temperate reefs to climate change requires exploring the recovery capacity of their habitat-forming species from recurrent marine heatwaves (MHWs). Here, we show that, in a Mediterranean highly enforced marine protected area established more than 40 years ago, habitat-forming octocoral populations that were first affected by a severe MHW in 2003 have not recovered after 15 years. Contrarily, they have followed collapse trajectories that have brought them to the brink of local ecological extinction. Since 2003, impacted populations of the red gorgonian Paramuricea clavata (Risso, 1826) and the red coral Corallium rubrum (Linnaeus, 1758) have followed different trends in terms of size structure, but a similar progressive reduction in density and biomass. Concurrently, recurrent MHWs were observed in the area during the 2003–2018 study period, which may have hindered populations recovery. The studied octocorals play a unique habitat-forming role in the coralligenous assemblages (i.e. reefs endemic to the Mediterranean Sea home to approximately 10% of its species). Therefore, our results underpin the great risk that recurrent MHWs pose for the long-term integrity and functioning of these emblematic temperate reefs.

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Thread-like tentacles in the Mediterranean corals Paramuricea clavata and Corallium rubrum

Mediterranean Marine Science ◽

10.12681/mms.13807 ◽

2018 ◽

Cited By ~ 1

Author(s):

PABLO J LOPEZ-GONZALEZ ◽

LORENZO BRAMANTI ◽

PABLO ESCRIBANO-ÁLVAREZ ◽

MARIA-CARLA BENEDETTI ◽

IRENE MARTÍNEZ-BARALDÉS ◽

...

Keyword(s):

Aggressive Behavior ◽

Corallium Rubrum ◽

Paramuricea Clavata ◽

The Mediterranean

The occurrence of modified tentacles (i.e. thread-like tentacles) in the Mediterranean octocorals Paramuricea clavata and Corallium rubrum is reported. Colonies of four species of Mediterranean gorgonians were maintained in aquarium conditions for more than 5 months. The development of thread-like tentacles has been observed only in two of the four species. The presence of modified tentacles in other cnidarians has been usually associated with defensive/aggressive behavior. Our observations showed that thread-like tentacles in P. clavata and C. rubrum can also be used for feeding.

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