scholarly journals Using historical genome‐wide DNA to unravel the confused taxonomy in a songbird lineage that is extinct in the wild

2020 ◽  
Author(s):  
Pratibha Baveja ◽  
Kritika M. Garg ◽  
Balaji Chattopadhyay ◽  
Keren R. Sadanandan ◽  
Dewi M. Prawiradilaga ◽  
...  
Keyword(s):  
Genome Wide ◽  
In The Wild

scholarly journals Population genetics of the coral Acropora millepora: Towards a genomic predictor of bleaching

2019 ◽  
Author(s):  
Zachary L. Fuller ◽  
Veronique J.L. Mocellin ◽  
Luke Morris ◽  
Neal Cantin ◽  
Jihanne Shepherd ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Balancing Selection ◽  
Genome Wide Association ◽  
Conservation Strategies ◽  
Genome Sequences ◽  
Acropora Millepora ◽  
Genome Wide ◽  
A Genome ◽  
In The Wild

AbstractAlthough reef-building corals are rapidly declining worldwide, responses to bleaching vary both within and among species. Because these inter-individual differences are partly heritable, they should in principle be predictable from genomic data. Towards that goal, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We then obtained whole genome sequences for 237 phenotyped samples collected at 12 reefs distributed along the Great Barrier Reef, among which we inferred very little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin. We further used 213 of the samples to conduct a genome-wide association study of visual bleaching score, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for the use of genomics-based approaches in conservation strategies.

scholarly journals Genome-wide identification and characterization of mRNAs and lncRNAs involved in cold stress in the wild banana (Musa itinerans)

PLoS ONE ◽  
2018 ◽  
Vol 13 (7) ◽  
pp. e0200002 ◽  
Author(s):  
Weihua Liu ◽  
Chunzhen Cheng ◽  
Yuling Lin ◽  
Xu XuHan ◽  
Zhongxiong Lai
Keyword(s):  
Cold Stress ◽  
Genome Wide ◽  
In The Wild ◽  
Wild Banana ◽  
Musa Itinerans ◽  
Identification And Characterization

scholarly journals Conservation Genomic Analyses of African and Asiatic Cheetahs (Acinonyx jubatus) Across Their Current and Historical Species Range

2020 ◽  
Author(s):  
Stefan Prost ◽  
Ana Paula Machado ◽  
Julia Zumbroich ◽  
Lisa Preier ◽  
Sarita Mahtani-Williams ◽  
...  
Keyword(s):  
Mhc Class Ii ◽  
Conservation Status ◽  
Nuclear Data ◽  
East African ◽  
Acinonyx Jubatus ◽  
Original Distribution ◽  
Genome Wide ◽  
Genome Wide Data ◽  
In The Wild ◽  
Uncertain Future

SummaryCheetahs (Acinonyx jubatus) are majestic carnivores and the fastest land animals; yet, they are quickly heading towards an uncertain future. Threatened by habitat loss, human-interactions and illegal trafficking, there are only approximately 7,100 individuals remaining in the wild. Cheetahs used to roam large parts of Africa, and Western and Southern Asia. Today they are confined to about 9% of their original distribution. To investigate their genetic diversity and conservation status, we generated genome-wide data from historical and modern samples of all four currently recognized subspecies, along with mitochondrial DNA (mtDNA) and major histo-compatibility complex (MHC) data. We found clear genetic differentiation between the sub-species, thus refuting earlier assumptions that cheetahs show only little population differentiation. Our genome-wide nuclear data indicate that cheetahs from East Africa may be more closely related to A. j. soemmeringii than they are to A. j. jubatus. This supports the need for further research on the classification of cheetah subspecies, as East African cheetahs are currently included in the Southern Africa subspecies, A. j. jubatus. We detected stronger inbreeding in individuals of the Critically Endangered A. j. venaticus (Iran) and A. j. hecki (Northwest Africa), and show that overall genome-wide heterozygosity in cheetah is lower than that reported for other threatened and endangered felids, such as tigers and lions. Furthermore, we show that MHC class II diversity in cheetahs is generally higher than previously reported, but still lower than in other felids. Our results provide new and important information for efficient genetic monitoring, subspecies assignments and evidence-based conservation policy decisions.

scholarly journals Whole-genome modeling accurately predicts quantitative traits, as revealed in plants

2015 ◽  
Author(s):  
Laurent Gentzbittel ◽  
Cécile Ben ◽  
Mélanie Mazurier ◽  
Min-Gyoung Shin ◽  
Martin Triska ◽  
...  
Keyword(s):  
Phenotypic Variation ◽  
Symbiotic Nitrogen Fixation ◽  
Natural Populations ◽  
Whole Genome ◽  
Population Admixture ◽  
Admixture Proportion ◽  
Genome Wide ◽  
Polygenic Adaptation ◽  
In The Wild ◽  
Wild Legume

AbstractMany adaptive events in natural populations, as well as response to artificial selection, are caused by polygenic action. Under selective pressure, the adaptive traits can quickly respond via small allele frequency shifts spread across numerous loci. We hypothesize that a large proportion of current phenotypic variation between individuals may be best explained by population admixture.We thus consider the complete, genome-wide universe of genetic variability, spread across several ancestral populations originally separated. We experimentally confirmed this hypothesis by predicting the differences in quantitative disease resistance levels among accessions in the wild legume Medicago truncatula. We discovered also that variation in genome admixture proportion explains most of phenotypic variation for several quantitative functional traits, but not for symbiotic nitrogen fixation. We shown that positive selection at the species level might not explain current, rapid adaptation.These findings prove the infinitesimal model as a mechanism for adaptation of quantitative phenotypes. Our study produced the first evidence that the whole-genome modeling of DNA variants is the best approach to describe an inherited quantitative trait in a higher eukaryote organism and proved the high potential of admixture-based analyses. This insight contribute to the understanding of polygenic adaptation, and can accelerate plant and animal breeding, and biomedicine research programs.

scholarly journals Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes

2021 ◽  
Author(s):  
Adam Ciezarek ◽  
Antonia Ford ◽  
Graham Etherington ◽  
Kasozi Nasser ◽  
Milan Malinsky ◽  
...  
Keyword(s):  
Native Species ◽  
Cichlid Fish ◽  
Snp Markers ◽  
Whole Genome ◽  
The Novel ◽  
Genome Resequencing ◽  
Genome Wide ◽  
In The Wild ◽  
Snp Panel ◽  
Whole Genome Resequencing

Cichlid fish of the genus Oreochromis form the basis of the global tilapia aquaculture and fisheries industry. Non-native farmed tilapia populations are known to be widely distributed across Africa and to hybridize with native Oreochromis species. However, many species are difficult to distinguish morphologically, hampering attempts to maintain good quality farmed strains or to identify pure populations of native species. Here, we describe the development of a single nucleotide polymorphism (SNP) genotyping panel from whole-genome resequencing data that enables targeted species identification in Tanzania. We demonstrate that an optimized panel of 96 genome-wide SNPs based on FST outliers performs comparably to whole genome resequencing in distinguishing species and identifying hybrids. We also show this panel outperforms microsatellite-based and phenotype-based classification methods. Case studies indicate several locations where introduced aquaculture species have become established in the wild, threatening native Oreochromis species. The novel SNP markers identified here represent an important resource for assessing broodstock purity and helping to conserve unique endemic biodiversity, and in addition potentially for assessing broodstock purity in hatcheries.

scholarly journals A genome-wide scan study identifies a single nucleotide substitution in MC1R gene associated with white coat colour in fallow deer (Dama dama)

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Gerald Reiner ◽  
Tim Weber ◽  
Florian Nietfeld ◽  
Dominik Fischer ◽  
Christine Wurmser ◽  
...  
Keyword(s):  
Pigment Cell ◽  
Coat Colour ◽  
Fallow Deer ◽  
Receptor Protein ◽  
Gene Marker ◽  
Genome Wide ◽  
A Genome ◽  
Gene Test ◽  
In The Wild ◽  
Genome Wide Scan

Abstract Background The coat colour of fallow deer is highly variable and even white animals can regularly be observed in game farming and in the wild. Affected animals do not show complete albinism but rather some residual pigmentation resembling a very pale beige dilution of coat colour. The eyes and claws of the animals are pigmented. To facilitate the conservation and management of such animals, it would be helpful to know the responsible gene and causative variant. We collected 102 samples from 22 white animals and from 80 animals with wildtype coat colour. The samples came from 12 different wild flocks or game conservations located in different regions of Germany, at the border to Luxembourg and in Poland. The genomes of one white hind and her brown calf were sequenced. Results Based on a list of colour genes of the International Federation of Pigment Cell Societies (http://www.ifpcs.org/albinism/), a variant in the MC1R gene (NM_174108.2:c.143 T > C) resulting in an amino acid exchange from leucine to proline at position 48 of the MC1R receptor protein (NP_776533.1:p.L48P) was identified as a likely cause of coat colour dilution. A gene test revealed that all animals of the white phenotype were of genotype CC whereas all pigmented animals were of genotype TT or TC. The study showed that 14% of the pigmented (brown or dark pigmented) animals carried the white allele. Conclusions A genome-wide scan study led to a molecular test to determine the coat colour of fallow deer. Identification of the MC1R gene provides a deeper insight into the mechanism of dilution. The gene marker is now available for the conservation of white fallow deer in wild and farmed animals.

scholarly journals Osmotic stress induces phosphorylation of histone H3 at threonine 3 in pericentromeric regions of Arabidopsis thaliana

2015 ◽  
Vol 112 (27) ◽  
pp. 8487-8492 ◽  
Author(s):  
Zhen Wang ◽  
Juan Armando Casas-Mollano ◽  
Jianping Xu ◽  
Jean-Jack M. Riethoven ◽  
Chi Zhang ◽  
...  
Keyword(s):  
Osmotic Stress ◽  
Protein Kinases ◽  
Double Mutant ◽  
Histone H3 ◽  
Epigenetic Mark ◽  
Wild Type ◽  
Protein Coding ◽  
Transcriptional Reprogramming ◽  
Genome Wide ◽  
In The Wild

Histone phosphorylation plays key roles in stress-induced transcriptional reprogramming in metazoans but its function(s) in land plants has remained relatively unexplored. Here we report that an Arabidopsis mutant defective in At3g03940 and At5g18190, encoding closely related Ser/Thr protein kinases, shows pleiotropic phenotypes including dwarfism and hypersensitivity to osmotic/salt stress. The double mutant has reduced global levels of phosphorylated histone H3 threonine 3 (H3T3ph), which are not enhanced, unlike the response in the wild type, by drought-like treatments. Genome-wide analyses revealed increased H3T3ph, slight enhancement in trimethylated histone H3 lysine 4 (H3K4me3), and a modest decrease in histone H3 occupancy in pericentromeric/knob regions of wild-type plants under osmotic stress. However, despite these changes in heterochromatin, transposons and repeats remained transcriptionally repressed. In contrast, this reorganization of heterochromatin was mostly absent in the double mutant, which exhibited lower H3T3ph levels in pericentromeric regions even under normal environmental conditions. Interestingly, within actively transcribed protein-coding genes, H3T3ph density was minimal in 5′ genic regions, coincidental with a peak of H3K4me3 accumulation. This pattern was not affected in the double mutant, implying the existence of additional H3T3 protein kinases in Arabidopsis. Our results suggest that At3g03940 and At5g18190 are involved in the phosphorylation of H3T3 in pericentromeric/knob regions and that this repressive epigenetic mark may be important for maintaining proper heterochromatic organization and, possibly, chromosome function(s).

scholarly journals Balance between short and long isoforms of cFLIP regulates Fas-mediated apoptosis in vivo

2016 ◽  
Vol 113 (6) ◽  
pp. 1606-1611 ◽  
Author(s):  
Daniel R. Ram ◽  
Vladimir Ilyukha ◽  
Tatyana Volkova ◽  
Anton Buzdin ◽  
Albert Tai ◽  
...  
Keyword(s):  
Splice Variants ◽  
Death Receptor ◽  
Liver Cells ◽  
Caspase 8 ◽  
Differential Splicing ◽  
Genome Wide ◽  
In The Wild ◽  
Induced Apoptosis

cFLIP, an inhibitor of apoptosis, is a crucial regulator of cellular death by apoptosis and necroptosis; its importance in development is exemplified by the embryonic lethality in cFLIP–deficient animals. A homolog of caspase 8 (CASP8), cFLIP exists in two main isoforms: cFLIPL (long) and cFLIPR (short). Although both splice variants regulate death receptor (DR)-induced apoptosis by CASP8, the specific role of each isoform is poorly understood. Here, we report a previously unidentified model of resistance to Fas receptor-mediated liver failure in the wild-derived MSM strain, compared with susceptibility in C57BL/6 (B6) mice. Linkage analysis in F2 intercross (B6 x MSM) progeny identified several MSM loci controlling resistance to Fas-mediated death, including the caspase 8- and FADD-like apoptosis regulator (Cflar) locus encoding cFLIP. Furthermore, we identified a 21-bp insertion in the 3′ UTR of the fifth exon of Cflar in MSM that influences differential splicing of cFLIP mRNA. Intriguingly, we observed that MSM liver cells predominantly express the FLIPL variant, in contrast to B6 liver cells, which have higher levels of cFLIPR. In keeping with this finding, genome-wide RNA sequencing revealed a relative abundance of FLIPL transcripts in MSM hepatocytes whereas B6 liver cells had significantly more FLIPR mRNA. Importantly, we show that, in the MSM liver, CASP8 is present exclusively as its cleaved p43 product, bound to cFLIPL. Because of partial enzymatic activity of the heterodimer, it might prevent necroptosis. On the other hand, it prevents cleavage of CASP8 to p10/20 necessary for cleavage of caspase 3 and, thus, apoptosis induction. Therefore, MSM hepatocytes are predisposed for protection from DR-mediated cell death.

scholarly journals Genome-wide analysis clarifies the population genetic structure of wild gilthead sea bream (Sparus aurata)

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0236230
Author(s):  
Francesco Maroso ◽  
Konstantinos Gkagkavouzis ◽  
Sabina De Innocentiis ◽  
Jasmien Hillen ◽  
Fernanda do Prado ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Gilthead Sea Bream ◽  
Sea Bream ◽  
North East ◽  
Genome Wide ◽  
Distribution Ranges ◽  
In The Wild ◽  
The Mediterranean

Gilthead 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 ranges from the Mediterranean to the African and European coasts of the North-East Atlantic. Until now, the population genetic structure of this species in the wild has largely been studied using microsatellite DNA markers, with minimal genetic differentiation being detected. In this geographically widespread study, 958 wild gilthead sea bream from 23 locations within the Mediterranean Sea and Atlantic Ocean were genotyped at 1159 genome-wide SNP markers by RAD sequencing. Outlier analyses identified 18 loci potentially under selection. Neutral marker analyses identified weak subdivision into three genetic clusters: Atlantic, West, and East Mediterranean. The latter group could be further subdivided into an Ionian/Adriatic and an Aegean group using the outlier markers alone. Seascape analysis suggested that this differentiation was mainly due to difference in salinity, this being 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.

scholarly journals Spatio-Temporal Ecological and Evolutionary Dynamics in Natural Butterfly Populations (2015 Field Season)

2015 ◽  
Vol 38 ◽  
pp. 29-32
Author(s):  
Zachariah Gompert ◽  
Lauren Lucas
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Molecular Evolution ◽  
Natural Populations ◽  
Spatial And Temporal Variation ◽  
Long Term Study ◽  
Genome Wide ◽  
In The Wild ◽  
Long Term Studies

The study of evolution in natural populations has advanced our understanding of the origin and maintenance of biological diversity. For example, long term studies of wild populations indicate that natural selection can cause rapid and dramatic changes in traits, but that in some cases these evolutionary changes are quickly reversed when periodic variation in weather patterns or the biotic environment cause the optimal trait value to change (e.g., Reznick et al. 1997, Grant and Grant 2002). In fact, spatial and temporal variation in the strength and nature of natural selection could explain the high levels of genetic variation found in many natural populations (Gillespie 1994, Siepielski et al. 2009). Long term studies of evolution in the wild could also be informative for biodiversity conservation and resource management, because, for example, data on short term evolutionary responses to annual fluctuations in temperature or rainfall could be used to predict longer term evolution in response to directional climate change. Most previous research on evolution in the wild has considered one or a few observable traits or genes (e.g., Kapan 2001, Grant and Grant 2002, Barrett et al. 2008). We believe that more general conclusions regarding the rate and causes of evolutionary change in the wild and selection’s contribution to the maintenance of genetic variation could be obtained by studying genome-wide molecular evolution in a suite of natural populations. Thus, in 2012 we began a long term study of genome-wide molecular evolution in a series of natural butterfly populations in the Greater Yellowstone Area (GYA). This study will allow us to quantify the contribution of environment-dependent natural selection to evolution in these butterfly populations and determine whether selection consistently favors the same alleles across space and through time.

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