scholarly journals Decimation by sea star wasting disease and rapid genetic change in a keystone species, Pisaster ochraceus

2018 ◽  
Vol 115 (27) ◽  
pp. 7069-7074 ◽  
Author(s):  
Lauren M. Schiebelhut ◽  
Jonathan B. Puritz ◽  
Michael N Dawson
Keyword(s):  
Population Dynamics ◽  
Allele Frequency ◽  
Keystone Species ◽  
Allele Frequencies ◽  
Sea Star ◽  
Sequencing Data ◽  
Wasting Disease ◽  
Genomic Change ◽  
Study Region ◽  
Pisaster Ochraceus

Standing genetic variation enables or restricts a population’s capacity to respond to changing conditions, including the extreme disturbances expected to increase in frequency and intensity with continuing anthropogenic climate change. However, we know little about how populations might respond to extreme events with rapid genetic shifts, or how population dynamics may influence and be influenced by population genomic change. We use a range-wide epizootic, sea star wasting disease, that onset in mid-2013 and caused mass mortality in Pisaster ochraceus to explore how a keystone marine species responded to an extreme perturbation. We integrated field surveys with restriction site-associated DNA sequencing data to (i) describe the population dynamics of mortality and recovery, and (ii) compare allele frequencies in mature P. ochraceus before the disease outbreak with allele frequencies in adults and new juveniles after the outbreak, to identify whether selection may have occurred. We found P. ochraceus suffered 81% mortality in the study region between 2012 and 2015, and experienced a concurrent 74-fold increase in recruitment beginning in late 2013. Comparison of pre- and postoutbreak adults revealed significant allele frequency changes at three loci, which showed consistent changes across the large majority of locations. Allele frequency shifts in juvenile P. ochraceus (spawned from premortality adults) were consistent with those seen in adult survivors. Such parallel shifts suggest detectable signals of selection and highlight the potential for persistence of this change in subsequent generations, which may influence the resilience of this keystone species to future outbreaks.

scholarly journals A simple method to estimate the in-house limit of detection for genetic mutations with low allele frequencies in whole-exome sequencing analysis by next-generation sequencing

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Takumi Miura ◽  
Satoshi Yasuda ◽  
Yoji Sato
Keyword(s):  
Next Generation Sequencing ◽  
Allele Frequency ◽  
Somatic Mutations ◽  
Limit Of Detection ◽  
Allele Frequencies ◽  
Genetic Mutations ◽  
Sequencing Data ◽  
Simple Method ◽  
Whole Exome ◽  
Generation Sequencing

Abstract Background Next-generation sequencing (NGS) has profoundly changed the approach to genetic/genomic research. Particularly, the clinical utility of NGS in detecting mutations associated with disease risk has contributed to the development of effective therapeutic strategies. Recently, comprehensive analysis of somatic genetic mutations by NGS has also been used as a new approach for controlling the quality of cell substrates for manufacturing biopharmaceuticals. However, the quality evaluation of cell substrates by NGS largely depends on the limit of detection (LOD) for rare somatic mutations. The purpose of this study was to develop a simple method for evaluating the ability of whole-exome sequencing (WES) by NGS to detect mutations with low allele frequency. To estimate the LOD of WES for low-frequency somatic mutations, we repeatedly and independently performed WES of a reference genomic DNA using the same NGS platform and assay design. LOD was defined as the allele frequency with a relative standard deviation (RSD) value of 30% and was estimated by a moving average curve of the relation between RSD and allele frequency. Results Allele frequencies of 20 mutations in the reference material that had been pre-validated by droplet digital PCR (ddPCR) were obtained from 5, 15, 30, or 40 G base pair (Gbp) sequencing data per run. There was a significant association between the allele frequencies measured by WES and those pre-validated by ddPCR, whose p-value decreased as the sequencing data size increased. By this method, the LOD of allele frequency in WES with the sequencing data of 15 Gbp or more was estimated to be between 5 and 10%. Conclusions For properly interpreting the WES data of somatic genetic mutations, it is necessary to have a cutoff threshold of low allele frequencies. The in-house LOD estimated by the simple method shown in this study provides a rationale for setting the cutoff.

scholarly journals Accurate allele frequencies from ultra-low coverage pool-seq samples in evolve-and-resequence experiments

2018 ◽  
Author(s):  
Susanne Tilk ◽  
Alan Bergland ◽  
Aaron Goodman ◽  
Paul Schmidt ◽  
Dmitri Petrov ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Model Organism ◽  
Software Tool ◽  
Allele Frequencies ◽  
Model Organisms ◽  
Sequencing Data ◽  
High Coverage ◽  
Next Generation Sequencing Technology ◽  
Low Coverage ◽  
Pooled Samples

AbstractEvolve-and-resequence (E+R) experiments leverage next-generation sequencing technology to track the allele frequency dynamics of populations as they evolve. While previous work has shown that adaptive alleles can be detected by comparing frequency trajectories from many replicate populations, this power comes at the expense of high-coverage (>100x) sequencing of many pooled samples, which can be cost-prohibitive. Here, we show that accurate estimates of allele frequencies can be achieved with very shallow sequencing depths (<5x) via inference of known founder haplotypes in small genomic windows. This technique can be used to efficiently estimate frequencies for any number of bi-allelic SNPs in populations of any model organism founded with sequenced homozygous strains. Using both experimentally-pooled and simulated samples of Drosophila melanogaster, we show that haplotype inference can improve allele frequency accuracy by orders of magnitude for up to 50 generations of recombination, and is robust to moderate levels of missing data, as well as different selection regimes. Finally, we show that a simple linear model generated from these simulations can predict the accuracy of haplotype-derived allele frequencies in other model organisms and experimental designs. To make these results broadly accessible for use in E+R experiments, we introduce HAF-pipe, an open-source software tool for calculating haplotype-derived allele frequencies from raw sequencing data. Ultimately, by reducing sequencing costs without sacrificing accuracy, our method facilitates E+R designs with higher replication and resolution, and thereby, increased power to detect adaptive alleles.

scholarly journals Virome Variation during Sea Star Wasting Disease Progression in Pisaster ochraceus (Asteroidea, Echinodermata)

Viruses ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1332
Author(s):  
Ian Hewson ◽  
Citlalli A. Aquino ◽  
Christopher M. DeRito
Keyword(s):  
Viral Genome ◽  
Marine Invertebrates ◽  
Scar Tissue ◽  
Sea Star ◽  
Wasting Disease ◽  
Viral Genomes ◽  
Normal Tissues ◽  
Pisaster Ochraceus ◽  
Affected Tissue ◽  
External Stimuli

Sea star wasting disease (SSWD) is a condition that has affected asteroids for over 120 years, yet mechanistic understanding of this wasting etiology remains elusive. We investigated temporal virome variation in two Pisaster ochraceus specimens that wasted in the absence of external stimuli and two specimens that did not experience SSWD for the duration of our study, and compared viromes of wasting lesion margin tissues to both artificial scar margins and grossly normal tissues over time. Global assembly of all SSWD-affected tissue libraries resulted in 24 viral genome fragments represented in >1 library. Genome fragments mostly matched densoviruses and picornaviruses with fewer matching nodaviruses, and a sobemovirus. Picornavirus-like and densovirus-like genome fragments were most similar to viral genomes recovered in metagenomic study of other marine invertebrates. Read recruitment revealed only two picornavirus-like genome fragments that recruited from only SSWD-affected specimens, but neither was unique to wasting lesions. Wasting lesion margin reads recruited to a greater number of viral genotypes (i.e., richness) than did either scar tissue and grossly normal tissue reads. Taken together, these data suggest that no single viral genome fragment was associated with SSWD. Rather, wasting lesion margins may generally support viral proliferation.

scholarly journals Genetic variation associated with lower susceptibility to sea star wasting syndrome in the keystone species, Pisaster ochraceus

2021 ◽  
Author(s):  
Andrea Burton ◽  
Sarah Gravem ◽  
Felipe Barreto
Keyword(s):  
Genetic Variation ◽  
Keystone Species ◽  
Disease Status ◽  
Sea Star ◽  
Sea Stars ◽  
Protein Coding ◽  
Functional Studies ◽  
Pisaster Ochraceus ◽  
Wasting Syndrome ◽  
Asymptomatic Individuals

The keystone species, Pisaster ochraceus, suffered mass mortalities along the northeast Pacific Ocean from Sea Star Wasting Syndrome (SSWS) outbreaks in 2013-2016. Causation of SSWS is still debated, leading to concerns as to whether outbreaks will continue to impact this species. Considering the apparent link between ocean temperature and SSWS, the future of this species and intertidal communities remains uncertain. We surveyed populations of sea stars along the Oregon coast in 2016, two years after the epidemic began. Cohabitation of asymptomatic and symptomatic individuals allowed us to ask whether lower susceptibility in asymptomatic individuals differed genetically. We performed restriction site-associated DNA sequencing (2bRAD-seq) to genotype thousands of single nucleotide polymorphism (SNP) loci. By comparing allele frequencies between symptomatic and asymptomatic individuals, we detected three loci that may be under selection. A multivariate analysis showed a clear separation between groups based on disease status in two of the three geographic regions, along with several regions across the genome having small statistical contributions to this separation. A draft annotation of protein-coding regions allowed us to identify 120 predicted genes that are linked to these markers and are putatively associated with lower susceptibility. Our results suggest that some variation in disease severity can be attributed to genetic variation. However, differences in phenotype have a highly polygenic nature with no single or few genomic regions having strong predictive effects. The genes associated with these regions may form the basis for functional studies aiming to understand disease progression in infected individuals.

scholarly journals Virome Temporal Variation During Sea Star Wasting Disease Progression in Pisaster ochraceus (Asteroidea, Echinodermata)

2020 ◽  
Author(s):  
Ian Hewson ◽  
Citlalli A. Aquino ◽  
Christopher M. DeRito
Keyword(s):  
Viral Genome ◽  
Marine Invertebrates ◽  
Scar Tissue ◽  
Sea Star ◽  
Wasting Disease ◽  
Viral Genomes ◽  
Normal Tissues ◽  
Pisaster Ochraceus ◽  
Affected Tissue ◽  
External Stimuli

Sea star wasting disease (SSWD) is a condition that has affected asteroids for over 120 years, yet mechanistic understanding of wasting etiology remains elusive. We investigated temporal virome variation in two Pisaster ochraceus specimens that wasted in the absence of external stimuli and two specimens that did not experience SSWD for the duration of our study, and compared viromes of wasting lesion margin tissues to both artificial scar margins and grossly normal tissues over time. Global assembly of all SSWD-affected tissue libraries resulted in 45 viral genome fragments represented in &amp;gt;1 library. Genome fragments mostly matched densoviruses and picornaviruses with fewer matching nodaviruses, narnaviruses and sobemoviruses. Picornavirus-like and densovirus-like genome fragments were most similar to viral genomes recovered in metagenomic study of other marine invertebrates. Read recruitment revealed only 2 picornavirus-like genome fragments that recruited from only SSWD-affected specimens, but neither was unique to wasting lesions. Wasting lesion margin reads recruited to a greater number of viral genotypes (i.e. richness) than did either scar tissue and grossly normal tissue reads. Taken together, these data suggest that no single viral genome fragment was associated with SSWD. Rather, wasting lesion margins may generally support viral proliferation.

scholarly journals RNA expression and disease tolerance are associated with a “keystone mutation” in the ochre sea star Pisaster ochraceus

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3696 ◽  
Author(s):  
V. Katelyn Chandler ◽  
John P. Wares
Keyword(s):  
Cellular Response ◽  
Constitutive Expression ◽  
Elongation Factor ◽  
Sea Star ◽  
Wasting Disease ◽  
Pisaster Ochraceus ◽  
The Pacific ◽  
Response To Temperature ◽  
Elongation Factor 1 ◽  
Lower Expression

An overdominant mutation in an intron of the elongation factor 1-α (EF1A) gene in the sea star Pisaster ochraceus has shown itself to mediate tolerance to “sea star wasting disease”, a pandemic that has significantly reduced sea star populations on the Pacific coast of North America. Here we use RNA sequencing of healthy individuals to identify differences in constitutive expression of gene regions that may help explain this tolerance phenotype. Our results show that individuals carrying this mutation have lower expression at a large contingent of gene regions. Individuals without this mutation also appear to have a greater cellular response to temperature stress, which has been implicated in the outbreak of sea star wasting disease. Given the ecological significance of P. ochraceus, these results may be useful in predicting the evolutionary and demographic future for Pacific intertidal communities.

scholarly journals Allele frequency-free inference of close familial relationships from genotypes or low depth sequencing data

2018 ◽  
Author(s):  
Ryan K Waples ◽  
Anders Albrechtsen ◽  
Ida Moltke
Keyword(s):  
Allele Frequency ◽  
Allele Frequencies ◽  
Model Organisms ◽  
Human Populations ◽  
Genotype Data ◽  
Sequencing Data ◽  
Diverse Range ◽  
Genomic Position ◽  
Familial Relationships ◽  
Similar Accuracy

AbstractKnowledge of how individuals are related is important in many areas of research and numerous methods for inferring pairwise relatedness from genetic data have been developed. However, the majority of these methods were not developed for situations where data is limited. Specifically, most methods rely on the availability of population allele frequencies, the relative genomic position of variants, and accurate genotype data. But in studies of non-model organisms or ancient human samples, such data is not always available. Motivated by this, we present a new method for pairwise relatedness inference, which requires neither allele frequency information nor information on genomic position. Furthermore, it can be applied to both genotype data and to low-depth sequencing data where genotypes cannot be accurately called. We evaluate it using data from SNP arrays and low-depth sequencing from a range of human populations and show that it can be used to infer close familial relationships with a similar accuracy as a widely used method that relies on population allele frequencies. Additionally, we show that our method is robust to SNP ascertainment, which is important for application to a diverse range of populations and species.

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