scholarly journals Allele specific expression and gene regulation explain transgressive thermal tolerance in non-native hybrids of the endangered California tiger salamander (Ambystoma californiense)

2019 ◽  
Author(s):  
Robert D. Cooper ◽  
H. Bradley Shaffer
Keyword(s):  
Thermal Tolerance ◽  
Regulatory Mechanisms ◽  
F1 Hybrids ◽  
Future Climate Change ◽  
Tiger Salamander ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Wide Range ◽  
Allele Specific ◽  
Ambystoma Californiense

AbstractHybridization between native and non-native species is an ongoing global conservation threat. Hybrids that exhibit traits and tolerances that surpass parental values are of particular concern, given their ability to outcompete the native parent. It is crucial to understand the mechanisms that drive these transgressive hybrid traits to diagnose and develop strategies to manage hybrid populations. Here, we explore several aspects of the hybridization between the endangered California tiger salamander (Ambystoma californiense; CTS) and the introduced barred tiger salamander (Ambystoma mavortium; BTS). We assayed critical thermal maximum (CTMax) to compare the ability of CTS, BTS and hybrids to tolerate acute thermal stress, and found that hybrids exhibit a wide range of CTMax values, with 40% (6/15) able to tolerate temperatures greater than either parent. We quantified the genomic response of each individual to discover and compare thermal abatement strategies. We found that CTS and BTS have strikingly different numbers and tissue-specific patterns of overall gene expression, with hybrids expressing intermediate values. We evaluated transgressive and variable phenotypes by uncovering regulatory mechanisms that give rise to these unique traits. F1 hybrids display abundant and variable degrees of allele specific expression (ASE), likely arising from extensive compensatory evolution in gene regulatory mechanisms of the parental lineages. We found that the proportion of genes with allelic imbalance in individual hybrids correlates with their CTMax, suggesting that BTS-biased expression confers improved thermal tolerance. We discuss the implications of these findings with respect to ongoing management of CTS in the face of future climate change.

Genome-wide analysis of spatiotemporal allele-specific expression in F1 hybrids of meat- and egg-type chickens

Gene ◽  
2020 ◽  
Vol 747 ◽  
pp. 144671 ◽  
Author(s):  
Peng Ren ◽  
Feilong Deng ◽  
Ye Wang ◽  
Jinshan Ran ◽  
Jingjing Li ◽  
...  
Keyword(s):  
F1 Hybrids ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Allele Specific

scholarly journals ASEP: gene-based detection of allele-specific expression in a population by RNA-seq

2019 ◽  
Author(s):  
Jiaxin Fan ◽  
Jian Hu ◽  
Chenyi Xue ◽  
Hanrui Zhang ◽  
Muredach P. Reilly ◽  
...  
Keyword(s):  
Association Studies ◽  
Genome Wide Association Studies ◽  
Rna Seq ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Wide Range ◽  
Gene Level ◽  
Shared Information ◽  
Allele Specific ◽  
Regulated Gene Expression

ABSTRACTAllele-specific expression (ASE) analysis, which quantifies the relative expression of two alleles in a diploid individual, is a powerful tool for identifying cis-regulated gene expression variations that underlie phenotypic differences among individuals. Existing methods for gene-level ASE detection analyze one individual at a time, therefore wasting shared information across individuals. Failure to accommodate such shared information not only loses power, but also makes it difficult to interpret results across individuals. However, ASE detection across individuals is challenging because the data often include individuals that are either heterozygous or homozygous for the unobserved cis-regulatory SNP, leading to heterogeneity in ASE as only those heterozygous individuals are informative for ASE, whereas those homozygous individuals have balanced expression. To simultaneously model multi-individual information and account for such heterogeneity, we developed ASEP, a mixture model with subject-specific random effect accounting for multi-SNP correlations within the same gene. ASEP is able to detect gene-level ASE under one condition and differential ASE between two conditions (e.g., pre-versus post-treatment). Extensive simulations have demonstrated the convincing performance of ASEP under a wide range of scenarios. We further applied ASEP to RNA-seq data of human macrophages, and identified genes showing evidence of differential ASE pre-versus post-stimulation, which were extended through findings in cardiometabolic trait-relevant genome-wide association studies. To the best of our knowledge, ASEP is the first method for gene-level ASE detection at the population level. With the growing adoption of RNA-seq, we believe ASEP will be well-suited for various ASE studies for human diseases.

scholarly journals Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
M. Joseph Tomlinson ◽  
Shawn W. Polson ◽  
Jing Qiu ◽  
Juniper A. Lake ◽  
William Lee ◽  
...  
Keyword(s):  
Broiler Chickens ◽  
Nucleotide Polymorphisms ◽  
Rna Seq ◽  
Specific Expression ◽  
Single Nucleotide ◽  
Allele Specific Expression ◽  
Detection Tool ◽  
Commercial Broiler ◽  
Significant Phenomenon ◽  
Allele Specific

AbstractDifferential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.

scholarly journals Analysis of Allele-Specific Expression in Mouse Liver by RNA-Seq: A Comparison With Cis-eQTL Identified Using Genetic Linkage

Genetics ◽  
2013 ◽  
Vol 195 (3) ◽  
pp. 1157-1166 ◽  
Author(s):  
Sandrine Lagarrigue ◽  
Lisa Martin ◽  
Farhad Hormozdiari ◽  
Pierre-François Roux ◽  
Calvin Pan ◽  
...  
Keyword(s):  
Mouse Liver ◽  
Genetic Linkage ◽  
Rna Seq ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Allele Specific
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