Elimination of reference mapping bias reveals robust immune related allele-specific expression in crossbred sheep

Salavati, Mazdak; Bush, Stephen J.; Palma-Vera, Sergio; McCulloch, Mary E. B.; Hume, David; Clark, Emily L.

doi:10.1101/619122

Cited by 3 publications

(3 citation statements)

References 81 publications

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“…In order to assess mapping sensitivity and specificity, we calculated the cumulative TPR (True where TPi and FPi represent the number of correctly and incorrectly mapped reads, respectively, at a given phred-scaled mapping quality threshold i (60,50,40,30,20,10,0), and n is the total number of reads mapped.…”

Section: Assessment Of the Read Mapping Accuracymentioning

confidence: 99%

“…Reads originating from DNA fragments that are highly diverged from corresponding reference nucleotides will either obtain low alignment scores, or align at incorrect locations, or remain un-mapped [18]. Reference bias compromises analyses that are sensitive to accurately mapped reads and prevents the precise estimation of allele frequencies [16,[19][20][21].…”

Section: Introductionmentioning

confidence: 99%

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Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery

Crysnanto

Pausch

2019

Preprint

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BackgroundThe current bovine genomic reference sequence was assembled from the DNA of a Hereford cow.The resulting linear assembly lacks diversity because it does not contain allelic variation. Lack of diversity is a drawback of linear references that causes reference allele bias. High nucleotide diversity and the separation of individuals by hundreds of breeds make cattle ideally suited to investigate the optimal composition of variation-aware references. ResultsWe augment the bovine linear reference sequence (ARS-UCD1.2) with variants filtered for allele frequency in dairy (Brown Swiss, Holstein) and dual-purpose (Fleckvieh, Original Braunvieh) cattle breeds to construct either breed-specific or pan-genome reference graphs using the vg toolkit. We find that read mapping is more accurate to variation-aware than linear references if pre-selected variants are used to construct the genome graphs. Graphs that contain random variants do not improve read mapping over the linear reference sequence. Breed-specific augmented and pangenome graphs enable almost similar mapping accuracy improvements over the linear reference.We construct a whole-genome graph that contains the Hereford-based reference sequence and 14 million alleles that have alternate allele frequency greater than 0.03 in the Brown Swiss cattle breed.We show that our novel variation-aware reference facilitates accurate read mapping and unbiased sequence variant genotyping for SNPs and Indels. ConclusionsWe developed the first variation-aware reference graph for an agricultural animal: https://doi.org/10.5281/zenodo.3570312. Our novel reference structure improves sequence read mapping and variant genotyping over the linear reference. Our work is a first step towards the transition from linear to variation-aware reference structures in species with high genetic diversity and many sub-populations.

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Section: Assessment Of the Read Mapping Accuracymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery

Crysnanto

Pausch

2019

Preprint

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“…We removed duplicate reads using picardtools, then used the mapped reads to call individual genotypes and compared across samples to find consistent single nucleotide polymorphisms (SNPs). ASE analyses are sensitive to read mapping bias that may arise from preferential mapping of the reference allele, a problem that is particularly severe if the reference genome is more closely related to one of the genotypes in the study (Degner et al, 2009; Salavati et al, 2019; Stevenson et al, 2013). Since the axolotl reference genome is more closely related to BTS than to CTS (CTS is the outgroup to the entire tiger salamander complex; see O’Neill et al, 2013; Shaffer & McKnight, 1996), we used the software wasp to remove this potential mapping bias for downstream ASE analyses (van de Geijn et al, 2015).…”

Section: Methodsmentioning

confidence: 99%

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

Cooper

Shaffer

2021

Molecular Ecology

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Hybridization 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 potential to outperform native species. Effective management of hybrid populations requires an understanding of both physiological performance and the underlying mechanisms that drive transgressive hybrid traits. 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 F1 hybrids to tolerate acute thermal stress, and found that hybrids exhibit a wide range of CTMax values, with 33% (4/12) able to tolerate temperatures greater than either parent. We then quantified the genomic response, measured at the RNA transcript level, of each salamander, to explore the mechanisms underlying thermal tolerance strategies. We found that CTS and BTS have strikingly different values and tissue‐specific patterns of overall gene expression, with hybrids expressing intermediate values. F1 hybrids display abundant and variable degrees of allele‐specific expression (ASE), likely arising from extensive compensatory evolution in gene regulatory mechanisms between CTS and BTS. We found evidence that the proportion of genes with allelic imbalance in individual hybrids correlates with their CTMax, suggesting a link between ASE and expanded thermal tolerance that may contribute to the success of hybrid salamanders in California. Future climate change may further complicate management of CTS if hybrid salamanders are better equipped to deal with rising temperatures.

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A mini-atlas of gene expression for the domestic goat (Capra hircus) reveals transcriptional differences in immune signatures between sheep and goats

Muriuki¹,

Bush²,

Salavati³

et al. 2019

Preprint

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Goats (Capra hircus) are an economically important livestock species providing meat and milk across the globe. They are of particular importance in tropical agri-systems contributing to sustainable agriculture, alleviation of poverty, social cohesion and utilisation of marginal grazing. There are excellent genetic and genomic resources available for goats, including a highly contiguous reference genome (ARS1). However, gene expression information is limited in comparison to other ruminants. To support functional annotation of the genome and comparative transcriptomics we created a mini-atlas of gene expression for the domestic goat. RNA-Seq analysis of 22 transcriptionally rich tissues and cell-types detected the majority (90%) of predicted protein-coding transcripts and assigned informative gene names to more than 1000 previously unannotated protein-coding genes in the current reference genome for goat (ARS1). Using network-based cluster analysis we grouped genes according to their expression patterns and assigned those groups of co-expressed genes to specific cell populations or pathways. We describe clusters of genes expressed in the gastro-intestinal tract and provide the expression profiles across tissues of a subset of genes associated with functional traits. Comparative analysis of the goat atlas with the larger sheep gene expression atlas dataset revealed transcriptional differences between the two species in macrophage-associated signatures. The goat transcriptomic resource complements the large gene expression dataset we have generated for sheep and contributes to the available genomic resources for interpretation of the relationship between genotype and phenotype in small ruminants.

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Elimination of reference mapping bias reveals robust immune related allele-specific expression in crossbred sheep

Cited by 3 publications

References 81 publications

Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery

Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery

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

A mini-atlas of gene expression for the domestic goat (Capra hircus) reveals transcriptional differences in immune signatures between sheep and goats

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