Identification of single nucleotide polymorphisms from the transcriptome of an organism with a whole genome duplication

Christensen, Kris A.; Brunelli, Joseph P.; Lambert, Matthew J; DeKoning, Jenefer; Phillips, Ruth B.; Thorgaard, Gary H.

doi:10.1186/1471-2105-14-325

Cited by 14 publications

(14 citation statements)

References 36 publications

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“…Several genomic resources have been developed for research to help improve rainbow trout commercial production traits including disease resistance. The list includes clonal lines (Young et al, 1996 ; Thorgaard et al, 2002 ), BAC libraries (Palti et al, 2004 ), genetic linkage maps (Young et al, 1998 ; Sakamoto et al, 2000 ; Rexroad et al, 2008 ; Palti et al, 2011 ; Guyomard et al, 2012 ), microarrays (Salem et al, 2008 ), expressed sequence tags (ESTs) (Rexroad et al, 2003 ; Sánchez et al, 2009 ; Boussaha et al, 2012 ), single nucleotide polymorphisms (SNPs) (Sánchez et al, 2009 ; Amish et al, 2012 ; Boussaha et al, 2012 ; Houston et al, 2012 ; Salem et al, 2012 ; Christensen et al, 2013 ; Colussi et al, 2014 ; Palti et al, 2014 ), next-generation sequence read archives (SRA) and genome as well as transcriptome reference assemblies (Salem et al, 2010 ; Sanchez et al, 2011 ; Berthelot et al, 2014 ; Fox et al, 2014 ). Several studies have identified many immune-related key genes and gene networks (Thorgaard et al, 2002 ; Cerdà et al, 2008 ; Chiu et al, 2010 ; Zhang et al, 2011 ).…”

Section: Introductionmentioning

confidence: 99%

Characterization of the rainbow trout spleen transcriptome and identification of immune-related genes

et al. 2014

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Resistance against diseases affects profitability of rainbow trout. Limited information is available about functions and mechanisms of teleost immune pathways. Immunogenomics provides powerful tools to determine disease resistance genes/gene pathways and develop genetic markers for genomic selection. RNA-Seq sequencing of the rainbow trout spleen yielded 93,532,200 reads (100 bp). High quality reads were assembled into 43,047 contigs. 26,333 (61.17%) of the contigs had hits to the NR protein database and 7024 (16.32%) had hits to the KEGG database. Gene ontology showed significant percentages of transcripts assigned to binding (51%), signaling (7%), response to stimuli (9%) and receptor activity (4%) suggesting existence of many immune-related genes. KEGG annotation revealed 2825 sequences belonging to “organismal systems” with the highest number of sequences, 842 (29.81%), assigned to immune system. A number of sequences were identified for the first time in rainbow trout belonging to Toll-like receptor signaling (35), B cell receptor signaling pathway (44), T cell receptor signaling pathway (56), chemokine signaling pathway (73), Fc gamma R-mediated phagocytosis (52), leukocyte transendothelial migration (60) and NK cell mediated cytotoxicity (42). In addition, 51 transcripts were identified as spleen-specific genes. The list includes 277 full-length cDNAs. The presence of a large number of immune-related genes and pathways similar to other vertebrates suggests that innate and adaptive immunity in fish are conserved. This study provides deep-sequence data of rainbow trout spleen transcriptome and identifies many new immune-related genes and full-length cDNAs. This data will help identify allelic variations suitable for genomic selection and genetic manipulation in aquaculture.

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Section: Introductionmentioning

confidence: 99%

Characterization of the rainbow trout spleen transcriptome and identification of immune-related genes

et al. 2014

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“…This problem has been efficiently addressed with a “filter” that used haploid genomic information because there should be no heterozygotes (Christensen et al . ; Larson et al . ).…”

Section: Discussionmentioning

confidence: 97%

“…These paralogs appeared to be a major problem here given the low conversion of sequence variants into functional assays in nuclear-encoded subunits of the mitochondrial machinery. This problem has been efficiently addressed with a "filter" that used haploid genomic information because there should be no heterozygotes (Christensen et al 2013;Larson et al 2014b).…”

Section: Discussionmentioning

confidence: 99%

Potentially adaptive mitochondrial haplotypes as a tool to identify divergent nuclear loci

et al. 2016

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Summary Genetic tools are commonly used for conservation and management of at‐risk species. Individuals are often sampled from mixtures that are composed of many populations, which creates a need to assign individuals to their source. This can be problematic when the genetic divergence among source populations is weak but can be improved using adaptive genetic loci, which should show stronger levels of divergence. We previously reported a signature of positive selection in the mitochondrial‐encoded ND5 subunit of complex I in diverse taxa. The respiratory machinery of the mitochondria in salmonids is composed of more than 80 nuclear genes and there is substantial interaction between nuclear and mitochondrial expressed gene products. Recent studies report adaptive variation in mitochondrial function as well as co‐evolution between mitochondrial and nuclear genomes. We used potentially adaptive ND5‐based mitochondrial haplotypes to identify nuclear loci that would display increased levels of genetic divergence compared to neutral nuclear loci in chum salmon (Oncorhynchus keta). Populations in a geographic area the size of France have previously demonstrated weak genetic divergence even after substantial discovery efforts by multiple laboratories for allozymes, microsatellites and SNPs over the last two decades. We used RAD‐based next‐generation sequencing and identified a nuclear‐encoded subunit of mitochondrial complex I that was a significant FST outlier and 14 other divergent nuclear markers that improve genetic assignment of individuals to their population of origin relative to assignments based on neutral markers alone. This work demonstrates how a known adaptive marker can be leveraged to increase the probability of identifying divergent markers for applied genetics tools that may be biologically linked to it.

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“…Single nucleotide polymorphisms (SNPs) have begun to replace microsatellites in many studies of relatedness and parentage because they are easier to score and becoming cheaper to develop (Morin, Luikart, & Wayne, ; Städele & Vigilant, ; Vignal, Milan, SanCristobal, & Eggen, ; Weinman, Solomon, & Rubenstein, ). However, in species with complicated genomes characterized by extensive gene duplication (including polyploidy), the presence of paralogs makes identifying SNPs challenging (Christensen et al., ; Dufresne, Stift, Vergilino, & Mable, ). In contrast, identifying polysomic microsatellite markers is easier because multiple alleles can be determined visually in genotyping output (David, Blum, Feldman, Lavi, & Hillel, ; Huang, Cipriani, Morgante, & Testolin, ).…”

Section: Introductionmentioning

confidence: 99%

Development of genome‐ and transcriptome‐derived microsatellites in related species of snapping shrimps with highly duplicated genomes

Gaynor

Solomon

Siller

et al. 2017

Molecular Ecology Resources

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Molecular markers are powerful tools for studying patterns of relatedness and parentage within populations and for making inferences about social evolution. However, the development of molecular markers for simultaneous study of multiple species presents challenges, particularly when species exhibit genome duplication or polyploidy. We developed microsatellite markers for Synalpheus shrimp, a genus in which species exhibit not only great variation in social organization, but also interspecific variation in genome size and partial genome duplication. From the four primary clades within Synalpheus, we identified microsatellites in the genomes of four species and in the consensus transcriptome of two species. Ultimately, we designed and tested primers for 143 microsatellite markers across 25 species. Although the majority of markers were disomic, many markers were polysomic for certain species. Surprisingly, we found no relationship between genome size and the number of polysomic markers. As expected, markers developed for a given species amplified better for closely related species than for more distant relatives. Finally, the markers developed from the transcriptome were more likely to work successfully and to be disomic than those developed from the genome, suggesting that consensus transcriptomes are likely to be conserved across species. Our findings suggest that the transcriptome, particularly consensus sequences from multiple species, can be a valuable source of molecular markers for taxa with complex, duplicated genomes.

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Identification of single nucleotide polymorphisms from the transcriptome of an organism with a whole genome duplication

Cited by 14 publications

References 36 publications

Characterization of the rainbow trout spleen transcriptome and identification of immune-related genes

Characterization of the rainbow trout spleen transcriptome and identification of immune-related genes

Potentially adaptive mitochondrial haplotypes as a tool to identify divergent nuclear loci

Development of genome‐ and transcriptome‐derived microsatellites in related species of snapping shrimps with highly duplicated genomes

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