Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing

Everett, Meredith V.; Miller, Michael R.; Seeb, James E.

doi:10.1186/1471-2164-13-521

Cited by 51 publications

(93 citation statements)

References 72 publications

(107 reference statements)

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“…Genetic maps from NGS have been developed quite extensively for salmonids, for example with RAD sequencing in O. nerka (Everett et al, 2012), O. mykiss (Hecht et al, 2012), and Atlantic salmon (Sm. salar) (Gonen et al, 2014).…”

Section: Genomic Organisationmentioning

confidence: 99%

Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

Elmer

2016

Hydrobiologia

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The past few years have seen an absolute revolution in genomic technologies and their potential applications to ecology and evolutionary biology research. Such advances open up a range of opportunities for research on non-model organisms and individuals drawn from wild populations. This has resulted in exciting new research seeking to identify the genetic polymorphisms important in adaptation and speciation and how they are organised within the genome. Building on this, there is great interest in the extent to which similar evolutionary patterns are found across multiple populations, particularly whether consistent genetic mechanisms are associated with recurrent phenotypes. A powerful context for disentangling these mechanisms is to focus on highly diverse radiations, where phenotypes vary in and across environments. Therefore, the high diversity found within and among species of salmonid fishes such as charr (Salvelinus) make for an ideal 'non'-model for genomic research. This paper outlines some of the current approaches available in ecological genomics and highlights some recent advances in salmonid research. It also suggests avenues for the sort of predictions that can be derived from ecological genomics, with the aim of understanding the genetics behind the fantastic diversity of salmonid fishes.Keywords Ecological genomics Á Transcriptomics Á Speciation Á Genetic mapping Á Salmonid fishes Á Charr Recent advances in the field of molecular biology have exciting implications for research on the ecology and evolution of natural populations. Particularly, high throughput 'next-generation' sequencing (NGS) (also known as 'second-generation', or 'massively parallel' sequencing) can generate huge amounts of genomic or transcriptomic data on almost any organism. NGS is dramatically decreasing in cost and the associated tools and pipelines are within reach of even modest research groups. This is therefore becoming an invaluable tool for understanding the origins and maintenance of biodiversity. These exciting new approaches can address long-standing questions in evolutionary biology, such as: What is the genetic basis of adaptations? How do closely related species differ? Why are some lineages more diverse than others?The challenge for 'omics' of non-model organisms now shifts away from raw data generation to focusing on informative evolutionary, ecological, and environmental contexts in order to most efficiently and

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Section: Genomic Organisationmentioning

confidence: 99%

Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

Elmer

2016

Hydrobiologia

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“…Construction of linkage maps has been facilitated using next generation sequencing (NGS). Everett et al [2012] used more than 1,000 genetic markers to rapidly constructed male and female linkage maps of the sockeye salmon (Onchorhynus nerka) that could be compared with more conventionally constructed maps of other salmonids.…”

Section: Bisexual Polyploidsmentioning

confidence: 99%

“…Despite these merits, the application of NGS in polyploid animals has largely lagged compared to diploids or even polyploidy plants [Bundock et al, 2009;Brenchley et al, 2012;Buggs et al, 2012;Trick et al, 2012]. Combined with transcriptome sequencing (RNA-seq) and genome reduction methods such as restriction site associated DNA tags (RADtags) [Miller et al 2007], NGS has been used to discover genome-wide SNPs in rainbow trout (O. mykiss) and westslope cutthroat trout (O. clarkii lewisi) [Hohenlohe et al, 2011] as well as in sockeye salmon (O. nerka) [Everett et al, 2011[Everett et al, , 2012. NGS has also been successfully used to study gene expression in the polyploid Lake Sturgeon (Acipenser fulvescens) [Hale et al, 2009].…”

Section: The Promise Of Ngs In Genomic Research Of Polyploidymentioning

confidence: 99%

Genetic and Genomic Interactions of Animals with Different Ploidy Levels

Bogart¹,

Bi²

2013

Cytogenet Genome Res

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Polyploid animals have independently evolved from diploids in diverse taxa across the tree of life. We review a few polyploid animal species or biotypes where recently developed molecular and cytogenetic methods have significantly improved our understanding of their genetics, reproduction and evolution. Mitochondrial sequences that target the maternal ancestor of a polyploid show that polyploids may have single (e.g. unisexual salamanders in the genus Ambystoma) or multiple (e.g. parthenogenetic polyploid lizards in the genus Aspidoscelis) origins. Microsatellites are nuclear markers that can be used to analyze genetic recombinations, reproductive modes (e.g. Ambystoma) and recombination events (e.g. polyploid frogs such as Pelophylax esculentus). Hom(e)ologous chromosomes and rare intergenomic exchanges in allopolyploids have been distinguished by applying genome-specific fluorescent probes to chromosome spreads. Polyploids arise, and are maintained, through perturbations of the ‘normal' meiotic program that would include pre-meiotic chromosome replication and genomic integrity of homologs. When possible, asexual, unisexual and bisexual polyploid species or biotypes interact with diploid relatives, and genes are passed from diploid to polyploid gene pools, which increase genetic diversity and ultimately evolutionary flexibility in the polyploid. When diploid relatives do not exist, polyploids can interact with another polyploid (e.g. species of African Clawed Frogs in the genus Xenopus). Some polyploid fish (e.g. salmonids) and frogs (Xenopus) represent independent lineages whose ancestors experienced whole genome duplication events. Some tetraploid frogs (P. esculentus) and fish (Squaliusalburnoides) may be in the process of becoming independent species, but diploid and triploid forms of these ‘species' continue to genetically interact with the comparatively few tetraploid populations. Genetic and genomic interaction between polyploids and diploids is a complex and dynamic process that likely plays a crucial role for the evolution and persistence of polyploid animals. See also other articles in this themed issue.

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“…Development of bioinformatic tools for RAD sequence data (e.g., Stacks, Catchen et al, 2011;PyRAD, Eaton, 2014) will promote its utility further. RAD sequencing has been successfully applied to linkage and quantitative trait locus (QTL) analyses using cross families (e.g., Baird et al, 2008;Baxter et al, 2011;Anderson et al, 2012;Everett et al, 2012;Hecht et al, 2012;Heliconius Genome Consortium, 2012;Martin et al, 2012;Takahashi et al, 2013), association studies using wild populations (Parchman et al, 2012;Hecht et al, 2013), population genomics (e.g., Hohenlohe et al, 2010;Bruneaux et al, 2012;Keller et al, 2013), phylogeny (e.g., Emerson et al, 2010;Heliconius Genome Consortium, 2012;Eaton and Ree, 2013;Jones et al, 2013;Wagner et al, 2013;Hipp et al, 2014;Cruaud et al, 2014), and identification of simple sequence repeat (SSR) markers (Barchi et al, 2011). However, practical questions remain about applying this method to phylogenetic studies of a group that includes variously related species (Rubin et al, 2012;McCormack et al, 2013).…”

Section: Introductionmentioning

confidence: 99%