Muller “Elements” in<i>Drosophila</i>: How the Search for the Genetic Basis for Speciation Led to the Birth of Comparative Genomics

Schaeffer, Stephen W.

doi:10.1534/genetics.118.301084

Cited by 42 publications

(32 citation statements)

References 121 publications

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“…Additionally, Sutherland et al (2016) and Savilammi et al (2019) have explored the utility of naming chromosomes based on homology to northern pike. This naming system has the potential to facilitate comparative genomics in salmonids by creating a “Mueller element”-like system (reviewed in Schaeffer 2018 ), where each chromosome arm has a universal identifier. However, there also remains value in species-specific identifiers; for example, Cart03 is the third named linkage group in the Cisco linkage map ( Table 2 ).…”

Section: Discussionmentioning

confidence: 99%

Comparative Genomic Analyses and a Novel Linkage Map for Cisco (Coregonus artedi) Provide Insights into Chromosomal Evolution and Rediploidization Across Salmonids

Blumstein

Campbell

Hale

et al. 2020

G3 Genes|Genomes|Genetics

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Whole-genome duplication (WGD) is hypothesized to be an important evolutionary mechanism that can facilitate adaptation and speciation. Genomes that exist in states of both diploidy and residual tetraploidy are of particular interest, as mechanisms that maintain the ploidy mosaic after WGD may provide important insights into evolutionary processes. The Salmonidae family exhibits residual tetraploidy, and this, combined with the evolutionary diversity formed after an ancestral autotetraploidization event, makes this group a useful study system. In this study, we generate a novel linkage map for cisco (Coregonus artedi), an economically and culturally important fish in North America and a member of the subfamily Coregoninae, which previously lacked a high-density haploid linkage map. We also conduct comparative genomic analyses to refine our understanding of chromosomal fusion/fission history across salmonids. To facilitate this comparative approach, we use the naming strategy of protokaryotype identifiers (PKs) to associate duplicated chromosomes to their putative ancestral state. The female linkage map for cisco contains 20,292 loci, 3,225 of which are likely within residually tetraploid regions. Comparative genomic analyses revealed that patterns of residual tetrasomy are generally conserved across species, although interspecific variation persists. To determine the broad-scale retention of residual tetrasomy across the salmonids, we analyze sequence similarity of currently available genomes and find evidence of residual tetrasomy in seven of the eight chromosomes that have been previously hypothesized to show this pattern. This interspecific variation in extent of rediploidization may have important implications for understanding salmonid evolutionary histories and informing future conservation efforts.

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Section: Discussionmentioning

confidence: 99%

Comparative Genomic Analyses and a Novel Linkage Map for Cisco (Coregonus artedi) Provide Insights into Chromosomal Evolution and Rediploidization Across Salmonids

Blumstein

Campbell

Hale

et al. 2020

G3 Genes|Genomes|Genetics

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“…Comparative genomics of Diptera (flies and mosquitoes) and Lepidoptera (butterflies and moths) has revealed high levels of chromosome conservation. For example, tephritid fruit flies have maintained chromosome arms, known as Muller elements (Schaeffer 2018), over at least 60 million years (Sved et al 2016). Conservation of gross chromosome structure is even more striking in mosquitos, where chromosome arms have been maintained for at least 150 million years despite substantial changes in genome size (Dudchenko et al 2017).…”

Section: Introductionmentioning

confidence: 99%

Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome

Mathers

Wouters

Mugford

et al. 2020

Preprint

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Large-scale chromosome rearrangements are arguably the most dramatic type of mutations, often leading to rapid evolution and speciation. However, chromosome dynamics have only been studied at the sequence level in a small number of model systems. In insects, Diptera (flies and mosquitoes) and Lepidoptera (butterflies and moths) have high levels of chromosome conservation. Whether this truly reflects the diversity of insect genome evolution is questionable given that many species exhibit rapid karyotype evolution. Here, we investigate chromosome evolution in aphids -an important group of hemipteran plant pests -using newly generated chromosome-scale genome assemblies of the green peach aphid (Myzus persicae) and the pea aphid (Acyrthosiphon pisum), and a previously published chromosome-scale assembly of the corn-leaf aphid (Rhopalosiphum maidis). We find that aphid autosomes have undergone dramatic reorganisation over the last 30 million years, to the extent that chromosome homology cannot be determined between aphids from the tribes Macrosiphini (M. persicae and A. pisum) and Aphidini (R. maidis). In contrast, gene content of the aphid sex (X) chromosome remained unchanged despite rapid sequence evolution, low gene expression and high transposable element load. To test whether rapid evolution of genome structure is a hallmark of Hemiptera, we compared our aphid assemblies to chromosome-level assemblies of two blood-feeding Hemiptera (Rhodnius prolixus and Triatoma rubrofasciata). Despite being more diverged, the blood-feeding hemipterans have conserved synteny and we detect only two chromosome fusion or fission events. The exceptional rate of structural evolution of aphid autosomes renders them an important emerging model system for studying the role of large-scale genome rearrangements in evolution.

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“…macro-synteny) over substantial periods of time. For example, tephritid fruit flies have maintained chromosome arms, known as Muller elements (Schaeffer 2018), over at least 60 million years (Sved et al 2016). Conservation of chromosome structure is even more striking in mosquitos, where chromosome arms have been maintained for at least 150 million years despite substantial changes in genome size (Dudchenko et al 2017).…”

Section: Introductionmentioning

confidence: 99%

Chromosome-Scale Genome Assemblies of Aphids Reveal Extensively Rearranged Autosomes and Long-Term Conservation of the X Chromosome

Mathers

Wouters

Mugford

et al. 2020

Molecular Biology and Evolution

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Chromosome rearrangements are arguably the most dramatic type of mutations, often leading to rapid evolution and speciation. However, chromosome dynamics have only been studied at the sequence level in a small number of model systems. In insects, Diptera and Lepidoptera have conserved genome structure at the scale of whole chromosomes or chromosome arms. Whether this reflects the diversity of insect genome evolution is questionable given that many species exhibit rapid karyotype evolution. Here, we investigate chromosome evolution in aphids – an important group of hemipteran plant pests – using newly generated chromosome-scale genome assemblies of the green peach aphid (Myzus persicae) and the pea aphid (Acyrthosiphon pisum), and a previously published assembly of the corn-leaf aphid (Rhopalosiphum maidis). We find that aphid autosomes have undergone dramatic reorganisation over the last 30 million years, to the extent that chromosome homology cannot be determined between aphids from the tribes Macrosiphini (M. persicae and A. pisum) and Aphidini (R. maidis). In contrast, gene content of the aphid sex (X) chromosome remained unchanged despite rapid sequence evolution, low gene expression and high transposable element load. To test whether rapid evolution of genome structure is a hallmark of Hemiptera, we compared our aphid assemblies to chromosome-scale assemblies of two blood-feeding Hemiptera (Rhodnius prolixus and Triatoma rubrofasciata). Despite being more diverged, the blood-feeding hemipterans have conserved synteny. The exceptional rate of structural evolution of aphid autosomes renders them an important emerging model system for studying the role of large-scale genome rearrangements in evolution.

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Muller “Elements” inDrosophila: How the Search for the Genetic Basis for Speciation Led to the Birth of Comparative Genomics

Abstract: The development of genetic maps multiple species of Drosophila to understand the basis for species formation became problematic because visible mutations were not easily compared among species and species-specific linkage groups lacked a standard nomenclature...

Cited by 42 publications

References 121 publications

Comparative Genomic Analyses and a Novel Linkage Map for Cisco (Coregonus artedi) Provide Insights into Chromosomal Evolution and Rediploidization Across Salmonids

Comparative Genomic Analyses and a Novel Linkage Map for Cisco (Coregonus artedi) Provide Insights into Chromosomal Evolution and Rediploidization Across Salmonids

Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome

Chromosome-Scale Genome Assemblies of Aphids Reveal Extensively Rearranged Autosomes and Long-Term Conservation of the X Chromosome

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