Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery

Warren, Wesley C.; Rice, Edward S.; Maggs, X; Roback, Emma; Keene, Alex; Martin, Fergal; Ogeh, Denye; Haggerty, Leanne; Carroll, Rachel A.; McGaugh, Suzanne; Rohner, Nicolas

doi:10.1101/2023.11.16.567450

“…The reference genome AstMex3_surface in FASTA format as well as annotation information and assembly report were downloaded from NCBI database, under RefSeq assembly accession GCF_023375975.1 (Warren et al, 2023). Illumina reads from A. mexicanus population resequencing data described in Herman et al (2018) were downloaded from European Nucleotide Archive (SRA accession: PRJNA260715).…”

Section: Data Acquisitionmentioning

confidence: 99%

The prevalence of copy number increase at multiallelic copy number variants associated with cave colonization

Pokrovac,

Rohner,

Pezer

2024

Molecular Ecology

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Copy number variation is a common contributor to phenotypic diversity, yet its involvement in ecological adaptation is not easily discerned. Instances of parallelly evolving populations of the same species in a similar environment marked by strong selective pressures present opportunities to study the role of copy number variants (CNVs) in adaptation. By identifying CNVs that repeatedly occur in multiple populations of the derived ecotype and are not (or are rarely) present in the populations of the ancestral ecotype, the association of such CNVs with adaptation to the novel environment can be inferred. We used this paradigm to identify CNVs associated with recurrent adaptation of the Mexican tetra (Astyanax mexicanus) to cave environment. Using a read‐depth approach, we detected CNVs from previously re‐sequenced genomes of 44 individuals belonging to two ancestral surfaces and three derived cave populations. We identified 102 genes and 292 genomic regions that repeatedly diverge in copy number between the two ecotypes and occupy 0.8% of the reference genome. Functional analysis revealed their association with processes previously recognized to be relevant for adaptation, such as vision, immunity, oxygen consumption, metabolism, and neural function and we propose that these variants have been selected for in the cave or surface waters. The majority of the ecotype‐divergent CNVs are multiallelic and display copy number increases in cavefish compared to surface fish. Our findings suggest that multiallelic CNVs – including gene duplications – and divergence in copy number provide a fast route to produce novel phenotypes associated with adaptation to subterranean life.

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The prevalence of copy number increase at multiallelic CNVs associated with cave colonization in Mexican tetra (Astyanax mexicanus)

Pokrovac,

Rohner,

Pezer

2023

Preprint

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Copy number variation is a common contributor to phenotypic diversity, yet its involvement in ecological adaptation is not easily discerned. Instances of parallelly evolving populations of the same species in a similar environment marked by strong selective pressures present opportunities to study the role of copy number variants (CNVs) in adaptation. By identifying CNVs that repeatedly occur in multiple populations of the derived ecotype and are not (or are rarely) present in the populations of the ancestral ecotype, the association of such CNVs with adaptation to the novel environment can be inferred. We used this paradigm to identify CNVs associated with recurrent adaptation of the Mexican tetra (Astyanax mexicanus) to cave environment. Using a read-depth approach, we detected CNVs from previously re-sequenced genomes of 44 individuals belonging to two ancestral surface and three derived cave populations. We identified 102 genes and 292 genomic regions that repeatedly diverge in copy number between the two ecotypes and occupy 0.8% of the reference genome. Functional analysis revealed their association with processes previously recognized to be relevant for adaptation, such as vision, immunity, oxygen consumption, metabolism, and neural function and we propose that these variants have been selected for in the cave or surface waters. The majority of the ecotype-divergent CNVs are multiallelic and display copy-number increases in cave fish compared to surface fish. Our findings suggest that multiallelic CNVs - including gene duplications, and divergence in copy number provide a fast route to produce novel phenotypes associated with adaptation to subterranean life.Significance StatementDuplications and deletions of genomic sequences occur frequently within a population. Such inter-individual difference in the amount of genetic material is known as copy number variation and is associated with differences in phenotypic traits. Despite its pervasiveness, the evolutionary impact of copy number variation in complex organisms is difficult to discern, primarily due to the infeasibility of setting up evolutionary experiments in the laboratory. Instances of multiple populations that evolved the same traits in similar environments represent naturally occurring evolutionary experiments and valuable opportunities to study the molecular basis of adaptation. Mexican tetra represents such a system and we use the genomes of surface and cave-dwelling populations to study the role of copy number variation in the recurrent cave adaptation.

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Investigation of Astyanax mexicanus (Characiformes, Characidae) chromosome 1 structure reveals unmapped sequences and suggests conserved evolution

Silva,

Mazzoni Zerbinato Andrade Silva,

Castro

et al. 2024

PLoS ONE

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Natural selection in the cave habitat has resulted in unique phenotypic traits (including pigmentation loss and ocular degeneration) in the Mexican tetra Astyanax mexicanus, considered a model species for evolutionary research. A. mexicanus has a karyotype of 2n = 50 chromosomes, and long-read sequencing and quantitative trait linkage maps (QTLs) have completely reconstructed the reference genome at the chromosomal level. In the current work, we performed whole chromosome isolation by microdissection and total amplification using DOP-PCR and Whole Chromosome Painting (WCP), followed by sequencing on the Illumina NextSeq platform, to investigate the microstructure of the large and conserved metacentric chromosome 1 of A. mexicanus. The sequences aligned to linkage block 3 of the reference genome, as determined by processing the reads with the DOPseq pipeline and characterizing the satellites with the TAREAN program. In addition, part of the sequences was anchored in linkage blocks that have not yet been assigned to the chromosomes. Furthermore, fluorescence in situ hybridization using WCP 1 carried out in other nearby species revealed a high degree of chromosome conservation, which allows us to hypothesize a common origin of this element. The physical mapping of the repetitive marker sequences provided a micro- and macrostructural overview and confirmed their position in chromosome pair 1. These sequences can serve as comparative tools for understanding the evolution and organization of this chromosome in other species of the family in future studies.

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Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery

Cited by 3 publications

References 41 publications

The prevalence of copy number increase at multiallelic copy number variants associated with cave colonization

The prevalence of copy number increase at multiallelic copy number variants associated with cave colonization

The prevalence of copy number increase at multiallelic CNVs associated with cave colonization in Mexican tetra (Astyanax mexicanus)

Investigation of Astyanax mexicanus (Characiformes, Characidae) chromosome 1 structure reveals unmapped sequences and suggests conserved evolution

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