A chromosome level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution.

Abstract

<jats:title>Abstract</jats:title> <jats:p>Identifying the genetic factors that underlie complex traits is central to understanding the mechanistic underpinnings of evolution. In nature, adaptation to severe environmental change, such as encountered following colonization of caves, has dramatically altered genomes of species over varied time spans. Genomic sequencing approaches have identified mutations associated with troglomorphic trait evolution, but the functional impacts of these mutations remain poorly understood. The Mexican Tetra, Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, and also inhabits at least 30 different caves in the region. Cave-dwelling A. mexicanus morphs are well adapted to subterranean life and many populations appear to have evolved troglomorphic traits independently, while the surface-dwelling populations can be used as a proxy for the ancestral form. Here we present a high-resolution, chromosome-level surface fish genome, enabling the first genome-wide comparison between surface fish and cavefish populations. Using this resource, we performed quantitative trait locus (QTL) mapping analyses for pigmentation and eye size and found new candidate genes for eye loss such as dusp26. We used CRISPR gene editing in A. mexicanus to confirm the essential role of a gene within an eye size QTL, rx3, in eye formation. We also generated the first genome-wide evaluation of deletion variability that includes an analysis of the impact on protein-coding genes across cavefish populations to gain insight into this potential source of cave adaptation. The new surface fish genome reference now provides a more complete resource for comparative, functional, developmental and genetic studies of drastic trait differences within a species.</jats:p>

Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River Basin

“…The image shows a good degree of synteny in terms of BUSCO genes; for a number of times entire chromosomes are syntenic. Figures 5 and 6 show similar analysis with C. auratus [44] and Astyanax mexicanus [45] of different levels of relatedness to C. macropomum, demonstrating the potential of this highly contiguous genome for studies of chromosome evolution.…”

A 3D molecular map of the cavefish neural plate illuminates eyefield organization and its borders in vertebrates

“…In zebrafish, medaka and Astyanax surface fish, the paired-type homeodomain transcription factor rx3 is critical for eye development, as all rx3 mutant fish are eyeless (Kennedy et al, 2004; Loosli et al, 2003; Loosli et al, 2001; Warren et al, 2021). There, rx3 controls survival of eye progenitors (Kennedy et al, 2004) as well as optic vesicle evagination and neuronal differentiation (Loosli et al, 2003), as revealed in the zebrafish chokh / rx3 loss-of-function background.…”

Characterizing the genetic basis of trait evolution in the Mexican cavefish

“…While our analysis was limited to phenotyping, previous studies have performed mapping studies to localize genomic regions associated with numerous traits including albinism, locomotor behavior, eye size, social behavior, nonvisual sensory systems (O'Quin and McGaugh 2016). Sequenced genomes for Pachón cave and surface populations of A. mexicanus are available and can be applied for mapping traits observed (McGaugh et al 2014;Warren et al 2021). The behavioral pipeline approach used in this study would be particularly powerful because it would allow for genomic mapping of many traits in a relatively small number of animals.…”