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The cavefish genome reveals candidate genes for eye loss.

ABSTRACT: Natural populations subjected to strong environmental selection pressures offer a window into the genetic underpinnings of evolutionary change. Cavefish populations, Astyanax mexicanus (Teleostei: Characiphysi), exhibit repeated, independent evolution for a variety of traits including eye degeneration, pigment loss, increased size and number of taste buds and mechanosensory organs, and shifts in many behavioural traits. Surface and cave forms are interfertile making this system amenable to genetic interrogation; however, lack of a reference genome has hampered efforts to identify genes responsible for changes in cave forms of A. mexicanus. Here we present the first de novo genome assembly for Astyanax mexicanus cavefish, contrast repeat elements to other teleost genomes, identify candidate genes underlying quantitative trait loci (QTL), and assay these candidate genes for potential functional and expression differences. We expect the cavefish genome to advance understanding of the evolutionary process, as well as, analogous human disease including retinal dysfunction.

SUBMITTER: McGaugh SE

PROVIDER: S-EPMC4218959 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature

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The cavefish genome reveals candidate genes for eye loss.

McGaugh Suzanne E SE Gross Joshua B JB Aken Bronwen B Blin Maryline M Borowsky Richard R Chalopin Domitille D Hinaux Hélène H Jeffery William R WR Keene Alex A Ma Li L Minx Patrick P Murphy Daniel D O'Quin Kelly E KE Rétaux Sylvie S Rohner Nicolas N Searle Steve M J SM Stahl Bethany A BA Tabin Cliff C Volff Jean-Nicolas JN Yoshizawa Masato M Warren Wesley C WC

Nature communications 20141020

Natural populations subjected to strong environmental selection pressures offer a window into the genetic underpinnings of evolutionary change. Cavefish populations, Astyanax mexicanus (Teleostei: Characiphysi), exhibit repeated, independent evolution for a variety of traits including eye degeneration, pigment loss, increased size and number of taste buds and mechanosensory organs, and shifts in many behavioural traits. Surface and cave forms are interfertile making this system amenable to genet ...[more]

PMID: 25329095

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Project description:BackgroundMango, Mangifera indica L., an important tropical fruit crop, is grown for its sweet and aromatic fruits. Past improvement of this species has predominantly relied on chance seedlings derived from over 1000 cultivars in the Indian sub-continent with a large variation for fruit size, yield, biotic and abiotic stress resistance, and fruit quality among other traits. Historically, mango has been an orphan crop with very limited molecular information. Only recently have molecular and genomics-based analyses enabled the creation of linkage maps, transcriptomes, and diversity analysis of large collections. Additionally, the combined analysis of genomic and phenotypic information is poised to improve mango breeding efficiency.ResultsThis study sequenced, de novo assembled, analyzed, and annotated the genome of the monoembryonic mango cultivar 'Tommy Atkins'. The draft genome sequence was generated using NRGene de-novo Magic on high molecular weight DNA of 'Tommy Atkins', supplemented by 10X Genomics long read sequencing to improve the initial assembly. A hybrid population between 'Tommy Atkins' x 'Kensington Pride' was used to generate phased haplotype chromosomes and a highly resolved phased SNP map. The final 'Tommy Atkins' genome assembly was a consensus sequence that included 20 pseudomolecules representing the 20 chromosomes of mango and included ~?86% of the ~?439?Mb haploid mango genome. Skim sequencing identified ~?3.3?M SNPs using the 'Tommy Atkins' x 'Kensington Pride' mapping population. Repeat masking identified 26,616 genes with a median length of 3348?bp. A whole genome duplication analysis revealed an ancestral 65 MYA polyploidization event shared with Anacardium occidentale. Two regions, one on LG4 and one on LG7 containing 28 candidate genes, were associated with the commercially important fruit size characteristic in the mapping population.ConclusionsThe availability of the complete 'Tommy Atkins' mango genome will aid global initiatives to study mango genetics.

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The cavefish genome reveals candidate genes for eye loss.

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The cavefish genome reveals candidate genes for eye loss.

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