Genome and Transcriptome Sequencing of casper and roy Zebrafish Mutants Provides Novel Genetic Clues for Iridophore Loss

Abstract

casper has been a widely used transparent mutant of zebrafish. It possesses a combined loss of reflective iridophores and light-absorbing melanophores, which gives rise to its almost transparent trunk throughout larval and adult stages. Nevertheless, genomic causal mutations of this transparent phenotype are poorly defined. To identify the potential genetic basis of this fascinating morphological phenotype, we constructed genome maps by performing genome sequencing of 28 zebrafish individuals including wild-type AB strain, roy orbison (roy), and casper mutants. A total of 4.3 million high-quality and high-confidence homozygous single nucleotide polymorphisms (SNPs) were detected in the present study. We also identified a 6.0-Mb linkage disequilibrium block specifically in both roy and casper that was composed of 39 functional genes, of which the mpv17 gene was potentially involved in the regulation of iridophore formation and maintenance. This is the first report of high-confidence genomic mutations in the mpv17 gene of roy and casper that potentially leads to defective splicing as one major molecular clue for the iridophore loss. Additionally, comparative transcriptomic analyses of skin tissues from the AB, roy and casper groups revealed detailed transcriptional changes of several core genes that may be involved in melanophore and iridophore degeneration. In summary, our updated genome and transcriptome sequencing of the casper and roy mutants provides novel genetic clues for the iridophore loss. These new genomic variation maps will offer a solid genetic basis for expanding the zebrafish mutant database and in-depth investigation into pigmentation of animals.

Phylogenetic Analysis of Core Melanin Synthesis Genes Provides Novel Insights Into the Molecular Basis of Albinism in Fish

“…We identified premature stop variations and gene loss that are potentially leading to melanin loss in fishes with the albinism phenotype, including Mexican tetra ( McGaugh et al, 2014 ), zebrafish ( Danio rerio, nacre/casper mutants) ( Howe et al, 2013 ; Bian et al, 2020 ), Chinese clearhead icefish ( Liu et al, 2017 ), deep-sea Mariana snailfish ( Pseudoliparis swirei ), and cave-restricted golden-line barbel fish ( Sinocyclocheilus anshuiensis ; Yang et al, 2016 ). These premature stop variants and gene loss could provide novel molecular interpretations for melanin loss and albinism in various vertebrates.…”

“…The tyrp1 gene might play an additional role in survival and proliferation of melanocytes. The expression of pmel (premelanosome protein) and tyrp1 genes is often regulated by mitf (microphthalmia-associated transcription factor a; see Figure 1 ; Braasch et al, 2009a ; Bian et al, 2020 ).…”

col1a2 + fibroblasts/muscle progenitors finetune xanthophore countershading by differentially expressing csf1a/1b in embryonic zebrafish

“…S1F). We further examined xanthophores in mpv17 mutants in which iridophores are severely defective ( 44 , 45 ). The xanthophore pattern was normal in mpv17 mutants, suggesting that iridophores were dispensable for embryonic xanthophore patterning (figs.…”

Evolutionary Genomics Reveals Multiple Functions of Arylalkylamine N-Acetyltransferase in Fish

“…AANAT plays critical roles in melatonin biosynthesis, and sometimes for potential dopamine metabolism, which are responsible for various physiological functions, such as seasonal migration, amphibious aerial vision, and cave or deep-sea adaptation. Interestingly, many transparent fish ( Liu et al, 2017 ; Bian et al, 2020 ) are short of melatonin, possibly due to an inactivation of AANAT or other melatonin biosynthesizing enzyme(s); their shorter life-time (half a year for a transparent roy zebrafish ( Bian et al, 2020 ), instead of 3–5 years for the wildtype) suggests that restoration of AANAT or melatonin may become an effective way to increase the lifetime of transparent fish. Meanwhile, accumulated genome and transcriptome data ( Li et al, 2015 ; Sun et al, 2016 ; Hughes et al, 2018 ) provide genetic resources to obtain more and more sequences of aanat genes, which will enrich our understanding of AANAT and melatonin functions in various fishes, and ultimately improve and standardize husbandry practices (such as management of light, feeding, and spawning) in fish aquaculture worldwide.…”