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

Chao Bian,Qiong Shi,Yu Huang,Weiting Chen,Tengfei Xu,Zhiqiang Ruan,Wei Ge,Zhe Hu,Yunyun Lv,Jia Li

doi:10.3390/ijms21072385

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.

Highlights

Laboratory zebrafish has been one of the most widely utilized models for developmental biology, genetics, in vivo imaging, and modeling of human genetic diseases, owing to its rapid development, high fecundity, and juvenile transparency [1,2,3,4]
To resolve the problem of this deficiency, a transparent casper mutant that lacks both light-absorbing melanophores and reflective iridophores was generated by crossing nacre and roy orbison mutants [5]
We found that only one private single nucleotide polymorphisms (SNPs) of the casper group was a nonsense mutation (g. chr6:43360485 C>T), which led to a premature termination codon

Summary

Introduction

Laboratory zebrafish has been one of the most widely utilized models for developmental biology, genetics, in vivo imaging, and modeling of human genetic diseases, owing to its rapid development, high fecundity, and juvenile transparency [1,2,3,4]. The nacre is a white mutant that carries a mutation in the gene of mitfa (microphthalmia-associated transcription factor) [6], leading to a recessive phenotype of a complete loss of black melanophores. How this inactivated mitfa regulates or impacts its upstream and downstream genes is still largely unknown. The nacre is a white zebrafish emxhutiabnittethdatacamrroieds earmatuetaltoiosnsionfthireigdeonpe hofomreitsfaa(lmoincrgopthhtehablmodiay-asasxoicsia[te8d].trAanrscercipetniotnsftaucdtoyr) [9] further demonstra[t6e],dleathdiantg ttho ea rmecpesvs1iv7e−p/−hezneotbyrpaefiosfha ckonmopclekteoulotss oefxbhlaicbkitmeedlaniroipdhooprehs.oHreowloevsesr., hIotwwthaiss postulated itnhaacttivthateedmmpivtf1a7regguenlaeteisnorziembpraacfitssihtscuopustlrdeapmlaayndadkoewynrsotrleeamingpenyersimis sidtililnlaergsyelnytuhneksnioswfon.r iridophore developmernedtuacTnthiodenrmooyfamimnuettleaannntaopsnhhcooewre[ss9.a].RreIectcseensdstievstetaupdilhieeedsnougtsyeipnnegowmcDitehNlAceosmciolponnlesitnehglaorvsespeoonrftoeirdtidbtohepaehtnomrsepsevqa1un7de(napcageretdinaeleither. A recent study [9] further demonstrated that the mpv17−/− zebrafish knockouts exhibited iridophore

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