玻璃鲶(Kryptopterus vitreolus)染色体水平的基因组组装揭示了其透明表型的分子线索。

IF 4 1区 生物学 Q1 ZOOLOGY
Chao Bian, Rui-Han Li, Zhi-Qiang Ruan, Wei-Ting Chen, Yu Huang, Li-Yue Liu, Hong-Ling Zhou, Cheong-Meng Chong, Xi-Dong Mu, Qiong Shi
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引用次数: 0

摘要

玻璃鲶(Kryptopterus vitreolus)因其高度透明的体型而在水族贸易中备受瞩目。这种透明性是由于主体失去了大部分反射性虹膜和吸光黑色素,但面部和头部仍保留了某些黑色和银色色素。然而,迄今为止,这种透明表型的分子机制在很大程度上仍然未知。为了探索这种透明现象的遗传基础,我们利用 PacBio 和 Hi-C 测序技术以及标准的组装和注释流程,构建了玻璃鲶染色体组水平的单倍型基因组组装,其中包括 32 条染色体和 23 344 个蛋白质编码基因。分析发现,编码酪氨酸酶相关蛋白 1 的推定白化病相关 tyrp1b 基因中存在一个过早终止密码子,使其成为一个无功能的假基因。值得注意的是,通过与其他 30 多种鱼类进行同源比较,发现玻璃鲶基因组中丢失了内皮素-3(edn3b)基因。为了研究 edn3b 的作用,我们生成了 edn3b -/- 突变体斑马鱼,与野生型斑马鱼相比,这些斑马鱼体表条纹中的黑色素显著减少。这些发现表明,edn3b的缺失导致了玻璃鲶的透明表型。我们高质量的染色体级基因组组装和关键基因的鉴定为玻璃鲶的透明表型提供了重要的分子见解。这些发现不仅加深了我们对玻璃鲶透明表型的分子机制的理解,而且为进一步研究各种动物的色素沉着提供了宝贵的基因资源。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Chromosome-level genome assembly of the glass catfish ( Kryptopterus vitreolus) reveals molecular clues to its transparent phenotype.

Glass catfish ( Kryptopterus vitreolus) are notable in the aquarium trade for their highly transparent body pattern. This transparency is due to the loss of most reflective iridophores and light-absorbing melanophores in the main body, although certain black and silver pigments remain in the face and head. To date, however, the molecular mechanisms underlying this transparent phenotype remain largely unknown. To explore the genetic basis of this transparency, we constructed a chromosome-level haplotypic genome assembly for the glass catfish, encompassing 32 chromosomes and 23 344 protein-coding genes, using PacBio and Hi-C sequencing technologies and standard assembly and annotation pipelines. Analysis revealed a premature stop codon in the putative albinism-related tyrp1b gene, encoding tyrosinase-related protein 1, rendering it a nonfunctional pseudogene. Notably, a synteny comparison with over 30 other fish species identified the loss of the endothelin-3 ( edn3b) gene in the glass catfish genome. To investigate the role of edn3b, we generated edn3b -/- mutant zebrafish, which exhibited a remarkable reduction in black pigments in body surface stripes compared to wild-type zebrafish. These findings indicate that edn3b loss contributes to the transparent phenotype of the glass catfish. Our high-quality chromosome-scale genome assembly and identification of key genes provide important molecular insights into the transparent phenotype of glass catfish. These findings not only enhance our understanding of the molecular mechanisms underlying transparency in glass catfish, but also offer a valuable genetic resource for further research on pigmentation in various animal species.

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来源期刊
Zoological Research
Zoological Research Medicine-General Medicine
CiteScore
7.60
自引率
10.20%
发文量
1937
审稿时长
8 weeks
期刊介绍: Established in 1980, Zoological Research (ZR) is a bimonthly publication produced by Kunming Institute of Zoology, the Chinese Academy of Sciences, and the China Zoological Society. It publishes peer-reviewed original research article/review/report/note/letter to the editor/editorial in English on Primates and Animal Models, Conservation and Utilization of Animal Resources, and Animal Diversity and Evolution.
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