Genome of a stage-dependent cave-dwelling frog reveals the genetic mechanism of an extremely divergent biphasic life cycle.

IF 7.5 1区生物学 Q1 CELL BIOLOGY

Cell reports Pub Date : 2025-04-29 DOI:10.1016/j.celrep.2025.115640

Ningning Lu, Wei Zhu, Chen-Yang Tang, Chaochao Yan, Qiheng Chen, Wei Wu, Liming Chang, Jianping Jiang, Jia-Tang Li, Bin Wang

{"title":"Genome of a stage-dependent cave-dwelling frog reveals the genetic mechanism of an extremely divergent biphasic life cycle.","authors":"Ningning Lu, Wei Zhu, Chen-Yang Tang, Chaochao Yan, Qiheng Chen, Wei Wu, Liming Chang, Jianping Jiang, Jia-Tang Li, Bin Wang","doi":"10.1016/j.celrep.2025.115640","DOIUrl":null,"url":null,"abstract":"<p><p>Cave-dwelling species offer unique insights into adaptive evolution. The stage-dependent cave frog, Oreolalax rhodostigmatus (Orho), exhibits troglomorphic traits as a tadpole in Karst caves, transitioning to a troglophilic/trogloxenic lifestyle after metamorphosis, characterized by developed pigment and eyes. We present the Orho genome (3.16 Gb, 26,192 protein-coding genes), revealing extensive expansion and positive selection in gene families associated with olfactory, taste, visual, and pain perceptions. Orho tadpoles exhibit suppressed visual function while retaining crystalline lens development. Adult eyes demonstrate high light-induced plasticity in the visual cycle. Orho tadpoles display both developmental and light-induced melanogenesis, which is associated with distinctive tyrosinases. A stage-dependent amphibian-specific tyrosinase subfamily, reported here, underpins their ontogenetic pigmentation. Additionally, prominent hepatic fat storage and genetic/transcriptional variations in lipid metabolism genes characterize tadpole development. These findings unveil the molecular mechanisms behind Orho's stage-dependent cave adaptation, which differs mechanistically from cavefishes, offering valuable insights into the highly divergent biphasic life cycle.</p>","PeriodicalId":9798,"journal":{"name":"Cell reports","volume":"44 5","pages":"115640"},"PeriodicalIF":7.5000,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Cell reports","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1016/j.celrep.2025.115640","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CELL BIOLOGY","Score":null,"Total":0}

引用次数: 0

Abstract

Cave-dwelling species offer unique insights into adaptive evolution. The stage-dependent cave frog, Oreolalax rhodostigmatus (Orho), exhibits troglomorphic traits as a tadpole in Karst caves, transitioning to a troglophilic/trogloxenic lifestyle after metamorphosis, characterized by developed pigment and eyes. We present the Orho genome (3.16 Gb, 26,192 protein-coding genes), revealing extensive expansion and positive selection in gene families associated with olfactory, taste, visual, and pain perceptions. Orho tadpoles exhibit suppressed visual function while retaining crystalline lens development. Adult eyes demonstrate high light-induced plasticity in the visual cycle. Orho tadpoles display both developmental and light-induced melanogenesis, which is associated with distinctive tyrosinases. A stage-dependent amphibian-specific tyrosinase subfamily, reported here, underpins their ontogenetic pigmentation. Additionally, prominent hepatic fat storage and genetic/transcriptional variations in lipid metabolism genes characterize tadpole development. These findings unveil the molecular mechanisms behind Orho's stage-dependent cave adaptation, which differs mechanistically from cavefishes, offering valuable insights into the highly divergent biphasic life cycle.

查看原文本刊更多论文

一个阶段依赖穴居青蛙的基因组揭示了一个极端不同的双相生命周期的遗传机制。

穴居物种为适应性进化提供了独特的视角。穴居蛙（Oreolalax rhodostimatus, Orho）是一种阶段依赖的洞穴蛙，在洞穴中作为蝌蚪表现出穴居动物的特征，在蜕变后过渡到穴居动物/穴居动物的生活方式，其特征是发育了色素和眼睛。我们展示了Orho基因组（3.16 Gb, 26,192个蛋白质编码基因），揭示了与嗅觉，味觉，视觉和疼痛感知相关的基因家族的广泛扩展和积极选择。小蝌蚪在保持晶状体发育的同时表现出抑制的视觉功能。成人的眼睛在视觉循环中表现出高度的光诱导可塑性。蝌蚪显示发育和光诱导黑素形成，这与独特的酪氨酸酶有关。一个阶段依赖的两栖动物特异性酪氨酸酶亚家族，在这里报道，支持他们的个体发生色素沉着。此外，突出的肝脏脂肪储存和脂质代谢基因的遗传/转录变异是蝌蚪发育的特征。这些发现揭示了Orho的阶段依赖洞穴适应背后的分子机制，这与洞穴鱼的机制不同，为高度分化的双相生命周期提供了有价值的见解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Cell reports CELL BIOLOGY-

CiteScore

13.80

自引率

1.10%

发文量

1305

审稿时长

77 days

期刊介绍： Cell Reports publishes high-quality research across the life sciences and focuses on new biological insight as its primary criterion for publication. The journal offers three primary article types: Reports, which are shorter single-point articles, research articles, which are longer and provide deeper mechanistic insights, and resources, which highlight significant technical advances or major informational datasets that contribute to biological advances. Reviews covering recent literature in emerging and active fields are also accepted. The Cell Reports Portfolio includes gold open-access journals that cover life, medical, and physical sciences, and its mission is to make cutting-edge research and methodologies available to a wide readership. The journal's professional in-house editors work closely with authors, reviewers, and the scientific advisory board, which consists of current and future leaders in their respective fields. The advisory board guides the scope, content, and quality of the journal, but editorial decisions are independently made by the in-house scientific editors of Cell Reports.