High Amplification of CLA-SAT-149 Satellite DNA in Bighead Catfish: Insights into Satellite DNA Evolution in Clariid Lineages.

IF 1.3 4区生物学 Q4 CELL BIOLOGY

Cytogenetic and Genome Research Pub Date : 2025-10-07 DOI:10.1159/000548841

Worapong Singchat, Wattanawan Jaito, Trifan Budi, Thitipong Panthum, Narongrit Muangmai, Chaiwut Grudpan, Jarungjit Grudpan, Suphada Kiriratnikom, Kyudong Han, Darren K Griffin, Prateep Duengkae, Yoichi Matsuda, Kornsorn Srikulnath

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引用次数: 0

Abstract

Introduction: Satellite DNA (satDNA) is an important component of eukaryotic genomes that influences chromosomal organization and evolution. This study investigates the sequence diversity, chromosomal distribution, and copy number variation of the CLA-SAT-149 satDNA family (149 bp) in four clariid catfish species, Clarias macrocephalus, C. gariepinus, C. batrachus, and C. nieuhofii, as well as in F1 hybrids and backcross (BC) progeny.

Methods: Fluorescence in situ hybridization (FISH) was used to map CLA-SAT-149 on metaphase chromosomes. Quantitative PCR (qPCR) quantified copy number variation. Amplicon sequencing was applied to characterize sequence variants, and Bayesian clustering analysis was used to assess genetic relationships among subfamilies.

Results: Chromosome mapping showed species-specific signals present in C. macrocephalus and F1 hybrids but absent in C. gariepinus and C. nieuhofii. qPCR revealed significantly higher copy numbers in C. macrocephalus. Two sequence variants were identified: the canonical 149-bp (subfamily A) and an 85-bp derivative (subfamily B). Bayesian analysis indicated multiple genetically distinct subgroups among species. F1 hybrids and BC progeny exhibited unique sequence profiles and copy number patterns, while C. nieuhofii lacked CLA-SAT-149 entirely.

Conclusion: The results support lineage-specific expansion, amplification, and loss of CLA-SAT-149 in clariid catfish, consistent with the satDNA library model. These patterns provide insights into satDNA evolution and have potential applications in aquaculture genetics, hybrid identification, and species differentiation.

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鳙鱼CLA-SAT-149卫星DNA的高扩增：对Clariid谱系中卫星DNA进化的见解。

卫星DNA （satDNA）是真核生物基因组的重要组成部分，影响染色体的组织和进化。本文研究了CLA-SAT-149 satDNA家族（149 bp）在大头鲶、加里平鲶、batrachus和nieuhofii四种鲶鱼以及F1杂交和回交（BC）后代中的序列多样性、染色体分布和拷贝数变异。方法：采用荧光原位杂交技术（FISH）对CLA-SAT-149进行中期染色体定位。定量PCR （qPCR）定量拷贝数变异。扩增子测序用于序列变异的表征，贝叶斯聚类分析用于评估亚家族之间的遗传关系。结果：染色体定位显示，大头棘球蚴和F1杂交体中存在物种特异性信号，而加里平棘球蚴和新霍菲棘球蚴中不存在。qPCR结果显示，大头虾的拷贝数显著增加。鉴定出两个序列变异：典型的149-bp （A亚家族）和85-bp的衍生物（B亚家族）。贝叶斯分析表明物种间存在多个遗传上不同的亚群。F1杂种和BC后代表现出独特的序列特征和拷贝数模式，而新霍氏球菌完全缺乏CLA-SAT-149。结论：结果支持CLA-SAT-149在澄清鲶鱼中特异性扩增、扩增和缺失，与satDNA文库模型一致。这些模式提供了对卫星dna进化的深入了解，并在水产养殖遗传学、杂交鉴定和物种分化方面具有潜在的应用价值。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Cytogenetic and Genome Research 生物-细胞生物学

CiteScore

3.10

自引率

5.90%

发文量

审稿时长

1 months

期刊介绍： During the last decades, ''Cytogenetic and Genome Research'' has been the leading forum for original reports and reviews in human and animal cytogenetics, including molecular, clinical and comparative cytogenetics. In recent years, most of its papers have centered on genome research, including gene cloning and sequencing, gene mapping, gene regulation and expression, cancer genetics, comparative genetics, gene linkage and related areas. The journal also publishes key papers on chromosome aberrations in somatic, meiotic and malignant cells. Its scope has expanded to include studies on invertebrate and plant cytogenetics and genomics. Also featured are the vast majority of the reports of the International Workshops on Human Chromosome Mapping, the reports of international human and animal chromosome nomenclature committees, and proceedings of the American and European cytogenetic conferences and other events. In addition to regular issues, the journal has been publishing since 2002 a series of topical issues on a broad variety of themes from cytogenetic and genome research.