Dinaíza Abadia Rocha-Reis, Igor Henrique Rodrigues-Oliveira, Rubens Pasa, Fabiano Bezerra Menegídio, John Seymour Pat Heslop-Harrison, Trude Schwarzacher, Karine Frehner Kavalco
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After the whole genome sequencing, the satDNAs were retrieved, amplified, and hybridized in chromosome preparations for male and female individuals.</p><p><strong>Results: </strong>We found 30 satellite families (47 variants, two superfamilies) in H. ancistroides and 38 satellite families (45 variants, four superfamilies) in H. aff. ancistroides. The sequences varied from 14 bp to 2,662 bp in H. ancistroides and from 14 bp to 2,918 bp in H. aff. ancistroides. We did not observe any tandem repeats that were exclusive to each of the libraries; however, many sequences showed very different abundances and copy numbers between the libraries. Four satDNAs did not hybridize on the chromosomes of either species. Conversely, one satDNA hybridized in both species, HxySat1-80. However, the phenotypes found varied among species, populations, and in the same individual. There was no sign of HanSat3-464 and HanSat11-335 in any individuals of H. aff. ancistroides, but markings were in the chromosomes of H. ancistroides. HxySat12-1127 and HxySat8-52, on the other hand, were only hybridized in H. aff. ancistroides, while H. ancistroides had a negative sign. No hybridization of satDNAs was found in the X and Y sex chromosomes as they were mostly composed of euchromatin.</p><p><strong>Conclusion: </strong>We distinguish H. aff. ancistroides as genetically different from H. ancistroides, recognizing that such characteristics go far beyond morphological, karyotypic, and molecular data. Our data support the differential abundance and location of satellite DNAs and confirm that many organisms, including fish, have repetitive sequences that validate the library hypothesis. All found and validated satDNAs and the characterization of the satellitomes of the two species represent important contributions to cytogenomic studies of the genus Hypostomus.</p>","PeriodicalId":11206,"journal":{"name":"Cytogenetic and Genome Research","volume":null,"pages":null},"PeriodicalIF":1.7000,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"In silico Characterization of Satellitomes and Cross-Amplification of Putative satDNAs in Two Species of the Hypostomus ancistroides Complex (Siluriformes, Loricariidae).\",\"authors\":\"Dinaíza Abadia Rocha-Reis, Igor Henrique Rodrigues-Oliveira, Rubens Pasa, Fabiano Bezerra Menegídio, John Seymour Pat Heslop-Harrison, Trude Schwarzacher, Karine Frehner Kavalco\",\"doi\":\"10.1159/000539429\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Introduction: </strong>The mapping of the satellite DNA on chromosomes is vital to understanding the distribution and evolution of repetitions in the genome since these chromosomal studies have shown the origin, evolutionary mode, and function of repetitive sequences. This study aimed to prospect the satellitome and determine its location in the genome of two cryptic species of Hypostomus, H. aff. ancistroides and H. ancistroides, with and without XX/XY sexual chromosome system.</p><p><strong>Methods: </strong>Mitotic chromosomes and DNA extraction were obtained according to protocols. After the whole genome sequencing, the satDNAs were retrieved, amplified, and hybridized in chromosome preparations for male and female individuals.</p><p><strong>Results: </strong>We found 30 satellite families (47 variants, two superfamilies) in H. ancistroides and 38 satellite families (45 variants, four superfamilies) in H. aff. ancistroides. The sequences varied from 14 bp to 2,662 bp in H. ancistroides and from 14 bp to 2,918 bp in H. aff. ancistroides. We did not observe any tandem repeats that were exclusive to each of the libraries; however, many sequences showed very different abundances and copy numbers between the libraries. Four satDNAs did not hybridize on the chromosomes of either species. Conversely, one satDNA hybridized in both species, HxySat1-80. However, the phenotypes found varied among species, populations, and in the same individual. There was no sign of HanSat3-464 and HanSat11-335 in any individuals of H. aff. ancistroides, but markings were in the chromosomes of H. ancistroides. HxySat12-1127 and HxySat8-52, on the other hand, were only hybridized in H. aff. ancistroides, while H. ancistroides had a negative sign. No hybridization of satDNAs was found in the X and Y sex chromosomes as they were mostly composed of euchromatin.</p><p><strong>Conclusion: </strong>We distinguish H. aff. ancistroides as genetically different from H. ancistroides, recognizing that such characteristics go far beyond morphological, karyotypic, and molecular data. 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All found and validated satDNAs and the characterization of the satellitomes of the two species represent important contributions to cytogenomic studies of the genus Hypostomus.</p>\",\"PeriodicalId\":11206,\"journal\":{\"name\":\"Cytogenetic and Genome Research\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":1.7000,\"publicationDate\":\"2024-01-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Cytogenetic and Genome Research\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1159/000539429\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/7/30 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q4\",\"JCRName\":\"CELL BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Cytogenetic and Genome Research","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1159/000539429","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/7/30 0:00:00","PubModel":"Epub","JCR":"Q4","JCRName":"CELL BIOLOGY","Score":null,"Total":0}
引用次数: 0
摘要
引言 染色体上卫星 DNA 的图谱对于了解基因组中重复序列的分布和进化至关重要，因为这些染色体研究显示了重复序列的起源、进化模式和功能。本研究的目的是对有性染色体系统为 XX/XY 和无性染色体系统为 XX/XY 的两个隐蔽种 Hypostomus（H. aff. ancistroides 和 H. ancistroides）的卫星染色体进行勘测，并确定其在基因组中的位置。方法 按照规程获得有丝分裂染色体并提取 DNA。全基因组测序后，对雌雄个体的卫星 DNA 进行检索、扩增和染色体制备杂交。结果 我们在 H. ancistroides 中发现了 30 个卫星家族（47 个变体，2 个超家族），在 H. aff. ancistroides 中发现了 38 个卫星家族（45 个变体，4 个超家族）。H. ancistroides 的序列从 14bp 到 2662bp 不等，而 H. aff. ancistroides 的序列从 14bp 到 2918bp 不等。我们没有观察到每个文库独有的串联重复序列，但是，许多序列在不同文库中的丰度和拷贝数非常不同。四个 satDNA 在两个物种的染色体上都没有杂交。相反，有一个 satDNA 在两个物种中都有杂交，即 HxySat1-80。然而，在不同物种、种群和同一个体中发现的表型各不相同。在 H. aff. ancistroides 的任何个体中都没有发现 HanSat3-464 和 HanSat11-335 的迹象，但在 H. ancistroides 的染色体中发现了标记。另一方面，HxySat12-1127 和 HxySat8-52 只在 H. aff. ancistroides 中杂交，而 H. ancistroides 的杂交则为负号。在 X 和 Y 性染色体上没有发现 satDNAs 杂交，因为它们主要由非染色体组成。结论 我们将 H. aff. ancistroides 与 H. ancistroides 区分开来，认为它们在遗传学上是不同的，这些特征远远超出了形态学、核型和分子数据的范畴。我们的数据支持卫星 DNA 的不同丰度和位置，并证实包括鱼类在内的许多生物都有重复序列，从而验证了文库假说。所有发现和验证的卫星 DNAs 以及两个物种卫星组的特征描述是对鳙鱼属细胞基因组研究的重要贡献。
In silico Characterization of Satellitomes and Cross-Amplification of Putative satDNAs in Two Species of the Hypostomus ancistroides Complex (Siluriformes, Loricariidae).
Introduction: The mapping of the satellite DNA on chromosomes is vital to understanding the distribution and evolution of repetitions in the genome since these chromosomal studies have shown the origin, evolutionary mode, and function of repetitive sequences. This study aimed to prospect the satellitome and determine its location in the genome of two cryptic species of Hypostomus, H. aff. ancistroides and H. ancistroides, with and without XX/XY sexual chromosome system.
Methods: Mitotic chromosomes and DNA extraction were obtained according to protocols. After the whole genome sequencing, the satDNAs were retrieved, amplified, and hybridized in chromosome preparations for male and female individuals.
Results: We found 30 satellite families (47 variants, two superfamilies) in H. ancistroides and 38 satellite families (45 variants, four superfamilies) in H. aff. ancistroides. The sequences varied from 14 bp to 2,662 bp in H. ancistroides and from 14 bp to 2,918 bp in H. aff. ancistroides. We did not observe any tandem repeats that were exclusive to each of the libraries; however, many sequences showed very different abundances and copy numbers between the libraries. Four satDNAs did not hybridize on the chromosomes of either species. Conversely, one satDNA hybridized in both species, HxySat1-80. However, the phenotypes found varied among species, populations, and in the same individual. There was no sign of HanSat3-464 and HanSat11-335 in any individuals of H. aff. ancistroides, but markings were in the chromosomes of H. ancistroides. HxySat12-1127 and HxySat8-52, on the other hand, were only hybridized in H. aff. ancistroides, while H. ancistroides had a negative sign. No hybridization of satDNAs was found in the X and Y sex chromosomes as they were mostly composed of euchromatin.
Conclusion: We distinguish H. aff. ancistroides as genetically different from H. ancistroides, recognizing that such characteristics go far beyond morphological, karyotypic, and molecular data. Our data support the differential abundance and location of satellite DNAs and confirm that many organisms, including fish, have repetitive sequences that validate the library hypothesis. All found and validated satDNAs and the characterization of the satellitomes of the two species represent important contributions to cytogenomic studies of the genus Hypostomus.
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.
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