Schemberger Michelle Orane, Nascimento Viviane Demetrio, Coan Rafael, Ramos Érica, Nogaroto Viviane, Ziemniczak Kaline, Valente Guilherme Targino, Moreira-Filho Orlando, Martins Cesar, Vicari Marcelo Ricardo
Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti, 4748, Ponta Grossa, Paraná, 84030-900, Brazil.
Programa de Pós-Graduação em Genética, Centro Politécnico, Universidade Federal do Paraná, Jardim das Américas, Caixa-Postal: 19071, Curitiba, Paraná, 81531-990, Brazil.
Chromosoma. 2019 Dec;128(4):547-560. doi: 10.1007/s00412-019-00721-9. Epub 2019 Aug 27.
Sex chromosome differentiation is subject to independent evolutionary processes among different lineages. The accumulation of repetitive DNAs and consequent crossing-over restriction guide the origin of the heteromorphic sex chromosome region. Several Neotropical fish species have emerged as interesting models for understanding evolution and genome diversity, although knowledge of their genomes is scarce. Here, we investigate the content of repetitive DNAs between males and females of Apareiodon sp. based on large-scale genomic data focusing on W sex chromosome differentiation. In Apareiodon, females are the heterogametic sex (ZW) and males are the homogametic sex (ZZ). The genome size estimate for Apareiodon was 1.2 Gb (with ~ 42× and ~ 47× coverage for males and females, respectively). In Apareiodon sp., approximately 36% of the genome was composed of repetitive DNAs and transposable elements (TEs) were the most abundant class. Read coverage analysis revealed different amounts of repetitive DNAs in males and females. The female-enriched clusters were located on the W sex chromosome and were mostly composed of microsatellite expansions and DNA transposons. Landscape analysis of TE contents demonstrated two major waves of invasions of TEs in the Apareiodon genome. Estimation of TE insertion times correlated with in situ locations permitted the inference that helitron, Tc1-mariner, and CMC EnSpm DNA transposons accumulated repeated copies during W chromosome differentiation between 20 and 12 million years ago. DNA transposons and microsatellite expansions appeared to be major players in W chromosome differentiation and to guide modifications in the genome content of the heteromorphic sex chromosomes.
性染色体分化在不同谱系中经历独立的进化过程。重复DNA的积累以及随之而来的交叉限制引导了异形性染色体区域的起源。尽管对新热带鱼类的基因组了解甚少，但几种新热带鱼类已成为理解进化和基因组多样性的有趣模型。在这里，我们基于聚焦W性染色体分化的大规模基因组数据，研究了无齿脂鲤属物种雌雄之间重复DNA的含量。在无齿脂鲤属中，雌性为异配性别（ZW），雄性为同配性别（ZZ）。无齿脂鲤属的基因组大小估计为1.2 Gb（雄性和雌性的覆盖度分别约为42倍和47倍）。在无齿脂鲤属物种中，约36%的基因组由重复DNA组成，转座元件（TEs）是最丰富的类别。读取覆盖度分析揭示了雌雄之间重复DNA的含量不同。雌性富集的簇位于W性染色体上，主要由微卫星扩增和DNA转座子组成。TE含量的景观分析表明，TEs在无齿脂鲤属基因组中有两次主要的入侵浪潮。对TE插入时间的估计与原位位置相关，这使得我们可以推断，在2000万至1200万年前W染色体分化期间，滚环转座子、Tc1-水手转座子和CMC EnSpm DNA转座子积累了重复拷贝。DNA转座子和微卫星扩增似乎是W染色体分化的主要因素，并引导异形性染色体基因组内容的修饰。
