Table1_Genomic Differences Between the Sexes in a Fish Species Seen Through Satellite DNAs.pdf

Neotropical fishes have highly diversified karyotypic and genomic characteristics and present many diverse sex chromosome systems, with various degrees of sex chromosome differentiation. Knowledge on their sex-specific composition and evolution, however, is still limited. Satellite DNAs (satDNAs) are tandemly repeated sequences with pervasive genomic distribution and distinctive evolutionary pathways, and investigating satDNA content might shed light into how genome architecture is organized in fishes and in their sex chromosomes. The present study investigated the satellitome of Megaleporinus elongatus, a freshwater fish with a proposed Z1Z1Z2Z2/Z1W1Z2W2 multiple sex chromosome system that encompasses a highly heterochromatic and differentiated W1 chromosome. The species satellitome comprises of 140 different satDNA families, including previously isolated sequences and new families found in this study. This diversity is remarkable considering the relatively low proportion that satDNAs generally account for the M. elongatus genome (around only 5%). Differences between the sexes in regards of satDNA content were also evidenced, as these sequences are 14% more abundant in the female genome. The occurrence of sex-biased signatures of satDNA evolution in the species is tightly linked to satellite enrichment associated with W1 in females. Although both sexes share practically all satDNAs, the overall massive amplification of only a few of them accompanied the W1 differentiation. We also investigated the expansion and diversification of the two most abundant satDNAs of M. elongatus, MelSat01-36 and MelSat02-26, both highly amplified sequences in W1 and, in MelSat02-26’s case, also harbored by Z2 and W2 chromosomes. We compared their occurrences in M. elongatus and the sister species M. macrocephalus (with a standard ZW sex chromosome system) and concluded that both satDNAs have led to the formation of highly amplified arrays in both species; however, they formed species-specific organization on female-restricted sex chromosomes. Our results show how satDNA composition is highly diversified in M. elongatus, in which their accumulation is significantly contributing to W1 differentiation and not satDNA diversity per se. Also, the evolutionary behavior of these repeats may be associated with genome plasticity and satDNA variability between the sexes and between closely related species, influencing how seemingly homeologous heteromorphic sex chromosomes undergo independent satDNA evolution.

新热带区鱼类具有高度多样化的核型与基因组特征，且存在多种不同的性染色体系统，性染色体分化程度各异。然而，学界对其性别特异性组成与演化的认知仍较为有限。卫星DNA (satDNAs) 是一类串联重复序列，在基因组中广泛分布且具有独特的演化路径，对其含量展开研究有助于解析鱼类及其性染色体的基因组结构组织方式。
本研究对长形大脂鲤（*Megaleporinus elongatus*）的卫星组（satellitome）进行了分析，该物种为淡水鱼类，被认为拥有Z1Z1Z2Z2/Z1W1Z2W2型多重性染色体系统，其中包含一条异染色质化且高度分化的W1染色体。该物种的卫星组包含140个不同的卫星DNA家族，涵盖此前已报道的序列以及本研究新发现的家族。考虑到卫星DNA在长形大脂鲤基因组中占比仅约5%，这一多样性水平颇为显著。
研究同时证实了该物种在卫星DNA含量上的性别差异：雌性基因组中的卫星DNA丰度较雄性高出14%。该物种卫星DNA演化所呈现的性别偏好特征，与雌性W1染色体相关的卫星DNA富集紧密相关。尽管雌雄两性几乎共享所有的卫星DNA家族，但仅少数卫星DNA家族发生了大规模扩增，这一过程伴随着W1染色体的分化。
本研究还对长形大脂鲤丰度最高的两种卫星DNA——MelSat01-36与MelSat02-26——的扩增与分化模式进行了分析。二者均在W1染色体中呈现高度扩增的特征；其中MelSat02-26还存在于Z2和W2染色体中。研究团队将这两种卫星DNA在长形大脂鲤及其近缘物种大头大脂鲤（*M. macrocephalus*，该物种拥有典型ZW型性染色体系统）中的分布情况进行了比较，结果显示：两种卫星DNA在两个物种中均形成了高度扩增的阵列，但在雌性限制性性染色体上呈现出物种特异性的组织模式。
本研究结果表明，长形大脂鲤的卫星DNA组成具有高度多样性，其W1染色体的分化主要源于卫星DNA的积累，而非卫星DNA本身的多样性。此外，这些重复序列的演化行为可能与基因组可塑性、不同性别间以及近缘物种间的卫星DNA变异相关，这会影响看似同源的异形性染色体如何经历独立的卫星DNA演化过程。