Instituto Latino-Americano de Ciências da Vida, Universidade Federal da Integração Latino-Americana, Foz do Iguaçu, Paraná, Brazil.
Departamento de Biologia Estrutural, Molecular e Genética, Programa de Pós-Graduação em Biologia Evolutiva, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil.
PLoS One. 2024 Nov 18;19(11):e0313896. doi: 10.1371/journal.pone.0313896. eCollection 2024.
Natural selection in the cave habitat has resulted in unique phenotypic traits (including pigmentation loss and ocular degeneration) in the Mexican tetra Astyanax mexicanus, considered a model species for evolutionary research. A. mexicanus has a karyotype of 2n = 50 chromosomes, and long-read sequencing and quantitative trait linkage maps (QTLs) have completely reconstructed the reference genome at the chromosomal level. In the current work, we performed whole chromosome isolation by microdissection and total amplification using DOP-PCR and Whole Chromosome Painting (WCP), followed by sequencing on the Illumina NextSeq platform, to investigate the microstructure of the large and conserved metacentric chromosome 1 of A. mexicanus. The sequences aligned to linkage block 3 of the reference genome, as determined by processing the reads with the DOPseq pipeline and characterizing the satellites with the TAREAN program. In addition, part of the sequences was anchored in linkage blocks that have not yet been assigned to the chromosomes. Furthermore, fluorescence in situ hybridization using WCP 1 carried out in other nearby species revealed a high degree of chromosome conservation, which allows us to hypothesize a common origin of this element. The physical mapping of the repetitive marker sequences provided a micro- and macrostructural overview and confirmed their position in chromosome pair 1. These sequences can serve as comparative tools for understanding the evolution and organization of this chromosome in other species of the family in future studies.
洞穴生境中的自然选择导致墨西哥脂鲤（Astyanax mexicanus）出现了独特的表型特征（包括色素丧失和眼部退化），它被认为是进化研究的模式物种。墨西哥脂鲤的染色体组型为 2n = 50 条染色体，长读测序和数量性状连锁图谱（QTL）已经完全重建了染色体水平的参考基因组。在当前的工作中，我们通过微切割和 DOP-PCR 及全染色体涂染（WCP）进行了全染色体分离和总扩增，然后在 Illumina NextSeq 平台上进行测序，以研究墨西哥脂鲤大型且保守的中央着丝粒染色体 1 的微结构。这些序列与参考基因组中通过 DOPseq 管道处理读段并通过 TAREAN 程序描述卫星所确定的连锁块 3 对齐。此外，部分序列锚定在尚未分配给染色体的连锁块中。此外，在其他附近物种中使用 WCP1 进行的荧光原位杂交揭示了高度的染色体保守性，这使我们可以假设该元件具有共同的起源。重复标记序列的物理图谱提供了微观和宏观结构概述，并确认了它们在染色体对 1 中的位置。这些序列可以作为比较工具，用于在未来的研究中了解该染色体在其他家族物种中的进化和组织。
