Urban John M, Gerbi Susan A, Spradling Allan C
Carnegie Institution for Science, Department of Embryology, Howard Hughes Medical Institute Research Laboratories, 3520 San Martin Drive, Baltimore, MD, 21218, USA.
Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA.
BMC Genomics. 2025 May 5;26(1):443. doi: 10.1186/s12864-025-11573-2.
The lower Dipteran fungus gnat, Bradysia (aka Sciara) coprophila, has compelling chromosome biology. Paternal chromosomes are eliminated during male meiosis I and both maternal X sister chromatids are retained in male meiosis II. Embryos start with three copies of the X chromosome, but 1-2 copies are eliminated from somatic cells as part of sex determination, and one is eliminated in the germline to restore diploidy. In addition, there is gene amplification in larval polytene chromosomes, and the X polytene chromosome folds back on itself mediated by extremely long-range interactions between three loci. These developmentally normal events present opportunities to study chromosome behaviors that are unusual in other systems. Moreover, little is known about the centromeric and telomeric sequences of lower Dipterans in general, and there are recent claims of horizontally-transferred genes in fungus gnats. Overall, there is a pressing need to learn more about the fungus gnat chromosome sequences.
We produced the first chromosome-scale models of the X and autosomal chromosomes where each somatic chromosome is represented by a single scaffold. Extensive analysis supports the chromosome identity and structural accuracy of the scaffolds, demonstrating they are co-linear with historical polytene maps, consistent with evolutionary expectations, and have accurate centromere positions, chromosome lengths, and copy numbers. The positions of alleged horizontally-transferred genes in the nuclear chromosomes were broadly confirmed by genomic analyses of the chromosome scaffolds using Hi-C and single-molecule long-read datasets. The chromosomal context of repeats shows family-specific biases, such as retrotransposons correlated with the centromeres. Moreover, scaffold termini were enriched with arrays of retrotransposon-related sequence as well as nucleosome-length (~ 175 bp) satellite repeats. Finally, the Hi-C data captured Mb-scale physical interactions on the X chromosome that are seen in polytene spreads, and we characterize these interesting "fold-back regions" at the sequence level for the first time.
The chromosome scaffolds were shown to be of exceptional quality, including loci harboring horizontally-transferred genes. Repeat analyses demonstrate family-specific biases and telomere repeat candidates. Hi-C analyses revealed the sequences of ultra-long-range interactions on the X chromosome. The chromosome-scale scaffolds pave the way for further studies of the unusual chromosome movements in Bradysia coprophila.
较低等的双翅目真菌蚋，即嗜粪迟眼蕈蚊（又名Sciara），具有引人注目的染色体生物学特性。父本染色体在雄性减数分裂I期间被消除，而母本的两条X姐妹染色单体在雄性减数分裂II中得以保留。胚胎开始时具有三条X染色体拷贝，但作为性别决定的一部分，体细胞中会消除1至2条拷贝，而生殖细胞中会消除一条以恢复二倍体状态。此外，幼虫多线染色体中存在基因扩增现象，并且X多线染色体通过三个位点之间的极远距离相互作用自身折叠回来。这些发育正常的事件为研究其他系统中不常见的染色体行为提供了机会。此外，一般而言，对于较低等双翅目的着丝粒和端粒序列知之甚少，并且近期有关于真菌蚋中水平转移基因的报道。总体而言，迫切需要更多地了解真菌蚋的染色体序列。
我们构建了X染色体和常染色体的首个染色体水平模型，其中每个体细胞染色体由单个支架表示。广泛的分析支持了支架的染色体身份和结构准确性，表明它们与历史多线图谱共线，符合进化预期，并且具有准确的着丝粒位置、染色体长度和拷贝数。通过使用Hi-C和单分子长读长数据集对染色体支架进行基因组分析，大致确认了核染色体中所谓水平转移基因的位置。重复序列的染色体背景显示出家族特异性偏差，例如与着丝粒相关的反转录转座子。此外，支架末端富含反转录转座子相关序列阵列以及核小体长度（约175 bp）的卫星重复序列。最后，Hi-C数据捕获了多线染色体铺展中可见的X染色体上兆碱基规模的物理相互作用，并且我们首次在序列水平上对这些有趣的“折叠回区域”进行了表征。
已证明染色体支架具有卓越的质量，包括含有水平转移基因的位点。重复序列分析显示出家族特异性偏差和端粒重复序列候选物。Hi-C分析揭示了X染色体上超长距离相互作用的序列。染色体水平的支架为进一步研究嗜粪迟眼蕈蚊中不寻常的染色体运动铺平了道路。
