Supplementary files: Recombination suppression drives expansion of the Drosophila dot chromosome

Genome size varies widely, even among closely related species, yet much less is known about chromosome size variation. Here we use the fourth chromosome of Drosophila, also known as the “Muller F element” or “dot chromosome”, as a model to investigate chromosome-specific size expansion. The F element of most Drosophila species is small (~1.3 Mb) and almost entirely heterochromatic, yet harbors approximately 80 protein-coding genes. Here, we study D. kikkawai, D. takahashii, D. ananassae, and D. bipectinata, whose F elements are 2- to 15-fold larger in size compared to D. melanogaster. Through manual gene curation and comparative genomic analysis, we find that their F elements have expanded primarily via accumulation of transposable elements (TEs) in introns and intergenic regions. Natural selection appears less efficient on these expanded F elements: they have smaller effective population sizes and their genes exhibit reduced usage of optimal codons, compared to D. melanogaster. We propose that F element size variation is driven by differences in F element recombination rates. The ultra-long (~20 Mb) F elements of D. ananassae and D. bipectinata display high rates of rearrangement and sequence evolution, and exhibit independent TE-driven expansions. Our results suggest the F elements of most Drosophila species likely recombine enough to prevent size expansion, while F element recombination in D. ananassae and D. bipectinata is either absent or rare enough to allow TEs and other deleterious mutations to accumulate via Muller’s ratchet; thus, these chromosomes evolve more like a Y chromosome than a typical Drosophila F element.File format information can be found:GFF: https://genome.ucsc.edu/FAQ/FAQformat.html#format3RepeatMasker: https://www.repeatmasker.org/webrepeatmaskerhelp.htmlFASTA: https://www.ncbi.nlm.nih.gov/genbank/fastaformat/PSL: https://genome.ucsc.edu/FAQ/FAQformat.html#format2Link file columns are as follows:1. Chrom12. Gene start3. Gene stop4. Chrom25. Ortholog start6. Ortholog stop即便在亲缘关系较近的物种间，基因组大小也存在显著差异，但我们对染色体大小变异的认知却相对匮乏。本研究以果蝇（Drosophila）的第四条染色体——亦被称为“穆勒F元件（Muller F element）”或“点染色体（dot chromosome）”——作为模型，探究染色体特异性的大小扩张现象。 多数果蝇物种的F元件体积较小（约1.3 Mb），且几乎完全为异染色质区域，却承载了约80个蛋白质编码基因。 本研究选取基克瓦果蝇（D. kikkawai）、高桥果蝇（D. takahashii）、安娜果蝇（D. ananassae）和双梳果蝇（D. bipectinata）作为研究对象，它们的F元件大小是黑腹果蝇（D. melanogaster）的2至15倍。 通过人工基因注释与比较基因组学分析，我们发现这些物种的F元件扩张主要源于转座因子（transposable elements, TEs）在内含子及基因间区域的积累。 相较于黑腹果蝇，这些扩张后的F元件上的自然选择效率似乎更低：它们的有效种群规模更小，且其基因对最优密码子的使用频率更低。 我们提出，F元件的大小变异由其重组率差异所驱动。 安娜果蝇与双梳果蝇的超长F元件（约20 Mb）表现出极高的重排速率与序列进化速率，且呈现出独立的转座因子介导的扩张过程。 我们的研究结果表明，多数果蝇物种的F元件重组频率足以阻止其大小扩张；而安娜果蝇与双梳果蝇的F元件要么完全不发生重组，要么重组频率极低，使得转座因子及其他有害突变可通过穆勒棘轮（Muller's ratchet）效应积累。因此，这类染色体的进化模式更接近于Y染色体，而非典型的果蝇F元件。 相关文件格式说明如下： GFF: 请参考 https://genome.ucsc.edu/FAQ/FAQformat.html#format3 RepeatMasker: 请参考 https://www.repeatmasker.org/webrepeatmaskerhelp.html FASTA: 请参考 https://www.ncbi.nlm.nih.gov/genbank/fastaformat/ PSL: 请参考 https://genome.ucsc.edu/FAQ/FAQformat.html#format2 关联文件的列字段说明如下： 1. Chrom1 2. Gene start 3. Gene stop 4. Chrom2 5. Ortholog start 6. Ortholog stop