Supporting data for "Genomic evidence of neo-sex chromosomes in the Eastern Yellow Robin"

Understanding sex-biased natural selection can be greatly enhanced by access to well-annotated chromosomes including ones inherited in sex-specific fashions. The Eastern Yellow Robin (EYR) is an endemic Australian songbird inferred to have experienced climate-driven sex-biased selection and is a prominent model for studying mitochondrial-nuclear interactions in the wild. However, the lack of an EYR reference genome containing both sex chromosomes (in birds, a female bearing Z and W chromosomes) is limiting current efforts to understand the mechanisms of these processes. Here, we assemble the genome for a female EYR and use low depth (10 ×) genome resequencing data from 19 individuals of known sex to identify chromosome fragments with sex-specific inheritance. <br> MaSurCA hybrid assembly using Nanopore and Illumina reads generated a 1.22 Gb EYR genome in 20,702 scaffolds (94.2% BUSCO completeness). Scaffolds were tested for W-linked (female-only) inheritance using a k-mer approach, and for Zlinked inheritance using median read-depth test in male and female reads (read-depths must indicate haploid female and diploid male representation). This resulted in 2,372 W-linked scaffolds (total length: 97,872,282 bp, N50: 81,931 bp) and 586 Z-linked scaffolds (total length: 121,817,358 bp, N50: 551,641 bp). Anchoring of the sex-linked EYR scaffolds to the reference genome of a female Zebra Finch revealed two categories of sex-linked genome region. First, 653 W-linked scaffolds (25.7 Mb) were anchored to the W sex chromosome and 215 Z-linked scaffolds (74.4 Mb) to the Z. Second, 1138 W-linked scaffolds (70.9 Mb), and 179 Z-linked scaffolds (51.0 Mb), were anchored to a large section (coordinates ~5 to ~60 Mb) of Zebra Finch chromosome 1A. The first ~5 Mb and last ~14 Mb of the reference chromosome 1A had only autosomally-behaving EYR scaffolds mapping to them. <br>We report a female (W-chromosome containing) EYR genome and provide genomic evidence for a neo-sex (neo-W and neo-Z) chromosome system in EYR, involving most of a large chromosome (1A) previously only reported to be autosomal in passerines.

对性别偏向自然选择的研究，可通过获取注释完善的染色体（包括以性别特异性方式遗传的染色体）得以显著深化。东部黄鸲（Eastern Yellow Robin, EYR）是澳大利亚特有的鸣禽，被推断经历过气候驱动的性别偏向选择，也是野外探究线粒体-核互作机制的主流研究模型。然而，目前缺乏同时涵盖两条性染色体的东部黄鸲参考基因组（鸟类中雌性携带Z与W染色体），这一短板限制了学界对上述过程分子机制的解析。为此，本研究组装了一只雌性东部黄鸲的基因组，并利用19个已知性别的个体的低深度（10×）基因组重测序数据，鉴定具有性别特异性遗传模式的染色体片段。
本研究结合纳米孔（Nanopore）与Illumina测序读长，通过MaSurCA混合组装策略构建了包含20702个支架序列（scaffold）的1.22 Gb东部黄鸲基因组，其BUSCO（Benchmarking Universal Single-Copy Orthologs）完整度达94.2%。我们采用k-mer方法检测支架序列的W连锁（仅雌性携带）遗传特征，同时通过对雌雄个体测序深度（read-depth）的中位值检验鉴定Z连锁支架序列（测序深度需符合雌性单倍型、雄性二倍型的分布特征）。最终得到2372个W连锁支架序列（总长度：97,872,282 bp，N50：81,931 bp）及586个Z连锁支架序列（总长度：121,817,358 bp，N50：551,641 bp）。
通过将东部黄鸲的性连锁支架序列与雌性斑胸草雀（Zebra Finch）参考基因组进行锚定比对，我们发现两类性连锁基因组区域：其一，25.7 Mb的653个W连锁支架序列被锚定至W性染色体，74.4 Mb的215个Z连锁支架序列被锚定至Z染色体；其二，70.9 Mb的1138个W连锁支架序列与51.0 Mb的179个Z连锁支架序列被锚定至斑胸草雀1号染色体1A上约5 Mb至约60 Mb的大片段区域。参考染色体1A的前约5 Mb与后约14 Mb区域，仅存在表现为常染色体遗传模式的东部黄鸲支架序列可比对锚定。
本研究报道了包含W染色体的雌性东部黄鸲参考基因组，并为东部黄鸲存在新性染色体（neo-W与neo-Z）系统提供了基因组学证据，该新性染色体系统涉及此前仅在雀形目鸟类中被报道为常染色体的大片段1号染色体1A的大部分区域。