Sequence and chromatin characteristics of the largest known plant sex chromosome

陆地植物孢子体的单性性已经进化了很多次，这意味着各种性别决定形式的独立起源，包括XY性别决定，无论是同态性染色体还是异型性染色体。后者是已知的大麻，Humulus, Silene， Rumex和Coccinia，葫芦科是本项目的重点，继续PI的工作，揭示植物性染色体进化的阶段和球虫属二态性染色体的进化。我们已经证实，C. grandis的Y染色体是陆地植物中最大的，而该物种的总基因组相对较小，并且在系统发育上接近于黄瓜，黄瓜是一个重要作物的全基因组注释的属。目前的工作将解决我们对植物性染色体的理解中的两个空白：(i)缺乏对异型性染色体DNA组成的分析，（ii）缺乏关于X和Y染色体是否显示组蛋白差异的信息，就像在剂量补偿动物XY系统中的情况一样。为了填补这些空白，我们将通过流式细胞术和显微解剖分离性染色体，并生成一株雄性植物、一株雌性植物、纯X染色体和纯Y染色体的illumina低覆盖率基因组。然后，生物信息学分析将揭示重复DNA的类型和相对频率，与常染色体和X染色体相比，重复DNA的类型和相对频率有望成为Y染色体大幅增加的基础。在（重复DNA和多倍体）期间，PI的实验室建立了Illumina数据的相关工作管道，并将适用于本项目。参与该项目的博士后在访问J. Fuchs和A. Houben， IPK， Gatersleben的实验室期间获得的试点数据表明，X和Y染色体可以被显微解剖，并且对分离的染色体进行Illumina测序是可行的。同样，组蛋白甲基化的初步数据显示了性别特异性模式。最后，利用基于重复dna的新探针，我们在培养的大球虫及其相关物种中进行FISH检测，将澄清其他球虫物种是否具有早期异型性染色体。

Unisexuality of land plant sporophytes has evolved many times, implying the independent origin of various forms of sex determination, including XY sex determination, with either homomorphic sex chromosomes or heteromorphic sex chromosomes. The latter are known from Cannabis, Humulus, Silene, Rumex, and Coccinia, the Cucurbitaceae that is the focus of the present project, continuing the PI's work on unveiling stages of sex chromosome evolution in plants and the evolution of dimorphic sex chromosomes in the genus Coccinia. We have confirmed that the Y chromosome of C. grandis is the largest in land plants, while the species' total genome is relatively small and phylogenetically close to Cucumis, a genus with >5 fully annotated genomes of important crops. The present work will address two gaps in our understanding of plant sex chromosomes: (i) lack of analysis of the DNA composition of heteromorphic sex chromosomes, (ii) lack of information on whether X and Y chromosomes show histone differences, as is the case in dosage-compensated animal XY systems. To fill these gaps, we will isolate sex chromosomes by flow cytometry and microdissection, and generate Illumina-sequenced low-coverage genomes of a male plant, a female plant, pure X chromosomes, and pure Y chromosomes. Bioinformatics analyses will then reveal the types and relative frequencies of the repetitive DNA that is expected to underlie the huge size increase in the Y chromosome compared to the autosomes and X chromosome. Relevant work pipelines for Illumina data were established in the PI's lab during (on repetitive DNA and polyploidy) and will be adapted for the present project. Pilot data obtained by the postdoc to be working in this project during visits to the labs of J. Fuchs and A. Houben, IPK, Gatersleben, show that the X and the Y chromosome can be microdissected and that Illumina sequencing of isolated chromosomes is feasible. Likewise, pilot data on histone methylation suggest sex-specific patterns. Lastly, using repetitive DNA-based new probes, FISH in Coccinia grandis and related species that we have in cultivation will clarify whether other Coccinia species have incipient heteromorphic sex chromosomes or not.