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Sequence and chromatin characteristics of the largest known plant sex chromosome

已知最大植物性染色体的序列和染色质特征

基本信息

批准号：
254585705
负责人：
Professorin Dr. Susanne Sabine Renner
金额：
--
依托单位：
Department of Biology
依托单位国家：
德国
项目类别：
Research Grants
财政年份：
2014
资助国家：
德国
起止时间：
2013-12-31 至 2017-12-31
项目状态：
已结题

来源：
https://gepris.dfg.de/gepris/projekt/254585705?language=en
关键词：
Sequence chromatin characteristics largest known

项目摘要

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.

陆生植物孢子体的单性经历了多次进化，暗示了各种形式的性别决定（包括XY性别决定）的独立起源，无论是同形性染色体还是异形性染色体。后者已知来自Cannabis，Humulus，Silene，Rumex和Coccinia，葫芦科是本项目的重点，继续PI关于揭示植物性染色体进化阶段和Coccinia属中二型性染色体进化的工作。我们已经证实了C. grandis是陆地植物中最大的，而该物种的总基因组相对较小，并且在遗传学上接近黄瓜属，黄瓜属具有>5个完全注释的重要作物基因组。目前的工作将解决我们对植物性染色体的理解中的两个差距：（i）缺乏对异形性染色体的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，就像在剂量补偿的动物XY系统中一样。为了填补这些空白，我们将通过流式细胞术和显微切割分离性染色体，并生成Illumina测序的雄性植物、雌性植物、纯X染色体和纯Y染色体的低覆盖率基因组。然后，生物信息学分析将揭示重复DNA的类型和相对频率，预计这些重复DNA是Y染色体与常染色体和X染色体相比尺寸大幅增加的基础。Illumina数据的相关工作管道在PI的实验室中建立（关于重复DNA和多倍性），并将适用于本项目。在访问J. Fuchs和A. Houben，IPK，Gatersleben，表明X和Y染色体可以被显微切割，并且分离的染色体的Illumina测序是可行的。同样，组蛋白甲基化的试验数据表明性别特异性模式。最后，使用重复的DNA为基础的新的探针，荧光原位杂交在大瓢虫和相关的物种，我们在培养将澄清是否其他瓢虫物种有初期异形性染色体或没有。