Aegilops ventricosa organellar-enriched DNA sequencing, assembly, and comparative genomics

Proper interactions between the nucleus and cytoplasmic organelles (mitochondria and plastids) are essential to eukaryotic cellular function. To improve our understanding of the role of organellar genomes and nuclear-cytoplasmic interactions in plant development and stress response, our first aim is to survey organellar genome diversity in wheat and across the broader Triticum-Aegilops complex. This will be followed by work to assess genome dynamics across developmental stages as well as during abiotic and biotic stress response. The results of this work will be important for improving crop traits. To accomplish our goals, it was critical to first establish improved methods for the isolation, sequencing, and assembly of organellar genomes from limited starting material without whole genome amplification. As a proof of concept, we optimized our methods using the Triticum aestivum cv. Chinese Spring, for which there is previous sequencing data available. The mitochondria and chloroplast genomes have large repeats (upto 10kb and 20kb in length, respectively). Previous studies have performed whole genome amplification and have manually stitched contigs to force a single master circle configuration of the organellar genomes, which may or may not reflect the true native state of the wheat organellar genomes. To resolve the long repeats and perform de novo assemblies without whole genome amplification and manual stitching of contigs, we utilized low input PacBio 20kb library preparations to generate long sequencing reads. In total, we sequenced 20 organellar-enriched samples with PacBio, including 13 diverse wild species, T. durum, T. aestivum cv. Chinese Spring, and three wheat alloplasmic lines. In addition we generated Illumina short-read sequences for many additional cultivars, wild species, and alloplasmic lines. This project includes data for one of these samples (Aegilops ventricosa). Raw sequencing reads are deposited here. Assemblies and annotations will be included once available.

细胞核与细胞质器官（如线粒体和叶绿体）之间的适当相互作用对于真核细胞功能至关重要。为了深化我们对细胞器基因组以及核-细胞质相互作用在植物发育和应激反应中作用的认知，我们的首要目标是调查小麦及其更广泛的 Triticum-Aegilops 复合群体中的细胞器基因组多样性。此研究将继之以评估基因组在发育阶段以及非生物和生物应激反应中的动态变化。该工作的成果对于改良作物性状具有重要意义。为实现我们的目标，首先建立改进的从有限起始材料中分离、测序和组装细胞器基因组的方法，且无需全基因组扩增，显得尤为关键。作为概念验证，我们利用具有先前测序数据的小麦品种 Triticum aestivum cv. Chinese Spring 优化了我们的方法。线粒体和叶绿体基因组存在大量重复序列（长度分别为 10kb 和 20kb）。先前的研究通过全基因组扩增并手动拼接连续片段，以强制形成细胞器基因组的单一主环结构，这可能或可能不会反映小麦细胞器基因组的真实原生状态。为了解决长重复序列，并在无需全基因组扩增和手动拼接连续片段的情况下进行从头组装，我们利用低输入 PacBio 20kb 库制备方案生成长测序读数。总计，我们使用 PacBio 测序了 20 个富含细胞器的样本，包括 13 个多样化的野生种、T. durum、T. aestivum cv. Chinese Spring 以及三个小麦异源多倍体系。此外，我们还为许多额外的栽培品种、野生种和异源多倍体系生成了 Illumina 短读序列。本项目包括其中一个样本（Aegilops ventricosa）的数据。原始测序读数已存档于此。一旦组装和注释完成，将包含在内。