Optimizing exome captures in species with large genomes using species-specific repetitive DNA blocker

Large and highly repetitive genomes are common. However, research interests usually lie within the non-repetitive parts of the genome, as they are more likely functional, and can be used to answer questions related to adaptation, selection, and evolutionary history. Exome capture is a cost-effective method for providing sequencing data from protein-coding parts of the genes. C0t-1 DNA blockers consist of repetitive DNA and are used in exome captures to prevent the hybridization of repetitive DNA sequences to capture baits or bait-bound genomic DNA. Universal blockers target repetitive regions shared by many species, while species-specific c0t-1 DNA is prepared from the DNA of the studied species, thus perfectly matching the repetitive DNA contents of the species. So far the use of species-specific c0t-1 DNA has been limited to a few model species. Here, we evaluated the performance of blocker treatments in exome captures of Pinus sylvestris, a widely distributed conifer species with a l..., The original Pinus tabuliformis reference genome (v1.0; Niu et al., 2022) was masked to increase mapping to the genome by correcting problems in the genome polishing, as many identical sequences were found at the ends of different chromosomes. To construct a masked version of the reference genome, chromosomes were first split back into contigs. Contigs were then aligned within chromosomes and between unplaced contigs using Minimap2 (Li, 2018). Alignments were then chained to longer ones using the ChainPaf module of Lep-Anchor (Rastas, 2020). Half of the aligning regions of > 10 kb were masked by masking the region in shorter of the two contigs involved in the alignment., , # Data from: Optimizing Exome Captures in Species with Large Genomes Using Species-specific Repetitive DNA Blocker [https://doi.org/10.5061/dryad.qfttdz0rw](https://doi.org/10.5061/dryad.qfttdz0rw) ## Description of the data and file structure The original *Pinus tabuliformis* reference genome (v1.0; Niu et al., 2022) was masked to increase mapping to the genome by correcting errors in the genome polishing, as many identical sequences were found at the ends of different chromosomes. To construct a masked version of the reference genome, chromosomes were first split back into contigs. Contigs were then aligned within chromosomes and between unplaced contigs using Minimap2 (Li, 2018). Alignments were then chained to longer ones using the ChainPaf module of Lep-Anchor (Rastas, 2020). Half of the aligning regions of > 10 kb were masked by masking the region in shorter of the two contigs involved in the alignment. ### Files and variables #### File: liftover\_gff3.awk **Description:*...大型且高度重复的基因组十分常见。然而，研究的核心关注点通常集中在基因组的非重复区域——这类区域更可能具备生物学功能，可用于解答与适应性演化、自然选择及进化历史相关的诸多科学问题。 外显子组捕获（exome capture）是一种经济高效的技术手段，能够获取基因编码蛋白区域的测序数据。C0t-1 DNA封闭剂由重复DNA序列构成，在外显子组捕获实验中用于阻断重复DNA序列与捕获探针（capture bait）或结合了探针的基因组DNA发生非特异性杂交。通用封闭剂靶向多个物种共有的重复序列区域，而物种特异性C0t-1 DNA则从研究对象物种的基因组DNA中制备，因此可完美匹配该物种自身的重复DNA组成。迄今为止，物种特异性C0t-1 DNA的应用仅局限于少数模式生物物种。本研究评估了封闭剂处理在欧洲赤松（Pinus sylvestris）外显子组捕获实验中的应用效果——欧洲赤松是一种分布广泛的针叶树，其基因组（原文此处有截断）。 原始油松（Pinus tabuliformis）参考基因组（v1.0；Niu等，2022）因在不同染色体末端发现大量高度相似的序列，通过修正基因组抛光流程中的错误以提升序列比对效率，故对其进行了重复序列屏蔽。为构建屏蔽后的参考基因组版本，首先将染色体拆解为重叠群（contig）；随后使用Minimap2工具（Li，2018）在染色体内部以及未定位重叠群之间进行序列比对；再通过Lep-Anchor的ChainPaf模块（Rastas，2020）将零散的比对结果拼接为更长的比对区段；最终将长度大于10kb的比对区域中，两个参与比对的重叠群内较短的那个的对应区域进行屏蔽，以此完成全基因组的重复序列屏蔽。 # 数据来源：利用物种特异性重复DNA封闭剂优化大型基因组物种的外显子组捕获 [https://doi.org/10.5061/dryad.qfttdz0rw](https://doi.org/10.5061/dryad.qfttdz0rw) ## 数据与文件结构说明 原始油松（Pinus tabuliformis）参考基因组（v1.0；Niu等，2022）因在不同染色体末端发现大量高度相似的序列，通过修正基因组抛光流程中的错误以提升序列比对效率，故对其进行了重复序列屏蔽。为构建屏蔽后的参考基因组版本，首先将染色体拆解为重叠群（contig）；随后使用Minimap2工具（Li，2018）在染色体内部以及未定位重叠群之间进行序列比对；再通过Lep-Anchor的ChainPaf模块（Rastas，2020）将零散的比对结果拼接为更长的比对区段；最终将长度大于10kb的比对区域中，两个参与比对的重叠群内较短的那个的对应区域进行屏蔽，以此完成全基因组的重复序列屏蔽。 ### 文件与变量 #### 文件：liftover_gff3.awk **描述：*...（原文截断）