兰州大学生物信息学课件：11-基因组分析-王则夫.pptx

基因组分析——以牦牛和胡杨等基因组为例王则夫2015年11月1日1. 基因组测序技术全基因组de novo测序：在不依赖于参考基因组的情况下对某一物种进行基因组测序及拼接，从而绘制该物种的全基因组序列图谱。1.1 基因组测序的里程碑1.2 基因组测序的发展2001200220042006200720082009201019982000201120121.3 基因组文章的发表趋势平均IF文章数量（不完全统计）1.4 基因组分析基本流程1材料准备、建库测序基因家族分析系统进化分析分化时间估算全基因组复制分析共线性分析群体历史分析(PSMC)重复序列注释基因结构注释（De novo预测、基于同源预测、基于表达序列预测）基因功能注释（GO、KEGG）基因组组装策略的选择（直接组装、复合式组装）基因组组装质量的评估（大小、N的比例、N50）2基因组组装流式细胞仪预估基因组大小根据基因组特征制定建库测序策略3基因组注释4流程化分析5个性化分析2. 基因组文献解读ⅠLETTERThe yak genome and adaptation to life at high altitude2012年度全国高校十大科研进展2.1 背景简介世界上生活在海拔最高处的哺乳动物，是高寒地区的特有牛种主要产于中国青藏高原海拔3000米以上地区适应高寒生态条件，有“高原之舟”之称在高寒牧区具有不可替代的生态、社会、经济地位牦牛(Bos grunniens) Wiener G, The Yak 2nd edition. (2013)2.2 科学问题牦牛的高海拔适应性 large lungs and hearts lack of hypoxic pulmonary vasoconstriction increased foraging ability strong environmental sense high energy metabolism 2.3 材料与测序a female domestic yak whole-genome shotgun strategy Illumina HiSeq 2000 platform4.4 billion reads from paired-end libraries~65X (Genome size ~3Gb)测序结果统计表2.4 基因组组装Contig N50 20.4 kbScaffold N50 1.4 MbTotal length 2,657 Mb (close to the cattle genome, 2,649Mb)2.4.1 基因组组装结果统计表 the largest scaffold spanning 8.8 Mb2.4.2 物种间比较评估Blank entries indicate that data are not available. Note that NGS assemblies may not be as contiguous as the Sanger-sequenced genomes with lower coverage.2.4.3 根据测序深度的分布进行评估The sequencing depth of 98% of the assembly was more than 20-fold2.4.4 结合fosmids进行评估Supplementary Figure 2: Comparison of scaffolds with sequence of fosmids (A) Yakbx, (B) Yakfx, (C) Yakgx, (D) Yakhx, (E) Yakjx and (F) Yakkx, to evaluate the completeness and accuracy of the yak assembly. Read depth on the fosmid was calculated by mapping the short reads onto the fosmid sequences. The predicted genes and annotated transposable elements (TEs) are shown in green and red, respectively. The remaining unclosed gaps on the scaffolds are marked as white blocks; most of these correspond to repetitive sequences.2.4.5 结合转录组数据进行评估 The genome assembly cover