分子遗传学-植物基因组学

Yang Qin, Li Zhi et al. 2013 PNAS
Epigenomics
a, Averaged DNA methylation levels along the gene bodies and 15 kilobases (kb) upstream of the transcription start sites (TSS) and 15 kb downstream of the transcription end sites (TES) of all RefSeq genes. b, Methylation landscape across each stage of human early embryos. The averaged DNA methylation level of each developmental stage is calculated based on the overlapped 100-base-pair (bp) tiles detected in all of the developmental stages analysed. c, Averaged DNA methylation levels of human sperm, ICM of the blastocysts and post-implantation embryos. d, Averaged DNA methylation levels of individual male and female pronuclei of zygotes at different time points after intra-cytoplasmic sperm injection (ICSI).
Many genomes sequenced
• Wheat • Cotton
• • • • • • • • • Maize Chickpea Cowpea Common bean Pigeonpea Rice barley Sorghum Soybean • • • • • • • • • • • • Ground nut Tomato Brassica Carrot Canola Sugar Beet Sugar Cane Wild grasses Pepper Cucumber Lettuce Arabidopsis • • • • • • • • • • • • Mouse Rat Zebra fish Pig Cow Sheep Goat Chicken Cod Salmon Camel Human
The gene number is similar in various plants?
Yandell and Ence, Nat Genet Rev, 2012, 13: 329-341
How to study genomics?
Mapping 作图 Sequencing 测序 Assemble 组装
Genetic map 遗传图
Physical map 物理图
Map-based sequencing 图谱测序
Random sequencing 随机测序
Framework mapping 骨架图
Gap mapping 空隙填图
Coordinating 整合
Correcting 校正
Draft and completed sequence 草图与精细图
(a) Percent coverage of TEs in nonoverlapping windows (window size = 500 kb). Outer tick marks show the calculated lengths of 13 G. arboreum pseudochromosomes. (b) Gene density estimated on the basis of the number of genes in non-overlapping 500-kb windows. (c) Transcription state. The transcript level for each gene was estimated by averaging values of reads per kilobase of mapped cDNA per million reads (RPKM) from different tissues in nonoverlapping 500-kb windows. (d) Marker density represented by the number of SNPs in non-overlapping 500-kb windows. (e) GC content estimated on the basis of the percentage of G+C nucleotides in 500-kb non-overlapping windows.
The history of the Human Genome Project (HGP)
1990 Official start of HGP with 3 billion $ and a 15 year horizon 1999 Sanger Centre publishes chromosome 22 1999 China is responsible for sequencing 1% of the human genome 2001 Draft Genome published: Celera & Public 2003 Completion (almost) of Human Genome
中国农业大学国家玉米改良中心 National Maize Improvement Center of China, CAU
植物基因组学Ⅰ Plant Genomics
杨小红 yxiaohong@cau.edu.cn
Plant Genomics
What is genomics? The history of genomics How to study the genomics? Molecular markers Libraries Sequencing Characterization of genome
基因组DNA
全基因组霰弹法 （Whole Genome Shotgun)
What is molecular markers
A molecular marker is a fragment of DNA that is associated with a certain location within the genome.
Structural Genomics (结构基因组) Functional Genomics (功能基因组) Postgenomics (后基因组) Epigenomics (表观基因组学) Metagenomics (宏基因组学)
Characterization of the G. arboreum cotton genome
Many genomes sequenced

Eukaryotes: 2398 Prokaryotes: 48665 Viruses: 4905 Plasmid: 6121 13572
http://www.ncbi.nlm.nih.gov/genome/browse/_2014.09.25

Summary of genomes sequenced in major plants
Year 2000 2002 2008 2009 2013 2014 Species Arabidopsis Rice Sorghum Maize Wheat Cotton Chr No. Geno Size Gene NO. Ref. 5 12 10 10 21 26 125 Mb 420 Mb 730 Mb 2300 Mb 4940 Mb (A/D) 1724 Mb 25,498 32,00050,000 34,496 32,000 34,87943,150 41,330 Nature, 408: 796-815 Science, 2002, 296(5565): 92-100; 296(5565):79-92 Nature, 457: 551-556 Science, 326: 1112-1115; 326: 1078 Nature, 496: 87-90; 496: 91-95 Nature Genetics, 46: 567-572
逐步克隆法（Clone by Clone）
完整的基因 组序列 基因组DNA
BAC文库wenku.baidu.com根据物理图谱 正确定位的 BAC 或contig
测序并进行 全基因组序 列组装
霰弹法克隆 用于霰弹法测 序的候选克隆 用于霰弹法测序 的亚克隆 测序并组装 ………ATGCCGTAGGCCTAGC TAGGCCTAGCTCGGA…… 完整的基因 组序列 ………ATGCCGTAGGCCTAGCTCGGA……
The history of genomics
1977, bacteriophage φX174, 5,375 bp (Sanger et al. Nature, 1977, 265: 687 - 695) 1995, Haemophilus influenzae, 1.8 Mb (Fleischmann et al. Science, 1995, 28: 269 (5223): 496-512 2001, Human, 3,200 Mb (International Human Genome Sequencing Consortium, Nature, 2001, 409: 860-921)
Barley
The importance of molecular markers in genome sequencing 基因组测序的基本策略是将整个基因组分割 成一些小的片段分别测序，然后将测序的片 段进行组装，使其回归到原来的位置。为了 确保分散的基因片段正确归位组装，必须寻 找一批标记，它们在染色体上的位置是已知 的、唯一的、确定的，并位于不同的测序片 段之中。
What is genomics?
Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyze the function and structure of genomes.
Li et al. Nat Genet. 2014, 46: 567-571
TE-related haplotypes displayed variable photoperiod sensitivities
Yang Qin, Li Zhi et al. 2013 PNAS
Transformation-mediated validation of ZmCCT
Guo et al. Nature, 2014, 511: 606-610
The pipeline to obtain high-quality population genomes from multiple deep metagenomes
Albertsen et al. Nat Biotech, 2013, 31: 533–538
Genetic map (遗传图谱) is a linkage map that shows the relative locations of various genes or markers, which are inferred by the recombinant rate between markers (cM).