1、比较基因组学定义及其研究意义：
定义:比较基因组学是在基因组学水平上研究不同
物种和品系之间在基因组结构与功能方面的亲源
关系及其内在联系的一门新兴学科。
研究意义 (1) 指导在遗传与基因组信息较为缺乏的物种中 进行基因的克隆和功能研究。 (2) 通过研究生物进化过程中，基因组所发生的 倍增、缺失、重组，对于生物进化研究，具 有重大意义。
Murphy et al. Genome Research 1999 1 9 9 9
共线性与同线性
共线性（Colinearity）
在不同的基因组中基因
和基因的排列顺序的一
致性称为共线性，它反 应了一种同源关系。 同线性（synteny） 连锁的同源基因在不同 物种基因组中有相同连 锁关系。
遗 传 图 与 物 理 图 的 共 线 性
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• Drosophila melanogaster (fruit fly) — model insect
• Danio rerio (zebrafish) — a good model for vertebrate developmental biology • Mus musculus (mouse) — model mammal, important for the study of human genome • Arabidopsis thaliana (thale cress ) — model dicot plant • Oryza sativa (rice) — model cereal and monocot plant
Gene comparison provides a possible way to predict gene association and protein interaction
• Gene association: Genes involved in the same metabolic pathway tend to appear together in a genome. Hence, by examining whether two genes are correlated in many genomes,
Sequence-based comparison
• Comparison of overall statistics of nucleotide sequence • Comparison of coding sequence (genes) • Comparison of segmental sequence or whole
物种间物理图距的保守性
禾本科类受体激酶LrK基因簇中的基因间距在大麦 (A)、水稻(B)和玉米(C)中几乎完全相同，约为4—5 kb， 并保持很好的共线性。
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Genome alignment
Long sequence alignment is problematic due to rearrangement. Presently, almost all of the alignment algorithms first identify large conserved sequence elements between the two genome sequences, and then generate the overall alignment. In general, similar genomes may result in better alignment.
– genome size
– overall (G+C) content
– regntent – genome signature
• codon usage biases • amino acid usage biases • the ratio of observed dinucleotide frequency and the expected frequency given random nucleotide distribution
比较基因组学 Comparative Genomics
Xiaofang Xie E-mail:xxf317@
Some well-known model organisms
• Escherichia coli — model prokaryote • Saccharomyces cerevisiae (baker’s yeast) — model unicellular eukaryote • Caenorhabditis elegans (nematode) — an excellent model for multicellular developmental biology
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宏观共线性和微观共线性
• 宏观共线性（macrosynteny） ：
• 指遗传连锁图上锚定标记排列次序的一致性。
• 微观共线性(microsynteny) ：
• 是指物理图上基因顺序的一致排列。
Approaches for genome comparison
figure, two chromosome maps
(I and 1) are shown, which are completely colinear.
Comparative maps of the wheat genome described in terms of the rice genome (A) and the Ae. umbellulata genome (B)
What the genomes of model organisms tell us
Almost every human gene has a counterpart in the mouse and some blocks of DNA are proving impossible to tell apart
Ortholog vs. Paralog
• Ortholog（直向同源物）: homologous genes
or DNA sequences in different genomes
(species)
• Paralog（横向同源物）: homologous genes
or DNA sequences in the same genome
(species)
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paralogs
orthologs
Colinearity vs. Synteny
• Colinearity: conservation of
gene content and order in
different genomes, which is a reflection of homology • Synteny: conserved linkage among genes in different genomes regardless of order • macrosynteny vs. microsynteny
Similarity vs. Homology (相似性与同源性)
• Similarity: a phenomenon that different genes or genome segments show similar sequences.
• Homology: a phenomenon that different
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Comparison of genes
• Gene number • Gene homology • Gene category • Gene structure • Gene functional relationship and interaction
it could be deduced that the proteins coded by genes A and B might interact either functionally Sequence-based comparison
or physically.
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then compare the order of orthologs in those
species. • The comparison will show the macro-colinearity among the species being tested.
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Comparative genetic
maps of five
grass species: rice, foxtail millet, sorghum,
maize and
barley
Five grass genomes, one consensus map.
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genes or genome segments have the same ancestor.
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相似性与同源性
相似性(similarity)： 是指一种很直接的数量关系，比如部分相 同或相似的百分比或其它一些合适的度量。 同源性(homology)： 指从一些数据中推断出的两个基因或蛋白 质序列具有共同祖先的结论，属于质的判断。
genome (genome alignment)
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Comparison of overall nucleotide statistics