植物比较基因组学

O. ridleyi
O. granulata
450 448 354 423 1124 653 1000 960
1283 338
1283
862
Mb
O. sativa O. glaberrima O. barthii O. glumaepatula
AA O. longstaminata
O. meridionalis O. nivara O. rufipogon O. spontanea
Arabidopsis 125
Lily
100,000
0.15 100.00
Repetitive DNA 重复序列
C-Value Paradox:
Variation in Genome Size among Plants
Species Mb/haploid
Barley
5000
Diploid
Wheat
Eleusine (finger millet)
Zizania (wild rice)
Oryza (rice)
Avena (oats) Hordeum (barley) Secale (rye) Triticum (wheat)
Example
Genus
Subfamily
Family
Ahn and Tanksley (1993) PNAS
Pooideae Ehrhartoideae Chloridoideae Panicoideae
Poaceae (Gramineae)
Saccharum (sugarcane)
Sorghum Zea (maize)
Tripsacum Setaria (foxtail millet) Pennisetum (pearl millet)
Retrotransposon 反转座子
The retrotransposons inserted into the maize genome 2 to 6 million years ago, which expanded the maize genome by a factor of 2.
PNAS 95: 1975 (1998)
禾本科植物具有很强的同线性
野生稻的系统进化关系
O. rufipogon O. nivara O. glaberrima O. punctata O. minuta O. officinalis O. alta O. australiensis
O. coarctata O. brachyantha
植物基因组的大小
4800 Mb
2800 Mb 450 Mb 360 Mb 140 Mb
16000 Mb
拟南芥
二穗 短柄草
水稻
玉米
大麦
栽培小麦
C-Value Paradox:
Variation in Genome Size among Plants
Species Mb/haploid pg/haploid
16000
Hexaploid
Polyploidy 倍性
C-Value Paradox:
Human Genome 3000 Mb
Fugu Fish
400 Mb
Repetitive DNA
Intron Size
1 222 3 45 678
12 3 45 678
A
B
Ancestral Segment
1 22 3 45 678
Colinearity and Exceptions in Adh1 region of maize and sorghum
PNAS 96: 7409 (1999)
Barley and Rice Colinear Regions
Zein gene family in maize, rice and sorghum genomes
(Domestication)
Impacts of Comparative Genomics
Improve annotation of genomes Evaluate the extent of synteny between species Analyze genes and genome evolution Help in cloning important genes Understand comparative biology and biodiversity
BB O. punctata
CC EE
O. eichingeri O. officinalis O. rhizomatis
O. australiensis
FF GG
O. brachyantha
O. granulata O. meyeriana O. neocaledonica
BBCC
O. minuta O. punctata
CCDD
O. alta O. grandiglumis O. latifolia
wk.baidu.com
HHJJ
O. longiglumis O. ridleyi
HHKK O. schlechteri
野生稻的系统进化关系
O. rufipogon O. nivara O. glaberrima O. punctata O. minuta O. officinalis O. alta O. australiensis
1 2 2 3 476 5 8 1 C
223
4 5 67
8
D
Maize

Sh2
Sorghum
B
B P CP C
P
BB C
C
Sn Sn
B C C Pm B
Sh2
Rice
B X S H Ss B
A1-a
XX
B
Bg S S X B
A1-b
Sh2
A1
A1
5 kb
Sorghum
Sh2

TT S-1
植物比较基因组学研究 Comparative Genomics
陈明生 中国科学院遗传发育所
2006年10月20日
植物比较基因组学研究 基因组物理图谱和遗传图谱 基因组加倍 禾本科作物的人工驯化
(Domestication)
植物比较基因组学研究 基因组物理图谱和遗传图谱 基因组加倍 禾本科作物的人工驯化
X1 X2
A1-a
A1-b
Solo LTR



S-2
T TT
SSRS-3
Rice
Sh2 X1 X2


A1


ESt SSR
Sn-1
TTSn-2D W T
5kb
Nested Retrotransposons in the Maize Genome Science 274: 765 (1996)