overview on arabidopsis and rice genome
TRANSCRIPT
Gopal Singh (Ph.D Scholar, CSIR-IHBT, Palampur
Subject- Genomics: Information Flow in Biological System
Overview of Arabidopsis and Rice Genome
Why Arabidopsis (Arabidopsis thaliana) ???
o Short generation time
o Small genome size (~125 Mb, 2n=10)
o Large number of offsprings
o Less complex architecture
o Easy to grow and maintain
o Easy phenotypic characterization
Arabidopsis Genome Sequencing
o 1st plant and 3rd multicellular organism to be sequenced
o Started in 1996 with an international collaboration known
as Arabidopsis Genome Initiative (AGI)
o Published the whole genome in 2000 (Nature, VOL 408,
14 DECEMBER 2000)
o Used Cosmid, PAC, BAC and TAC libraries for sequencing
oThe genetic map of Columbia accession compiling by CSHL
NATURE |VOL 408 | 14 DECEMBER 2000
1983 Publication of first genetic map
1988-89 Publication of RFLP maps
1990 Multinational Coordinated Arabidopsis thaliana Genome Research Project initiated
1991Arabidopsis Stock Centers at Ohio State (USA) and Nottingham (UK), as well as the
Arabidopsis Data Base (AtDB), were established
1991 First YAC libraries and anchoring of YAC clones to RFLP map
1992 Publication of first chromosome walk
1994-8Collections of cDNA (EST) clones sequenced linking up genetic and cytogenetic with
physical maps
1995-8 Physical map of all 5 chromosomes delineated
Jan 98 Publication of 1.9 Mb of contiguous DNA sequence from chromosome 4
June 98 29 Mb of genomic DNA sequenced
Oct. 98 Arabidopsis featured in genome issue of "Science“>46 Mb of genomic DNA sequenced
2000 Completion of genome sequencing (expected date)
Multinational Coordinated Arabidopsis thaliana Genome Research Project
Historical Perspective and Progress
NATURE |VOL 408 | 14 DECEMBER 2000
Gene Density and Repeats Distribution
Arabidopsis thaliana: Genetic Portrait of a Model Plant
Physical mapping of chromosome 1
Genome Attributes of Arsabidopsis
Chr. 1 Chr. 2 Chr. 3 Chr. 4 Chr. 5 ∑
Length (bp) 29,105,111 19,646,945 23,172,617 17,549,867 25,953,409 115,409,949
Number of genes
6,543 4,036 5,220 3,825 5,874 25,498
Gene density(kb/gene)
4.0 4.9 4.5 4.6 4.4 4.0 4.9 4.5 4.6 4.4
Average genelength (bp)
2,078 1,949 1,925 2,138 1,974
Average peptidelength (bp)
446 421 424 448 429
Exons 35,482 19,631 26,570 20,073 31,226 13,2982
Introns 28,939 15,595 21,350 16,248 25,352 107,484
ESTs 30,522 14,989 20,732 16,605 22,885 105,733
NATURE |VOL 408 | 14 DECEMBER 2000
Genome Features of Three Genomes
NATURE |VOL 408 | 14 DECEMBER 2000
Functional Analysis of Arabidopsis Genes
Arabidopsis thaliana: Genetic Portrait of a Model Plant
Why Rice (Oryza sativa) ???
o One of the important crop plant
o Rice (+ wheat and maize) account for
about half of the world’s food production,
o Principal food of half of the world’s
population
o Smallest gemone in major cereal crops
(~ 400 - 430 Mb, 2n=24)
o Wheat genome is ~ 37 times larger
Eckardt, Plant Cell. 2000 Nov; 12(11): 2011–2018
Institute Chromosome
Eckardt, Plant Cell. 2000 Nov; 12(11): 2011–2018
Participating Organizations of IRGSP
Rice Genome Sequencing
o Began in September 1997 as The International Rice
Genome Sequencing Project (IRGSP)
oPAC and BAC TAC libraries were used for sequencing
o Nipponbare variety was selected as template (except for
chromosome 4 which sequenced with indiaca Guang Lu
Ai 4 by Chinese group
o Monsanto release a draft genome of rice in 2000
Eckardt, Plant Cell. 2000 Nov; 12(11): 2011–2018
Contd….
o Two draft were release in 2000: indica (Goff et al.,
SCIENCE, Vol 296, 2002) and japinica (Syngenta a private
company)
o Finally, the complete map-based genome of rice was
released by IRGSP in 2005 (NATURE, Vol 436, 2005)
o Provide the sequence date for 389Mb with 95% accuracy
Sequence Data for Each Chromosome
NATURE, Vol 436, 2005
Summery for Rice Genome Sequencing
o According to Rice Genome Annotation Project
Kawahara et al., Rice 6:4, 2013
