ArabidopsisArabidopsis thalianathaliana genomegenome

Carmen Martínez FernándezCarmen Martínez Fernández

AdvancedAdvanced GeneticsGenetics. . GenomicsGenomics

• Introduction

• Sequencing strategy and progresses

• Characterization of the coding regions

• Genome organization and duplication

• Repeats

• Three genomes in the plant cell

• Transposable elements

• Araport

IndexIndex

A. thaliana as a model organism • Fast life cycle

• Produces numerous self progeny

• Limited requirements

• Easy grown

• Relatively small genome (125 Mb) can be manipulated easily and rapidly • 5 Chromosomes

• 25,498 genes encoding proteins from 11,000 families

• The evolution of Arabidopsis genome

IntroductionIntroduction

Breakdown of 54000 Arabidopsis publications by research area, from 1965 to 2015 (partial data for 2015)

Provart N.J et al. (2015) New Phytologist.

http://bar.utoronto.ca/50YearsOfArabidopsis/

1. BAC, P1 and TAC libraries and cosmid clones

2. Physical maps construction by restriction fragment fingerpint analysis

3. Integration of physical maps with the genetic maps

SequencingSequencing strategystrategy and and progressesprogresses

• Progress in sequencing, reassembly and annotation of the genome

(Bevan M. and Walsh S. (2005) Genome Res. 15: 1632-1642 )

CharacterizationCharacterization of of thethe codingcoding regionsregions

(The Arabidopsis Genome Initiative 2000)

a. Proportion of predicted Arabidopsis genes in different functional categories b. Comparison of functional categories between organisms

GenomeGenome organizationorganization and and duplicationsduplications

(The Arabidopsis Genome Initiative 2000)

• Explanations of amplifications and ancestral duplications:

Independent amplification of individual genes by unequal crossing over (predominant mechanism involved)

Tandem and dispersed gene families

Ancestral duplication of the entire genome and subsequent rearrangements

Segmental duplications

GenomeGenome organizationorganization and and duplicationsduplications

RepeatsRepeats

(Zemach et al., 2013)

-Heterochromatin regions surrounding the centromere. In there we can found retroelements, transposons, microsatellites and middle-repetitive sequences.

- Two rDNA loci at the northern ends of chromosomes 2 and 4 - It also has shown that intersticial heterochromatin regions (or knobs)

DDM1 –dependent methylation: nucleosome remodeler

ThreeThree genomesgenomes in in thethe plan plan cellcell

(The Arabidopsis Genome Initiative 2000)

- Organelle-to-nuclear gene transfers from other species’ - Organelle-to-nuclear gene transfers in the plant cell

TransposableTransposable elementselements

(The Arabidopsis Genome Initiative 2000)

Class I: 2,109 Class II: 2,203 New groups: 1,209

AraportAraport

AraportAraport

[1] Krishnakumar. V et al. (2014). Araport: the Arabidopsis Information Portal. Nucleic Acid Research, Vol.43.

[2] Bevan M. and Walsh S. (2005). The Arabidopsis genome: A foundation for plant research. Genome Research. 15: 1632-1642.

[3] The Arabidopsis Genome Initiative 2000. NATURE. Vol. 408.

[4] Provart N.J et al. (2015). New Phytologist.

ReferencesReferences