Lecture 4
- How do you compare (plant) genomes? Compare genomes by looking
at the size of the genome genes, make use of a sequence alignment
- Major mechanisms for gene expansion? To get more genes use gene
duplication events with whole genomes, chromosomes can break and fuse
again.
- Driving force for genome evolution? Transposons are the
driving force of the evolution of genomes. Gene and genome duplications
are major driving forces of gene diversification and evolution
- What are gene families, how do they arise? Gene families have the
same ancestor (the same function). Eukaryotic gene family sizes differ
mainly because of different rates of gene duplication and retention, and
gene content differences may reflect species- specific adaptions.
- What is gene ontology? Standard way of gene function annotation
- How many domains does a protein have?Domains are highly conserved
regions and maintain a function. In higher organisms proteins have more
domains.
- How do you determine the position of introns in the genomic
sequence of a gene?
- What are non-coding genes and pseudo genes? Non-coding
genes; tRNA rRNA, SiRNA. Only mRNA is a coding gene. Pseudo-genes;
genes that have lost there function
- What is the size of plant genomes? 100 million ~ billion bp
- Plant model species? For example Arabidopsis or rice
- How many protein coding genes do (flowering) plant genomes
contain? 25000, this is more than humans (yeast had 6000)
- What is the size of a typical plant (Arabidopsis) promoter?
Promoter regulates the expression of the DNA. Arabidopsis has 28000
genes.
- What does At3g57810 stand for?
Article 1
- How long ago did Moss diverge from the lineage of flowering
plants? Moss diverges from the lineage 400 million years ago.
- What is the size of the Moss genome, how many chromosomes and
what is the number of genes? Genome size of the moss is 480
mega-basepairs long. It contains 27 chromosomes (ara has 5) and has
28000 genes.
- Do gene families in primitive (plant) genomes always contain less
members than in genomes from more advanced organisms? Explain
moss is a primitive plant, it has 1381 families. Gene families become
bigger during time; more genomes.
- Does alternative splicing occur in plants? Alternative splicing
occurs in plants; it has to have introns and exons to do alternative splicing.
- What are the most abundant type of repeat sequences? The most
abundant type of repeats in plants are long terminal repeats.
- What can you learn from the analysis of repeat sequences that are
present in a genome? From the long terminal repeats we can learn
something about the age of the insert; you find peaks
- What could be the cause of activity peaks in fig 2? Evolutionary
stress.
, Article 2
- Why compare genomes? To get information (about relationships and
evolution) about gene function. Comparing has problems like genome
duplication
- How many genome duplications have been detected in the
Arabidopsis thaliana genome? 12 genome duplications in
Arabidopsis. 70% of Arabidopsis genome consists of duplication blocks. Only
23% is duplicated.
- What is meant with chromosome condensation? Chromosome
condensation: chromosome number varies, chromosomes fuse this
causes problems
- What is complicating the comparison of Arabidopsis with other
angiosperms? differences in gene density make it harder to compare
Arabidopsis.
- Which events complicate the detection of synteny and collinearity
between (plant) genomes? Synthetic matches have the same origin.
Collineartiy means that it is in the same region. Genes with no synthetic
matches go lost or are gained by the organism. (compare it with other
members to explain this event). Improved synteny and collinearity
alignments emerging from top-down approaches applied to multiple
genomes and subgenomes are a potential foundation for reconstruction of
the ancestral state(s) of angiosperm genomes
- In fig 2, genes with no syntenic matches to the selected regions are
not plotted. Explain the presence of such non-synthetic genes in
these collinear regions. Collinearity, a more specific form of synteny,
requires common gene order. Collinearity and synteny have traditionally
been identified by looking for one-to-one (pairwise) conservation between
species.
- What is meant with deletion resistant ancestral genes, and what is
the opposite case of that? Deletion resistant ancestral genes;
consistently being preserved in syntenic subgenomes. Such preferential
conservation of genes from particular families such as MADS-box genes and
other transcription factors may contribute to increasing morphological
complexity.
Article 3
- What is the function of the MADS domain, and of the MADS-box
genes? MADS domain regulates transcription by binding the
DNA. (has binding domain and activation domain). Many different
transcription families.
- Do plants and animals have a similar set of transcription factor
gene families? Plants and animals both have MADS domain, but they
have a different function.
- How do you compare (plant) genomes? Compare genomes by looking
at the size of the genome genes, make use of a sequence alignment
- Major mechanisms for gene expansion? To get more genes use gene
duplication events with whole genomes, chromosomes can break and fuse
again.
- Driving force for genome evolution? Transposons are the
driving force of the evolution of genomes. Gene and genome duplications
are major driving forces of gene diversification and evolution
- What are gene families, how do they arise? Gene families have the
same ancestor (the same function). Eukaryotic gene family sizes differ
mainly because of different rates of gene duplication and retention, and
gene content differences may reflect species- specific adaptions.
- What is gene ontology? Standard way of gene function annotation
- How many domains does a protein have?Domains are highly conserved
regions and maintain a function. In higher organisms proteins have more
domains.
- How do you determine the position of introns in the genomic
sequence of a gene?
- What are non-coding genes and pseudo genes? Non-coding
genes; tRNA rRNA, SiRNA. Only mRNA is a coding gene. Pseudo-genes;
genes that have lost there function
- What is the size of plant genomes? 100 million ~ billion bp
- Plant model species? For example Arabidopsis or rice
- How many protein coding genes do (flowering) plant genomes
contain? 25000, this is more than humans (yeast had 6000)
- What is the size of a typical plant (Arabidopsis) promoter?
Promoter regulates the expression of the DNA. Arabidopsis has 28000
genes.
- What does At3g57810 stand for?
Article 1
- How long ago did Moss diverge from the lineage of flowering
plants? Moss diverges from the lineage 400 million years ago.
- What is the size of the Moss genome, how many chromosomes and
what is the number of genes? Genome size of the moss is 480
mega-basepairs long. It contains 27 chromosomes (ara has 5) and has
28000 genes.
- Do gene families in primitive (plant) genomes always contain less
members than in genomes from more advanced organisms? Explain
moss is a primitive plant, it has 1381 families. Gene families become
bigger during time; more genomes.
- Does alternative splicing occur in plants? Alternative splicing
occurs in plants; it has to have introns and exons to do alternative splicing.
- What are the most abundant type of repeat sequences? The most
abundant type of repeats in plants are long terminal repeats.
- What can you learn from the analysis of repeat sequences that are
present in a genome? From the long terminal repeats we can learn
something about the age of the insert; you find peaks
- What could be the cause of activity peaks in fig 2? Evolutionary
stress.
, Article 2
- Why compare genomes? To get information (about relationships and
evolution) about gene function. Comparing has problems like genome
duplication
- How many genome duplications have been detected in the
Arabidopsis thaliana genome? 12 genome duplications in
Arabidopsis. 70% of Arabidopsis genome consists of duplication blocks. Only
23% is duplicated.
- What is meant with chromosome condensation? Chromosome
condensation: chromosome number varies, chromosomes fuse this
causes problems
- What is complicating the comparison of Arabidopsis with other
angiosperms? differences in gene density make it harder to compare
Arabidopsis.
- Which events complicate the detection of synteny and collinearity
between (plant) genomes? Synthetic matches have the same origin.
Collineartiy means that it is in the same region. Genes with no synthetic
matches go lost or are gained by the organism. (compare it with other
members to explain this event). Improved synteny and collinearity
alignments emerging from top-down approaches applied to multiple
genomes and subgenomes are a potential foundation for reconstruction of
the ancestral state(s) of angiosperm genomes
- In fig 2, genes with no syntenic matches to the selected regions are
not plotted. Explain the presence of such non-synthetic genes in
these collinear regions. Collinearity, a more specific form of synteny,
requires common gene order. Collinearity and synteny have traditionally
been identified by looking for one-to-one (pairwise) conservation between
species.
- What is meant with deletion resistant ancestral genes, and what is
the opposite case of that? Deletion resistant ancestral genes;
consistently being preserved in syntenic subgenomes. Such preferential
conservation of genes from particular families such as MADS-box genes and
other transcription factors may contribute to increasing morphological
complexity.
Article 3
- What is the function of the MADS domain, and of the MADS-box
genes? MADS domain regulates transcription by binding the
DNA. (has binding domain and activation domain). Many different
transcription families.
- Do plants and animals have a similar set of transcription factor
gene families? Plants and animals both have MADS domain, but they
have a different function.
