Chapter6 Lec2 + 3

Question 1

Discuss the A.thaliana genome over the genome structure.

Answer 1

The genome structure reveals both local and genome-wide duplications; they were probably 5 polyploidizations, with the last two having occurred 90 and 40 MYA

In addition, the local duplications have affected ~17% of genes

Close relatives, such as cabbage and cauliflower, have since underwent additional polyploidizations in the 12 MY after split from Arabidopsis.

Question 2

Discuss organellar genomes in the A.thaliana genome.

Answer 2

The A.thaliana has a mitochondrial(mt) and chloroplast(cp) genomes.

cp genomes are relatively gene dense,but with preserved gene order; in contrast, my genes are more widely-spaced and recombination is more common.

my and co genes contain fewer introns, respectively accounting for 12% and 18,4% vs 80% in nuclear genome.

Question 3

Discuss the A.thaliana proteome.

Answer 3

It expresses many proteins that are plant-specific, including photosynthesis and cell well-regulated components.

Protein homologues between A.thaliana and humans vary depending on functional category.

Functional category ‘protein synthesis ‘:60% of nuclear-derived proteins in A.thaliana have human homologues; ‘transcriptional regulation’ , the figure is only 30%.

• importantly, this doesn’t mean that transcription regulators are lacking in plant genomes; however, it implies that plants use different role-players
• in fact, plants have developed specific transcription factor families that are not present in animals.

Question 4

Discuss the genes and functions detected from the genome.

Answer 4

• As weed, A.thaliana is rich in genes that encode water-transporting channels, peptide- hormones transporters, metabolic and baiosynthetic enzymes involved in defence, detoxification and environmental sensing.
• Plant-specific functions include light sensors that regulate development and circadian responses; pollinator attractors and seed-dispersal agents formed by molecules (pigments termed flavonoids and carotenoids) that have relevance in traditional ‘herbal medicine ‘ and pharmacology.
• Many genes have homologues in humans; eg. A.thaliana has a BRCA2 homologue (whose mutations causes breast cancer in humans).
• In some instances, plant genes encode products tha0t are more similar to human-encoded proteins than those from other vertebrates.

Question 5

Genomes of animals; sea squirt( Ciona intestinalis), one of the most primitive chordates; thus it’s genome reveals insight into ___ and origins.

How many bp and genes were deduced following genome sequencing?

How is the sea squirt genes compared to humans genes?

Answer 5

1. Chordate, vertebrate
2. ~160 Mbp and ~16000 genes
3. Sea squirt has a high density(i.e 7.5kb/gene) ,humans (i.e. 100kb/gene)

Question 6

In other genome features, ~60% of genes have___in C.elegans and/or fruit fly; these represent the component____with____ and chordates.

Answer 6

Homologues, shared, invertebrates

Question 7

True/ false

More genes are more similar to vertebrate genes than worm and/or fly genes; these are not vestiges of the common ancestor lost in the lineage leading to vertebrates.

Answer 7

False

Less genes are more similar to worm and/or fly genes than vertebrate genes; these are vestiges of the common ancestor lost in the lineage leading to vertebrates.

Question 8

Ciona lacks genes for_____,____receptors, or_____,thus,these are a vertebrate invention(though lacking from___vertebrates including_____and_____.

Answer 8

Immunoglobulins, T-cells, MHC proteins, primitive, lamprey, hagfish

Question 9

Fifth of Ciona Gene’s have homologues in vertebrates and invertebrates; perhaps they are still to be discovered or may be very divergent.

True/false

Answer 9

False, have no homologues

Question 10

Some genes encode proteins that are_____and these include ___ and___(also found in termites as they feed on______)

Answer 10

Urochordate-specific, cellulose synthases,endogluconases,cellulose-rich plant matter

Question 11

Discuss pufferfish(Tetraodon nigrovirdis) compared to humans.

Answer 11

1) common ancestor of human and fish parted ways ~450MYA, thus the genome of the pufferfish should reveal properties of vertebrates.
2) with a genome of ~340Mb;which is smaller than humans due to having less transposable elements (TEs), with shorter introns and intergenic regions.
3) with a genome 40% protein-coding; and 28000 protein-coding gene.

Question 12

What two features were found between the T.nigrovirdis genome and structure of vertebrate genomes.?

Answer 12

● First, there exist evidence for whole-genome duplications(WGDs). This was followed by chromosome rearrangements that complicated genome structure further. The WGD + chromosome rearrangements led to considerable degree of synteny between groups of paralogous genes on different chromosomes.

● Secondly, syntenic groups between pufferfish and human genomes. Found evidence that most human regions (e.g chr2) map to two separate regions in pufferfish genome supports the WGD + chr rearrangement theory. Also, that pufferfish and humans have roughly same no.of genes suggests that some duplicated genes were subsequently lost(seemingly, at random)

Question 13

What are paralogous genes?

Answer 13

Are similar genes that occur within the genome of a species.

Question 14

What are orthologous genes?

Answer 14

Are similar genes that occur in different species.

Question 15

Chicken genome was the ____ of a bird.
It was useful for ____ genomics vs mammals.
Birds and mammals diverged about ___.
They were domesticated from ___ in Asia, about ___yrs ago.

Answer 15

1st complete sequence
Study of comparative
310 MYA
Grey jungle fowl( Galllus sonneratii), 4000

Question 16

Chicken genome information.
How long is it?
How many autosomes does it have and what are it’s sex chromosomes?
How are the chromosomes distributed between two genders?
Are synteny between human and mouse more conserved than between human and chicken? T/F
Why are chicken genome smaller than in mammals?

Answer 16

~1.2 Gbp
38 and one pair of sex chromosomes Z and W.
Females are heterogametic ZW and males are homogametic ZZ
False , human and chicken are more conserved than human and mouse.
Because they have less interspersed repeats and psuedogenes, also greater expansion of genes families in mammalian genomes.

Question 17

When comparing genomes of human vs pufferfish vs chicken it exposes a common gene set of ______from chicken have ______in both pufferfish and human. These genes are therefore likely to implement common necessary ____ and are expected in most _____.

Answer 17

~7000 protein-coding genes, orthologues, functions higher vertebrates

Question 18

What were the observation when comparing humans and chicken only?

Answer 18

1) there were about 60% of ~23000 chicken protein-coding genes have unique human homologues.
2) average seq conservation between such gene pairings is about 75.3%
3) proteins homologues in different functional categories differ in seq conservation; for e.g, transport proteins show 60% seq conservation.

Question 19

What were other notable features of chicken genome?

Answer 19

1) there are avian-specific proteins including keratins(that form feathers;in mammals, a different gene family diversified to form hair) and avidin (protein found in egg-white of birds, reptiles and amphibians; thought to protect eggs from bacteria?

2)relative to humans, chicken lack genes for:
Milk proteins (e.g. casein)

Enamel proteins (associated with loss of teeth in bird lineage since a primitive bird called Archaepteryx had teeth)

Vomeronasal receptors- part of secondary chemosensory/odour detection system ; absence from chicken and other birds signifies a loss in the avian lineage, rather than an invention in mammalian one.

Question 20

The genome of platypus classification order____(which includes platypus and echidna),is a single orifice that serve both____and____. They have mixture of _____and ____ features. For e.g. __,__,(but not teats,rather modified _____serve as ______in the skin that releases milk), they ____and ___ (only in males, delivered via ankels)

Answer 20

Monotremes, urogenital and digestive systems, mammalian and reptilian, hair, mammary glands,localized pores,lay eggs and produce venom.

Question 21

Give all the genome features of platypus.

Answer 21

1) 10 sex chromosomes with males being XYXYXYXYXY, yet, sex determination system is closer to that of birds than most mammals
2) lacks the SRY gene(sex determination gene on the Y chromosome of placental mammals marsupials)
3) the 1st monotreme to be sequenced; 2.2 billion base pair and 18527 protein-coding genes.
4) most genes have orthologues in marsupials (e.g. opossum), placental (e.g. humans) and chicken

Question 22

Name other notable features of platypus.

Answer 22

1) odours receptors
2) milk
3) eggs
4) venom