What have we learned from whole genome sequencing of animals?

Question 1

key landmarks in whole genome sequences

Answer 1

C elegans first one in 1998

Humans in 2001

But had been doing gene-by-gene sequencing since Sanger sequencing emerged in the 70s

Question 2

3 kinds of things we can learn from whole genome sequences

Answer 2

global characteristics- e.g. gene content, gene duplication, gene loss
weird stuff- HGT, chromosome heterogeneity
expression analyses

Question 3

examples of gene duplications relating to organism function

Answer 3

octopus- protocadherin genes, nervous system function?
oysters- expansion in stress response genes, potentially due to living in fluctuating conditions

Question 4

gene loss examples

Answer 4

barnacles- losing Hox genes for abdomen, don’t need it i guess
tapeworms/other parasites- loss of a lot of genes
naked mole rat- pseudogenes in visual perception, suggesting gene loss actively occurring

Question 5

extreme example of gene loss

Answer 5

Dicyema japonicum (classification uncertain)- parasite living in kidneys of cephalopods- only around 5000 genes, v extreme gene loss due to parasitism

Question 6

expression analysis method

Answer 6

RNAseq- taking short reads of RNA from samples and mapping to the genome- differential gene expression

Question 7

example of HGT

Answer 7

cellulose making/breaking genes in Ciona are likely from bacteria- only real way of proving this is from WGS (proving that it’s actually IN the genome and not just in the organism)
spider mites- plant protein degrading genes from fungi
bdelloid rotifers !!