Genome Projects Flashcards
What is heterosis
Hybrid vigour (only in F1 offspring) utilised by farmers to increase yields of hybrids by 15 - 60% relatice to inbred parents.
size of maize genome
how much is TE?
2.9Gb size
85%
which approaches were used to sequence maize genome
- Cultivar B73 selected because of widespread use in breeding
- hierarchial approach to get sequence - BAC to BAC (30x coverage). 3 different BAC lbraries produced with 3 restriction enzymes.
- 350253 BAC clones fingerprinted and assembled to 1500 contigs.
- minimum tiling path of 16848 BACS picked for sequencing.
- predicted protein encoding genes and miRNA genes from assembled BAC contigs using mix of evidence based and ab inito approaches.
What are Helitrons?
How are they important for variation btw maize cultivars?
Very active class of DNA transposons in plants animals and fungi. Maize has 8 families of helitrons, forming 20000 copies. located in gene rich regions and often move gene fragments when transposed, moving genes and creating variation.
mechanism of helitrons translocating
transposase molecules cleave donor and target sites.
ss TE inserts into target and may also move a flanking sequence from donor into target DNA.
replication of inserted sequence.
What did anchoring reference sequence of B73 maize to a genetic map show?
Unequal rate of meiotic recombination per megabase.
Highest recombination rate observed at the end of the chromosomes
low recombination rates were found surrounding the centromere.
Correlates with gene density
What caused a lot of chromosomal rearrangements in maize genome?
Whole genome duplication event, 5-12mya.
returned to diploid state.
Associated with numerous chr breakages and fusions - seen by alignment with genomes of sorghum and rice.
-most duplicated genes lost sue to extensive chr rearrangement, has retained just 8110 genes as duplicates.
what other methods was used to genetate maize genome, in 2017
whole genome shotgun approach.
using PacBio SMRT, assembled almost 3000 contigs. N50contig = 1.18Mb.
high quality optical map used on this assembly to create 625 scaffolds N50 scaffold length = 9.56Mb.
Error correction using Illumina short read seq.
new B73 assembly total size 2,105Mb.
difference in no genes in 2 versions of maize genome
version 2 had 39,324 genes, 6,784 more than version 1. 20%
Result of differences in assembly and annotation. no biological significance.
what is the Pan genome idea
pan-genome describes all genes and genetic variation within a species. - core genome portion common to all individuals, - dispensable genome is only in a subset or unique to individuals.
What is the HapMap project?
Haplotype map
- 2012 published for maize
- focussed on sequence diversity across 103 different maize lines +19 wild relatives.
- sequenced with illumina and aligned to 2009 B73 reference genome. 4.2x coverage of each maize line.
- 55million SNPs identified. 21% associated with genic region (a lot since only 1-2% of genome codes genes).
- thousands of structural rearrangements.
When was th ehuman genome project completed
What methods.
june 2000. 10 year effort.
Competition between public hierarchal approach, sector and private, Shotgun approach.
agreed a tie in june 2000.
what is the 1000 genomes project?
description of common human genetic variation.
whole genome sequencing to diverse set of individuals from multiple pops.
Completed 2015.
Discovered 60,000 structural variants.
How many structural variants in a typical human genome?
2100 - 2500
affect approx 20 million bases
How did the 1000 genomes project support ‘out of africa’ model of human origin?
showed individuals from African acestry had greatest number of variant sites.
