The bonobo genome compared with the chimpanzee and human genomes

Kay Pruüfer et al. Nature (June,2012)Presenter: Chia-Ying Chen

Materials

a female bonobo (Ulindi, Leipzig Zoo) -- 454 sequencing -- paired-end reads of insert sizes of 3, 9 and 20 kb (a total depth of 26 X )

19 individuals: 3 bonobos 2 western chimpanzees 7 eastern chimpanzees 7 central chimpanzees -- Illumina 76 or 101 paired end (about 1X coverage)

Assessment of the Bonobo Genome

panTro2 (Clint) (6X Sanger sequneced)

Retrotransponson Evolution in the Bonobo Genome

using GMAP to align all available bonobo (198 million reads) and chimpanzee (46 million reads) sequence traces to hg18

99.7%991 27 30

Using Alu retrotransposon to estimate split times

2.2M

6.5M

15M

B C H O

Ontology analysis of transposon

• to create 2 million simulated insertions• to count numbers of observed vs. simulated transposon integrants inside or within +/- 50 kb Refseq genes• to query the PANTHER data

Enrichment or depletion of L1 integrants

biological processes molecular functions

5 955

1

100 978 9781

5 2,748,175 2,748,175i

Divergence, Site Pattern Analysis and Signals of Admixture

to gain insight into the relationship between and within bonobo and chimpanzee populations

Data: illumina reads of 16 chimpanzees and 3 bonobos the 454 reads of Ulindi the Sanger sequencing reads of Clint (panTro2)

Divergence times

Bonobo - Chimpanzee : 2.2 million years

Clint - Central chimpanzee : 1.3 million years

Clint - Eastern chimpanzee : 1.3 million years

Clint - Western chimpanzee : 0.5 millions years

Ulindi - Bonobo : 0.5 million years

Nc: A equals B, and C different

Nb: A equals C, and B different

Divergence between A and B :2 b

b c

N

N N

C1 C2 B H

( )

( )

ABBA BABAD

ABBA BABA

in blocks of 5 mega bases

Site Pattern Analysis and Signals of Admixture

Speciation Times, Ancestral Population Size and Incomplete Lineage sorting

The scenarios may lead to gene trees with a topology different from the species tree :

The population size of the ancestral species is sufficiently large.

The time span between speciation events is sufficiently small.

These areas are termed incomplete lineage sorting (ILS)

Based on the 4-way alignment (HCBO) set phred score=30 masked RepeaatMasker track removed over-collapsing of regions due to duplications

CoalHMM analysis is run on each mega base of alignment chunks

Correlation between ILS and gene ontology classes

to count the bases in each of the four ILS states for the entire length of genes including introns

to carry out GO enrichment test using FUNC

to identify GO categories that are either enriched or depleted for CH and BH bases using Wilcoxon rank test

Genes depleted in ILS : intracellular, transcription, translationGenes enriched in ILS : protein signal to the membrane cell adhesion

But, no preferential GO terms when the analyses separately identify GO categories for CH and BH bases.

Incomplete Lineage Sorting Regions and Balancing Selection

The regions may be enriched in incomplete lineage sorting (ILS) due to long-standing balancing selection.

We considered ILS assignment in 50 kb windows to identify candidate regions

If balancing selection remains active until present times, it may also affect the patterns of polymorph in present-day populations.

Balancing selection candidates: • to exhibit high diversity in chimpanzee• to be enriched for shared SNPs