Aequatous browser: Visualising complex similarity relationships among species

The Genome Analysis Centre

Building Excellence in Genomics and Computa5onal Bioscience

Anil Thanki Scien&fic Programmer

Core Bioinforma&cs Team

[email protected]

Synteny Browser: Visualising rela&onships among species

14-‐May-‐2014

The Genome Analysis Centre The Genome Analysis Centre

Synteny Browser Concept

•  Evolu&on •  Synteny •  Homology •  Paralogous •  Orthologous •  Mul&ple sequence alignment •  CIGAR line

•  Ensembl Compara •  Database •  Synteny Browser Pipeline

•  Examples in Browser •  Future work


Evolu;on


Synteny

-‐  Synteny the occurrence of two or more genes on the same chromosome within one species

-‐ Conserved Synteny The occurrence of synteny of orthologous genes in two different organisms.

conserved synteny

human chr7

mouse chr5

mblab.wustl.edu/svn/mblab/trunk/web_internal/presenta&ons/MJB/Synteny.ppt synteny ppt


Homology

… existence of shared ancestry between a pair of structures, or genes, in different species.

-‐ Wikipedia

The principle of homology:


Orthologs

… if homologous sequences are inferred to be descended from the same ancestral sequence separated by a specia&on.

•  i.e. Phenylalanine Hydroxylase (PheOH) •  is an enzyme that catalyzes the hydroxyla&on of the aroma&c side-‐chain of phenylalanine to

generate tyrosine

h[p://www.bio.davidson.edu/courses/molbio/molstudents/spring2010/piper/orthologs.html

•  Orthologs o_en, but not always, have the same func&on.


Paralogs

… if homologous sequences were created by a duplica&on event within the genome.

•  o_en belong to the same species, but this is not necessary •  the haemoglobin gene of humans and the myoglobin gene of chimpanzees are paralogs

MATTHEW2262'S BLOG


*.ology

•  Ohnology •  … paralogous genes that have originated by a process of

whole-‐genome duplica&on (WGD). •  Xenology •  Homologs resul&ng from horizontal gene transfer between

two organisms are termed xenologs. •  Typically have similar func&on in both organisms. •  Can have different func&ons, if the new environment is

vastly different for the horizontally moving gene. •  Gametology •  Gametology denotes the rela&onship between homologous

genes on nonrecombining, opposite sex chromosomes. -‐ Wikipedia


Sequence Alignment Mul&ple Sequence Alignment •  Sequence alignment of three or more sequences. •  Used to infer homology


CIGAR Line


CIGAR Line


CIGAR Line •  Compact Idiosyncra&c Gapped Alignment Report •  The CIGAR string is a mix of le[ers and numbers to represent the alignment in shorter and efficient way.

•  They are used to indicate things like which bases align (either a match/mismatch) with the reference, are deleted from the reference, and are inser&ons that are not in the reference.




•  E.g •  Ref: CCATACTGAACTGACTAAC •  Read: ACTAGAATGGCT

•  Ref: C C A T A C T G A A C T G A C T A A C •  Read: A C T A G A A T G G C T

h[p://genome.sph.umich.edu/wiki/SAM






•  CIGAR: 3M h[p://genome.sph.umich.edu/wiki/SAM






•  CIGAR: 3M1I h[p://genome.sph.umich.edu/wiki/SAM






•  CIGAR: 3M1I3M h[p://genome.sph.umich.edu/wiki/SAM






•  CIGAR: 3M1I3M1D h[p://genome.sph.umich.edu/wiki/SAM






•  CIGAR: 3M1I3M1D5M h[p://genome.sph.umich.edu/wiki/SAM


CIGAR Line in Compara •  CIGAR Line in Ensembl Compara •  Read1: CCATACTGAACTGACTAAC •  Read2: ACTAGAATGGCT •  Read3: CCAACTAGAACTGACTAAC



•  Read1: C C A T A C T - G A A C T G A C T A A C!•  Read2: - - - - A C T A G A A - T G G C T - - -!•  Read3: C C A - A C T A G A A C T G A C T A A C




•  CIGAR1: 7M




•  CIGAR1: 7MD




•  CIGAR1: 7MD12M




•  CIGAR1: 7MD12M •  CIGAR2:




•  CIGAR1: 7MD12M •  CIGAR2: 4D




•  CIGAR1: 7MD12M •  CIGAR2: 4D7M




•  CIGAR1: 7MD12M •  CIGAR2: 4D7MD




•  CIGAR1: 7MD12M •  CIGAR2: 4D7MD5M




•  CIGAR1: 7MD12M •  CIGAR2: 4D7MD5M3D




•  CIGAR1: 7MD12M •  CIGAR2: 4D7MD5M3D •  CIGAR3:




•  CIGAR1: 7MD12M •  CIGAR2: 4D7MD5M3D •  CIGAR3: 3M




•  CIGAR1: 7MD12M •  CIGAR2: 4D7MD5M3D •  CIGAR3: 3MD




•  CIGAR1: 7MD12M •  CIGAR2: 4D7MD5M3D •  CIGAR3: 3MD16M


Compara

•  A single database which contains precalculated compara&ve genomics data

•  Raw genomic sequence •  Whole genome alignments •  (tBLAT, BlastZ-‐net, PECAN)

•  Syntenic regions (based on BlastZ-‐net)

•  Protein Sequences •  Raw Protein Alignments •  Protein Family clusters •  Protein trees •  Gene orthology / paraology predic&ons

Stephen Fitzgerald


Compara

•  Compara is divided into main three parts: 1.  General Tables (12) 2.  Genomic alignments tables (8) 3.  Gene trees and homologies tables (24)

•  Link to Ensembl Core tables for core genomic informa&on •  i.e. Gene Structure, Chromosome etc

compara


Pipeline Get Species Get

Chromosomes Get Member

Genes Get Gene Tree with Alignment

Get Gene Structure Draw Genes Draw CIGARs

















Pipeline

e! COMPARA

Get Species Get Chromosomes

Get Member Genes

Get Gene Tree with Alignment


L

BC

A

EF

G

HI


Pipeline

e! COMPARA


Get Member Genes



L

BC

A

EF

G

HI

R1

R2

R3


Pipeline

e! COMPARA


Get Member Genes



L

BC

A

EF

G

HI

R1

R2

R3

A1 A2 A3

A6 A5 A4


Pipeline

e! COMPARA


Get Member Genes



A D

L

J M

O


Pipeline

e! COMPARA


Get Member Genes



A


Pipeline

e! COMPARA


Get Member Genes



A


Pipeline

e! COMPARA


Get Member Genes



A

BC

D


Pipeline

e! COMPARA


Get Member Genes



select m1.stable_id, m2.stable_id, m3.*, gam.CIGAR_line from member m1 join member m2 on (m1.canonical_member_id = m2.member_id) join gene_tree_node gtn1 on (m2.member_id = gtn1.member_id) join gene_tree_root gtr on (gtr.root_id = gtn1.root_id) join gene_align_member gam using (gene_align_id) join member m3 on (gam.member_id = m3.member_id) where gtr.clusterset_id = "default" and m1.source_name = "ENSEMBLGENE" and m1.stable_id = "LOC_Os01g01010";!


Pipeline

e! COMPARA


Get Member Genes



select m1.stable_id, m2.stable_id, m3.*, gam.CIGAR_line from member m1 join member m2 on (m1.canonical_member_id = m2.member_id) join gene_tree_node gtn1 on (m2.member_id = gtn1.member_id) join gene_tree_root gtr on (gtr.root_id = gtn1.root_id) join gene_align_member gam using (gene_align_id) join member m3 on (gam.member_id = m3.member_id) where gtr.clusterset_id = "default" and m1.source_name = "ENSEMBLGENE" and m1.stable_id = "LOC_Os01g01010";!


Pipeline

e! O. sa&va

e! Brachy

e! A. tauschii

e! COMPARA


Get Member Genes



select g.gene_id, g.seq_region_start as gene_start, g.seq_region_end as gene_end, g.seq_region_strand as gene_strand, g. description as gene_name, t.transcript_id, t.seq_region_start as transcript_start, t.seq_region_end as transcript_end, t.description as transcript_name, e.exon_id, e.seq_region_start as exon_start, e.seq_region_end as exon_end, tl.translation_id, tl.seq_start as translation_start, tl.seq_end as translation_end, tl.start_exon_id, tl.end_exon_id from gene g left join transcript t on t.gene_id = g.gene_id left join exon_transcript et on t.transcript_id = et.transcript_id left join exon e on et.exon_id = e.exon_id left join translation tl on tl.transcript_id = t.transcript_id where t.gene_id = g.gene_id and t.transcript_id = et.transcript_id and et.exon_id = e.exon_id and g.stable_id = ?";!


Pipeline

e! O. sa&va

e! Brachy

e! A. tauschii

e! COMPARA


Get Member Genes




Pipeline

e! O. sa&va

e! Brachy

e! A. tauschii

e! COMPARA


Get Member Genes








For Reference: 1.  Expand CIGAR

•  7MD12M







•  7MD12M •  MMMMMMMDMMMMMMMMMMMM








2.  Mul&ply 3 &mes 1.  MMMMMMMMMMMMMMMMMMMMMDDDMMMMMMMMMMMMMMM

MMMMMMMMMMMMMMMMMMMMM









MMMMMMMMMMMMMMMMMMMMM 3.  Split on exons

•  MMMMMMMMMMMM MMMMMMMM MDDDMMMMMM MMMMMMMMMMMMMMMMM MMMMMM MMMMMMM!









MMMMMMMMMMMMMMMMMMMMM 3.  Split on exons

•  MMMMMMMMMMMM MMMMMMMM MDDDMMMMMM MMMMMMMMMMMMMMMMM MMMMMM MMMMMMM!

4.  Draw






For Homologous gene: 1.  Expand CIGAR

•  MD9MD5M3D •  MDMMMMMMMMMDMMMMMDDD

2.  Mul&ply 3 &mes •  MMMDDDMMMMMMMMMMMMMMMMMMMMMMMMMMMDDDMMM

MMMMMMMMMMMMDDDDDDDDD









MMMMMMMMMMMMDDDDDDDDD 3.  Map to Reference CIGAR

•  MMMMMMMMMMMMMMMMMMMMMDDDMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM!•  MMMDDDMMMMMMMMMMMMMMMMMMMMMMMMMMMDDDMMMMMMMMMMMMMMMDDDDDDDDD











4.  Split on exons matching to Reference •  MMMMMMMMMM MMMMMMMMMM MDDDMMMMMM MMMMMMMMMMMMMMMMM MMMMMM MMMMMMM!•  MMMDDDMMMM MMMMMMMMMM MMMMMMMMMM MMMDDDMMMMMMMMMMM MMMMDD DDDDDDD!












5.  Split on exons of homologous gene •  MMMDDDMMMM MMMMMMM MMMMMMMMM MMMMMMMDDDM MMMMMMMMMM MMMMDD DDDDDDD












5.  Split on exons of homologous gene •  MMMDDDMMMM MMMMMMM MMMMMMMMM MMMMMMMDDDM MMMMMMMMMM MMMMDD DDDDDDD!

6.  Draw







Examples in Browser

•  TGAC’s data •  Ensembl core 73


Examples in Browser



Examples in Browser



Examples in Browser



Examples in Browser



Exis;ng Tools -‐ Genomicus


Exis;ng Tools -‐ SynView


Future Work

•  Synteny Browser to make tes&ng prototype –  h[p://tgac-‐browser.tgac.ac.uk/homology_73_4way/

•  Search for a par&cular gene •  Set a homologous gene as a reference and look into gene tree

nodes related to it •  Brassica, Wheat

–  For different genome A,B and D •  Release •  BioJS

–  Data format –  CIGAR string to represent rela&onships

•  Create MySQL views for easy query on Ensembl Compara tables

72

Acknowledgements

The Genome Analysis Centre

Robert Davey Group Leader, Sequencing Informa&cs,

TGAC

Sarah Ayling Group Leader, Computa&onal

Biology, TGAC

Mario Caccamo Director, TGAC

Javier Harrero Head of the Bill Lyons Informa&cs Centre, UCL Cancer Ins&tute

Past: TGAC

Gemy G. KaithakoVl Scien&fic

Programmer, Genome Analysis,

TGAC

Xingdong Bian

Scien&fic Programmer, Sequencing Informa&cs,

TGAC

THANKS!

Science

Aequatous browser: Visualising complex similarity relationships among species