Ensembl: A Genomic Toolset for pigs, poultry, plants, pests, pathogens and pollinators. Paul Kersey

Transcription

1 Ensembl: A Genomic Toolset for pigs, poultry, plants, pests, pathogens and pollinators Paul Kersey

2 A brief history of genome sequencing 1995 Haemophilus influenzae 1.8 Mb 1996 Saccharomyces cerevisiae 12 Mb 1999 Drosophila melanogaster 140 Mb 2001 Homo sapiens 3.1 Gb Sequencing technology is continuously improving, but (massively parallel) next generation techniques really were game-changers 2 pkersey@ebi.ac.uk

3 Cost of Sequencing a Human Genome

4 A brief history of genome sequencing genomes project (2500 human genomes) genomes project (1,0001 Arabidopsis genomes) Genomics England (100,000 human genomes) 4 pkersey@ebi.ac.uk

5 What can we do with thousands of genome sequences? Statistical association of traits with markers Increased marker resolution to find causative variants Understand population structure and evolutionary processes Track epidemics Assay for known variation Environmental distribution Tool for managing crosses More genomes More statistical power, find rarer causative alleles 5 pkersey@ebi.ac.uk

6 Thousands of genomes a tool for breeding Characterize germplasm of land races and wild relatives Understand what s actually present in an existing line Find alleles associated with traits Combine genotyping with various (laboratory, greenhouse, field) phenotyping mechanisms, themselves increasingly automated and high-throughput Manage crosses 6 pkersey@ebi.ac.uk

7 Everyone can do their own experiments, but EMBL-EBI would like to maintain a cataologue of reference genomes and variants for all majorly studied species Selected lines can be re-phenotyped and analysed against the same reference data One major challenge: organising the pan-genome No single genome is enough to serve as a reference for many species Variants, functional elements present in some strains but not in the reference Reference is still a useful concept: but needs to be extended choose your own reference according to need 7 pkersey@ebi.ac.uk

8 Phenotyping data Immensely varied Dependent on an environment (GxPxE) Anything you can measure from molecular assays to in-field imaging Increasing use of structured controlled vocabularies for human readable, inter-operable data summaries Meta data is critical What has been assayed? Where was it assayed? How has it been assayed? 8 pkersey@ebi.ac.uk

9 The EBI mission EMBL-EBI provides freely available data from life science experiments, performs basic research in computational biology and offers an extensive user training programme, supporting researchers in academia and industry. We also coordinated the ELIXIR pilot phase and are hosting the ELIXIR hub 9 pkersey@ebi.ac.uk

10 EBI provides Structured archives (and associated submission services) for most major types of molecular biological data e.g. European Nucleotide Archive (part of the ENA-GenBank- DDBJ International Nucleotide Sequence Database Consortium) European Variation Archive now accepting submissions in VCF format ArrayExpress, PRIDE, Metabolights Integrative, interpreted services providing access to that data in a biologically meaningful context e.g. Ensembl 10 pkersey@ebi.ac.uk

11 Ensembl A modular suite of software for genome analysis and visualisation developed jointly by the Wellcome Trust Sanger Institute and the European Bioinformatics Institute Now used for genomes from across the taxonomic space Offers a standard set of interfaces to a wide range of genome-scale data, including: Web-based GUI Public mysql server Perl and REST-ful APIs FTP Data mining tool (constructed using BioMart) framework with its own set of interfaces: web GUI, web services, command line and local client 1 1 pkersey@ebi.ac.uk 2015 ELIXIR Innovation and SME Forum Wageningen 18th-19th March

12 vertebrates bacteria fungi protists plants metazoa 26 th July 2013 ELIXIR Innovation and SME Forum Wageningen 18th-19th March 2015

13 Agriculturally relevant species in Ensembl Farm animals Crop plants Pests Vectors Pollinators Pathogens Symbionts and commensuals

14 14 ELIXIR Innovation and SME Forum Wageningen 18th-19th March 2015

15 15 ELIXIR Innovation and SME Forum Wageningen 18th-19th March 2015

16 16 ELIXIR Innovation and SME Forum Wageningen 18th-19th March 2015

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18 Gene tree pipeline Take canonical protein for each gene belonging to one Ensembl Genomes clade Cluster: WU-BLASTP + Smith-Waterman allversus-all, hcluster_sg Align: multiple aligners consensified by M- Coffee Build trees: PhyML-WAG + PhyML-HKY + NJ-p + NJ-dN + NJ-dS + species tree TreeBeST-merge O r t h o l o g s & P a r a l o g s Infer orthologues and paralogues

19 Orthologues and paralogues Paralogues: Any gene pairwise relationship where the ancestor node is a duplication event Orthologues: Any gene pairwise relationship where the ancestor node is a speciation event

20 Orthology / paralogy types ortholog_one2one ortholog_one2many ortholog_many2many apparent_ortholog_one2one possible_ortholog (weakly supported duplication node) within_species_paralog other_paralog (too distant to be in the same tree) contiguous_gene_split (artefact) putative_gene_split (artefact)

21 ELIXIR Innovation and SME Forum Wageningen 18th-19th March 2015

22 Pairwise whole genome alignments & synteny Only for certain combinations of species Generated using (B)LASTz-net Synteny Organisms of relatively recent divergence show similar blocks of genes in the same relative positions in the genome Shows how the genome is cut and pasted in the course of evolution Calculated using pairwise whole genome alignments Only for certain combinations of species

23 Ensembl Ensembl supports many livestock species Ensembl provides automatic gene annotation for these species Ensembl works with Havana to support manual annotation in Pigs Ensembl provides Variation databases and functional annotation where the data exists Ensembl is playing an active role in FAANG and will integrate the functional data generated as it becomes available

24 FAANG Functional Annotation of Animal Genomes High quality transcriptomic and regulatory annotation of Animal Genomes Open Data released pre-publication Common data and analysis standards EBI leading establishment of infrastructure for data sharing and standard

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27 The bread wheat genome Large haploid genome size is > 5 Gb But in fact, the genome is an alloxhexaploid (triploid genome size ~ 16 Gb) Each diploid genome is quite homozygous 27 pkersey@ebi.ac.uk

28 Evolution of hexaploid bread wheat 2 8 pkersey@ebi.ac.uk

29 The bread wheat genome Genome has been sequenced by Illumina after chromosome sorting Assembly is fragmented, but gene models are broadly comparable to other grasses Chromosome 3B has been sequenced BAC-by-BAC 29

30 Wheat in Ensembl Plants We represent the IWGSC chromosome survey sequence with the addition of the finished 3B sequence. We also use PopSeq data (from IPK, Gatersleben) to group scaffolds into bins based on genetic locations 30

31 1:1 orthology calls over 19 cereals including the three sub-genomes of bread wheat 3 1 ELIXIR Innovation and SME Forum Wageningen 18th-19th March 2015

32 32 ELIXIR Innovation and SME Forum Wageningen 18th-19th March 2015

33 33 ELIXIR Innovation and SME Forum Wageningen 18th-19th March 2015

34 Polymorphism data for bread wheat ~900,000 SNPs provided by CerealsDB, as follows: The Axiom 820K SNP Array contains 820,000 SNPs of which ~684,000 have been mapped. The iselect 80K Array contains over 80,000 SNP loci of which ~58,000 have been mapped. The KASP probeset contains ~3,900 SNP loci of which ~3,100 have been loaded in Ensembl Plants 34

35 35 ELIXIR Innovation and SME Forum Wageningen 18th-19th March 2015

36 36 ELIXIR Innovation and SME Forum Wageningen 18th-19th March 2015

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38 Inter-homoeologous variants Genome combination Mismatch length (in reference genome), bp Alignment length, bp % mismatch B on A 2,881,969 41,739, D on A 2,665,562 43,228, A on B 2,892,005 41,749, D on B 2,739,967 44,238, A on D 2,689,840 43,252, B on D 2,745,993 43,244, Mismatch defined as length on reference not matched in non reference 38 pkersey@ebi.ac.uk

39 39 ELIXIR Innovation and SME Forum Wageningen 18th-19th March 2015

40 Bread wheat whole genome alignment DNA-DNA pairwise alignments with lastz Brachypodium distachyon: 617,996,145 Mb (14% of bread wheat) in 1,310,922 blocks Hordeum vulgare: 423,284,874 Mb (9% of bread wheat) in 2,902,234 blocks Oryza sativa Japonica: 312,857,683 Mb out of 4,460,951,632 (7% of bread wheat) in 718,036 blocks 40

41 Additional alignment data for bread wheat Repbase repeats Triticeae repeats from TREP Wheat RNA-Seq, ESTs, and UniGene datasets have been aligned to the Triticum aestivum genome: 454 RNA-seq data for the following INSDC studies: SRP02455 (Akhuvnova et al.), ERP (Brenchley et al.), SRP Sequences from TriFLDB Transcriptome assembly from diploid einkorn wheat Triticum monococcum (Fox et al.) 41

42 Diploid progenitors of bread wheat Aegilops tauschii (DD) and Triticum urartu (AA) are also included in Ensembl Plants In addition, we have RNA-seq data from Triticum monococcum (AA) These genomes have been aligned to rice, and barley Relevant RNA-seq reads have been also aligned ELIXIR Innovation and SME Forum Wageningen 18th-19th March 2015

43 Bread wheat whole genome alignment DNA-DNA pairwise alignments with lastz Brachypodium distachyon: 617,996,145 Mb (14% of bread wheat) in 1,310,922 blocks Hordeum vulgare: 423,284,874 Mb (9% of bread wheat) in 2,902,234 blocks Oryza sativa Japonica: 312,857,683 Mb out of 4,460,951,632 (7% of bread wheat) in 718,036 blocks 43

44 Accessing Ensembl Data Programatically 5 easy methods

45 Access method 1:FTP downloads ftp://ftp.ensemblgenomes.org/pub/ Genomic, cdna and protein sequence (FASTA) Annotated sequence (EMBL / GenBank) Gene sets (GTF) Resequencing alignments individuals / strains (EMF) Whole-genome multiple alignments (EMF) Gene-based multiple alignments (EMF) Constrained elements (BED) Database dumps (MySQL)

46 Access method 2: mysql MySQL: an open-source relational database management system (RDBMS) Used as the back end to support most Ensembl pipelines and applications You get the database from and install locally On the Ensembl Genomes FTP site, you can download the Ensembl schema as a.sql file. You can also download the data files /data/mysql/bin/mysql -u mysqldba create database zea_mays_core_24_77_6; exit; /data/mysql/bin/mysql -u mysqldba zea_mays_core_24_77_6 < zea_mays_core_24_77_6 /data/mysql/bin/mysqlimport -u mysqldba --fields_escaped_by=\\ zea_mays_core_24_77_6 -L *.txt 4 6 pkersey@ebi.ac.uk Gramene Workshop, Plant and Animal Genomes XIII

47 Access method 3: Ensembl Perl API Mature, fully featured Perl API (Applications Programming Interface) for Ensembl resources Perl: a commonly used programming language in bioinformatics, designed to make easy thing easy and hard things possible Provides access to: Genomic sequence Genome features e.g. genes, translations Annotation e.g. cross-references

48 Access method 4: REST API REpresentational State Transfer is an abstraction of the architecture of the World Wide Web; more precisely, REST is an architectural style consisting of a coordinated set of architectural constraints applied to components, connectors, and data elements, within a distributed hypermedia system. REST ignores the details of component implementation and protocol syntax in order to focus on the roles of components, the constraints upon their interaction with other components, and their interpretation of significant data elements (Wikipedia) A style for structuring URLs (i.e. web addresses) according to the content they contain RESTful web service or RESTful web API Allows users to access data simply by invoking the URL Often returns a data structure defined in a simple grammar (e.g. JSON) which can be imported into an object in any programming language

49 Access method 5: BioMart A generic tool to facilitate the design and query of data warehouses Data warehouses are databases designed to optimise the performance of certain commonly performed queries May be less flexible than normalised schema Less suitable for maintaining primary data (harder to automatically define constraints due to form of data model) Nonetheless, can still be implemented within RDBMS BioMart uses mysql We have gene-centric and variant centric BioMarts for all Ensembl divisions BioMart comes with its own web interface

50 BioMart Web UI

51 Access Method 6: Virtual Machines Download an environment containing all of Ensembl to run on your machine In effect, you are downloading/running a model of a computer As long as your computer can support running the VM, there should be no problem with library incompatibilities etc. - all the resources Ensembl needs are within the VM Increasingly, a model of choice for running web-based services (e.g. in cloud environments) you don t deploy into a platform, you deploy a whole platform We use OpenBox, an open source virtualisation platform 51 pkersey@ebi.ac.uk Gramene Workshop, Plant and Animal Genomes XIII

52 Funding Ensembl Genomes Funded by EMBL EU (INFRAVEC, Microme, transplant, AllBio) BBSRC (PhytoPath, wheat/barley/midge sequencing, UK-US collaboration, RNAcentral) Wellcome Trust (PomBase) NIH/NIAID (VectorBase) NSF (Gramene collaboration) Bill and Melinda Gates Foundation (wheat rust) 52

53 People James Allen, Irina Armean, Dan Bolser, Bruce Bolt, Mikkel Christensen, Paul Davis, Thomas Down, Christoph Grabmueller, Kevin Howe, Arnaud Kerhornou, Julia Khobdova, Eugene Kulesha, Nick Langridge, Dan Lawson, Mark McDowall, Uma Maheswari, Gareth Maslen, Michael Nuhn, Chuang Kee Ong, Michael Paulini, Helder Pedro, Anton Petrov, Dan Staines, Brandon Walts, Gary Williams The vertebrate genomics EBI (Paul Flicek) 53 pkersey@ebi.ac.uk

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