Defining chromosomes for VGP assemblies

Kerstin Howe
Wellcome Sanger Institute, UK

Transcript

1. Defining chromosomes in VGP assemblies Kerstin Howe, Wellcome Sanger Institute, UK 16.01.2019
2. VGP Assembly Curation 1. Correcting/improving produced assemblies • Removal of contaminations and haplotypic duplications • Rearrangements of scaffolds/contigs • Correct erroneous interchromosomal fusions and translocations • Correct erroneous intrachromosomal rearrangements • Complete fragmented genes • Identification and naming of chromosomal units • Based on Genome Reference Consortium’s data model and curation • No changes without sufficient evidence • Changes are documented • Assemblies are curated as TPFs and AGPs 2. Improving assembly strategy • Identify shortcomings in current software • Advise on process inclusions/order
3. Assembly curation assembly decontamination feedback, adjustment curated assembly with chromosome assignment Manual curation gEVAL – Genome Evaluation Browser cDNAs gene sets whole genome comparisons gene synteny genetic maps stuff… centromeres telomeres previous assemblies Evolution Highway data PacBio 10X BioNano HiC vgp-geval.sanger.ac.uk
4. Identifying chromosomes bTaeGut1 before curation bTaeGut1 after curation • Ideally through karyotyping and FISH - not possible for majority of samples • HiC provides suitable alternative => inferred karyotype
5. Chromosome naming Existing INSDC terminology • Chromosome • Unlocalised • Unplaced bTaeGut1
6. Chromosome naming By synteny • Align close relative with sound chromosome naming • Compare BUSCO annotation
7. Chromosome naming By synteny • Align close relative with sound chromosome naming • Compare BUSCO annotation By size Keep the naming consistent in future releases! 1 2 3 4 5 6 7 8 9 10
8. VGP 1st release assemblies
9. Telomeres and centromeres • Mechanisms for identification and visualization (gEVAL) exists • INSDC approved mark-up framework exists • Assembling those regions is not trivial… GRCh38 … …
10. More curation MT often excluded from assembly pipeline • Dedicated MT assembly and curation (Giulio Formenti, Peter Houde, Ed Braun) Sex chromosome identification • help from Kateryna Makova and Paul Medvedev Capel, B. (17) Vertebrate sex determination: evolutionary plasticity of a fundamental switch. Nature Reviews Genetics volume18, pages675–689
11. Summary • Continue with current system for v1/1.5 assemblies • Annotate centromeres and telomers for v2 assemblies • HiC for all, karyotyping where possible • More dedicated work on mtDNA curation and sex chromosomes
12. Acknowledgements Sanger Will Chow Joanna Collins Sarah Pelan James Torrance Jonathan Wood Yin Yang Iliana Bista Milan Malinsky Shane McCarthy Zemin Ning Karen Oliver Mike Quail Michelle Smith Richard Durbin VGP assembly group Erich Jarvis Sergey Koren Harris Lewin Adam Phillippy Martin Pippel Arang Rhie Guojie Zhang Yang Zhou …and many more…