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Defining chromosomes for VGP assemblies

January 16, 2019

Defining chromosomes for VGP assemblies

Kerstin Howe
Wellcome Sanger Institute, UK


January 16, 2019

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  1. 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
  2. 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
  3. 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
  4. Chromosome naming By synteny • Align close relative with sound

    chromosome naming • Compare BUSCO annotation
  5. 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
  6. Telomeres and centromeres • Mechanisms for identification and visualization (gEVAL)

    exists • INSDC approved mark-up framework exists • Assembling those regions is not trivial… GRCh38 … …
  7. 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
  8. 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
  9. 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…