AGBT talk: James Giovannoni, Cornell University

Title: Utilization of Next Generation Sequencing for Creation and Exploitation of the Tomato Genome.

[He’s creating tomato genomes?  Odd phrasing, but we’ll see how this works out.]

Think of this as a side dish to the genome technology you’ve been hearing. [nice…]

Tomato has a lot uses: eating, ketchup, de-skunking.  Most important source of vitamin A and C, simply because the amount of it that we eat.

Looking for a reference genome – a great biological system for studying fruit ripening.  Synteny of tomato and potato is high.  So, high quality reference for one of these will be a big help.  Related to pepper & eggplant as well.

Also a wide variety of tomato species, in a wide variety of environments.  (Picture shown of the wild progenitor of the tomato, but it’s really hard to see, unfortunately) Originated in south america, but domestication happened in Europe after Cortez brought it back. Modern breeding of tomatoes has all descended from european stock, so there is a LOT of diversity in the americas that has not yet been tapped.

International consortium working on this. Sequencing efforts started in 2004.  Originally started with a BAC approach.  1500 bacs were sequenced by the consortium.  Things have changed fast, and there is now 454 (31x), Sanger (3.6x), Illumina (82x) and Solid (141x) reads.

Assembler strategy covered – (sequencing, filtering and assembly – using all available information).

Very pretty genetic map and FISH slides. Also a summary of metrics from version 1.0 to 2.3, which is currently frozen for publication. Validation summary as well. [I’m sure all of this will be in the paper, so I’m not copying out details.]

An automated annotation pipeline, run by collaborators in Belgium, also frozen for publication.

Sequence is available: http://solgenomics.net

Still working on the sequence – setting a high target.  apx 1/3 of gaps can be closed by in silico means. (using Celera CABOG assembly).  using 100 bacs that spanned gaps, most of the sequences match the gap. [I may have missed something]

IMAGE2 used for closure and finishing – Iterative mapping and assembly for gap elimination.  Closed 11 of 12 gaps, and was able to reduce size of 12th gap.  Very resource intensive, tho.

Insights:

  • duplications common to plant genomes are found here.
  • triplication event for dicot clade
  • etc.

New carotenoid genes with novel tissue-specificities.

Neat explanation/slide of the genetic regulation of the development and maturation of fleshy fruit. Chlorophyll degradation is inversely related to non-photosynthetic pigments.

Decoding the fruit transcriptome using large-scale strand-specific transcriptome sequencing.  Looking at both strands has caused them to revise how they believe expression occurs in the fruit. (skipped over examples in the interest of time.) About 5% of genes needed to be revised when strand-specific was taken into account.

Also doing ChIP-Seq, for tomato epigenome, both TF and histone data. (plant specific transcription factors)

Only fleshy fruits ripen, histone methylation seems to be correlated with regulation of genes involved – processes are tied together. [again, I missed part of the explanation] (Manning et al, 2006, Nat Gen 38)

Conclusions:

  • high quality assembly of tomato genome
  • continuing to refine it
  • 97% of assembly is in 91 scaffolds, linked to 12 tomato chromosomes
  • annotation of 35,000 genes.
  • evidence of whole duplication events.
  • epigenetic and RNA-Seq providing novel insights into control of fruit ripening.

[Interesting talk… I knew nothing about the tomato, and little about fruit ripening beyond what you learn in undergrad… There seem to be good papers on this, which would make a nice blog entry one day.]

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