Michelle Stitzer
@mcstitzer
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Interested in transposable elements. NSF postdoc at Cornell. @PopBioUCD alum. she/her.
Joined September 2014
Let us know what you think! We're excited about further characterizing the evolutionary forces that interact to give rise to the highly polymorphic, absolutely beautiful TE landscape of the maize genome🌽.
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Fun to bring along current (@MerKhaiBurch, Arcadio) and former (Asher, @baoxing_song, @GuillRamstein) labmates into the world of TEs, their help on quantitative genetics and genomics was a*maiz*ing, as well as @CedricFeschotte and @EdBuckler for all their support.
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This works out to a loss of about 1 kernel for every 14 megabases of TE sequence. Young TE insertions (which selection hasn't had time to purge), and TEs within 1 kilobase of a gene (which may alter gene expression), have stronger deleterious effects.
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We use large-scale maize mapping populations to find variation in both genome size and TE content. We then use grain yield phenotypes of almost a million individual hybrid corn plants to show that the effect of TEs on fitness is weak, but measurably deleterious
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TEs are really good at breaking genes (like pigment producing genes in kernels), and as selfish DNA are generally thought to be bad for the host genome. But there are hundreds of thousands of TEs in the maize genome, just how bad could they be?
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The maize genome is bursting with TEs, jumping genes that can move to new positions - but do TEs matter for maize fitness?.
Transposable element abundance subtly contributes to lower fitness in maize #bioRxiv.
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We've tested it out on lots of plant species (and even a goldfish!) and recover not only large scale structural variation, but also base pair resolution of conserved regulatory sequence, and gapped alignment across TE-rich regions.
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It works by finding conserved gene anchors between assemblies, then uses an implementation of the wavefront algorithm that allows for two gap penalties to perform a global alignment of each anchor and interanchor region.
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Really excited about AnchorWave! @baoxing_song taught me so much about alignment, and put together an approach that works for the real life messy stuff about genomes - like lots of TEs and paleopolyploidy.
Our genome alignment tool - AnchorWave has published online at:..It has a big improvement for plant genome comparison.
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RT @PLOSGenetics: Transposable elements (TEs) are #DNA pieces that move around the #genome. Stitzer et al model the roles of TEs & reveal a….
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It’s out! A natural history of the MANY transposable elements found in the maize genome.
journals.plos.org
Author summary Transposable elements (TEs) are pieces of DNA that can jump to new positions in the genome. When they land at a new location, they generate a mutation. Such mutations in genes affect...
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So absolutely honored! Thanks to @PopBioUCD and the whole evolution and ecology community at UC Davis.
Congratulating to Michelle Stitzer (@mcstitzer) this year's winner of the @ucdavis Outstanding Dissertation in Ecology and Evolution Merton Love Award. She'll give her seminar "The Genomic Ecosystem of Transposable Elements in Maize." on May 28th.
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The maize genome is an ecosystem, full of transposable elements! With @sna8 @SpringerNathan and @jrossibarra
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RT @jrossibarra: @sna8 @mcstitzer @abrohamm1 @SpringerNathan @HirschCandice In only four maize genomes we find 100's of thousands of variab….
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Had such a great time at #UppTransposon2018 and so excited to now have the complete Mobile DNA trilogy on my shelf! Thanks again to organizers Patric Jern, @ClaudiaKutter, and @alexander_suh.
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