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On bioRxiv: Incomplete epigenetic reprogramming during asexual reprodu...

Posted on February 20, 2018

Epigenetic reprogramming during regeneration depends on tissue type read more

Incomplete reprogramming of cell-specific epigenetic marks during asexual reproduction leads to heritable phenotypic variation in plants

Wibowo et al. bioRxiv 2018/02/19/267955

Plants differ from animals in their capability to easily regenerate fertile adult individuals from terminally differentiated cells. This unique developmental plasticity is commonly observed in nature where many species can reproduce asexually through the ectopic initiation of organogenic or embryogenic developmental programs. However, it is not currently known if this developmental reprogramming is coupled to a global epigenomic resetting, or what impact it has on the phenotype of the clonal progeny. Here we show that plants asexually propagated via induction of a zygotic developmental program do not fully reset cell-specific epigenetic imprints. These imprints are instead inherited even over multiple rounds of sexual reproduction, becoming fixed in hybrids and resulting in heritable molecular and physiological phenotypes that depend on the founder cell used. Our results demonstrate how novel phenotypic variation in plants can be unlocked through the incomplete reprogramming of cell-specific epigenetic marks during asexual propagation.


Accumulation of mutations in A. thaliana over 400 years

Posted on February 13, 2018

We used a unique natural "experiment" to measure long-time substitution rates read more

The rate and potential relevance of new mutations in a colonizing plant lineage

Exposito-Alonso et al.

A consequence of an increasingly interconnected world is the spread of species outside their native range—a phenomenon with potentially dramatic impacts on ecosystem services. Using population genomics, we can robustly infer dynamics of colonization and successful population establishment. We have compared hundred genomes of a single Arabidopsis thaliana lineage in North America, including genomes of contemporary individuals as well as 19th century herbarium specimens. These differ by an average of about 200 mutations, and calculation of the nuclear evolutionary rate enabled the dating of the initial colonization event to about 400 years ago. We also found mutations associated with differences in traits among modern individuals, suggesting a role of new mutations in recent adaptive evolution.

Impressive A. thaliana long-read genome assemblies

Posted on February 07, 2018

Both PacBio and Oxford Nanopore produce impressive assemblies read more

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

Todd P. Michael, Florian Jupe, Felix Bemm, S. Timothy Motley, Justin P. Sandoval, Christa Lanz, Olivier Loudet, Detlef Weigel & Joseph R. Ecker

The handheld Oxford Nanopore MinION sequencer generates ultra-long reads with minimal cost and time requirements, which makes sequencing genomes at the bench feasible. Here, we sequence the gold standard Arabidopsis thaliana genome (KBS-Mac-74 accession) on the bench with the MinION sequencer, and assemble the genome using typical consumer computing hardware (4 Cores, 16?Gb RAM) into chromosome arms (62 contigs with an N50 length of 12.3?Mb). We validate the contiguity and quality of the assembly with two independent single-molecule technologies, Bionano optical genome maps and Pacific Biosciences Sequel sequencing. The new A. thaliana KBS-Mac-74 genome enables resolution of a quantitative trait locus that had previously been recalcitrant to a Sanger-based BAC sequencing approach. In summary, we demonstrate that even when the purpose is to understand complex structural variation at a single region of the genome, complete genome assembly is becoming the simplest way to achieve this goal.


Dynamics of A. thaliana/Pseudomonas pathosystem (bioRxiv)

Posted on January 23, 2018

With Kemen and Neher labs, we describe the natural dynamics of the A. thaliana/Pseudomonas pathsystem over several years and locations read more

Arabidopsis thaliana populations support long-term maintenance and parallel expansions of related Pseudomonas pathogens

Talia L Karasov, Juliana Almario, Claudia Friedemann, Wei Ding, Michael Giolai, Darren Heavens, Sonja Kersten, Derek S Lundberg, Manuela Neumann, Julian Regalado, Richard A Neher, Eric Kemen, Detlef Weigel

Crop disease outbreaks are commonly associated with the clonal expansion of single pathogenic lineages. To determine whether similar boom-and-bust scenarios hold for wild plant pathogens, we carried out a multi-year multi-site 16S rDNA survey of Pseudomonas in the natural host Arabidopsis thaliana. The most common Pseudomonas lineage corresponded to a pathogenic clade present in all sites. Sequencing of 1,524 Pseudomonas genomes revealed this lineage to have diversified approximately 300,000 years ago, containing dozens of genetically distinct pathogenic sublineages. The coexistence of diverse sublineages suggests that in contrast to crop systems, no single strain has been able to overtake these A. thaliana populations in the recent past. An important question for the future is how the maintenance of pathogenic diversity is influenced by host genetic variation versus an environment with more microbial and abiotic heterogeneity than in agricultural systems.

IOMAP collaboration: Comparative genomics of rice and its relatives

Posted on January 22, 2018

Now out in Nature Genetics read more

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young ‘AA’ subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 ‘Miracle Rice’, which relieved famine and drove the Green Revolution in Asia 50 years ago.

Detlef seminar on adaptation to the environment

Posted on January 17, 2018

Learn more about some of our recent work: read more

Seminar at UC San Diego at the Minisymposium of the "Food & Fuel for the 21st Century" group.

Detlef discussed collaborative work with Pepe Gutierrez-Marcos, led by Anjar Wibowo and Claude Becker, on epigenetics and transgenerational inheritance of stress resilience, as well as work led by Moises Exposito, on predicting future adaptation to climate change (also a recent bioRxiv preprint).


Upcoming Events


MiKo Talk John Diffley

March 21, 3 pm
MPH Lecture Hall

Title: "How our genomes are copied"


MiKo Talk Regina Baucom

October 25, 3 pm
MPH Lecture Hall

Title: "TBA"


MiKo Talk Matthew Rockman

April 18, 3 pm
MPH Lecture Hall

Title: "TBA"