Latest News

2017 Campus Soccer Tournament

Posted on August 11, 2017

Two awesome WeigelWorld soccer teams participated in this year’s campus tournament. read more

Denisovans

The Elephants

 

 

In Science: Ancient maize adaptation to temperate climate

Posted on August 04, 2017

Genomic estimation reveals when ancient maize became adapted to temperate climate read more

Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America

Swarts, K., Gutaker, R. M., Benz, B., Blake, M., Bukowski, R., Holland, J., Kruse-Peeples, M., Lepak, N., Prim, L., Romay, M. C., Ross-Ibarra, J., Sanchez-Gonzalez, J. d. J., Schmidt, C., Schuenemann, V. J., Krause, J., Matson, R. G., Weigel, D., Buckler, E. S., Burbano, H. A. (2017)

People introduced maize to the southwestern US by 4,000 years ago; full agriculture was established quickly in the lowland deserts but delayed in the temperate uplands for 2,000 years. We test if the earliest upland maize was adapted for early flowering, a characteristic of modern temperate maize. We sequenced fifteen 1,900-year old maize cobs from Turkey Pen Shelter in the temperate Southwest. Indirectly validated genomic models predicted that Turkey Pen maize was marginally adapted with respect to flowering, as well as short, tillering and segregating for yellow kernel color. Temperate adaptation drove modern population differentiation and was selected in situ from ancient standing variation. Validated prediction of polygenic traits improves our understanding of ancient phenotypes and the dynamics of environmental adaption.

 

Collaboration with Huq lab: Splicing and phytochrome signaling

Posted on July 31, 2017

Out in PNAS: SPF45-related splicing factor, phytochrome signaling & pre-mRNA splicing read more

Xin et al. (2017) SPF45-related splicing factor for phytochrome signaling promotes photomorphogenesis by regulating pre-mRNA splicing in Arabidopsis. Proc Natl Acad Sci USA, doi: 10.1073/pnas.1706379114

Pre-mRNA processing not only enhances the diversity encoded in the genome without the need to increase the number of genes but also provides a means to adjust cellular transcript abundance. Environmental light has a profound effect on transcript accumulation, but how this is partitioned between transcriptional and posttranscriptional processes is largely unknown. Here we describe the identification and characterization of the splicing factor for phytochrome signaling (SFPS), which directly interacts with the photoreceptor phytochrome B. sfps seedlings are hyposensitive to light and display pre-mRNA splicing defects in a large number of genes, many of which regulate light signaling and the circadian clock. Thus, light might control pre-mRNA splicing in addition to transcription of many genes through SFPS to promote photomorphogenesis.

Congrats Danelle: Dissertation Award of Teufel Foundation

Posted on July 17, 2017

Danelle received today the dissertation award of the Reinhold-und-Maria-Teufel-Stiftung. read more

Danelle Seymour defended her PhD thesis on "Exploring the genetics and genomics of Arabidopsis thaliana and its relatives" last year. The dissertation award of the Reinhold-und-Maria-Teufel-Stiftung, which includes a personal purse of €5,000, recognizes the outstanding quality of her work. Congratulations, Danelle!

Danelle is currently a postdoc at UC Irvine, with Brandon Gaut.

On bioRxiv: Segregation distortion in Arabidopsis thaliana

Posted on July 10, 2017

The genetic architecture of recurrent segregation distortion in Arabidopsis thaliana read more

The genetic architecture of recurrent segregation distortion in Arabidopsis thaliana

Danelle K. Seymour, Eunyoung Chae, Burak I. Ariöz, Daniel Koenig, Detlef Weigel

doi.org/10.1101/158527

The equal probability of transmission of alleles from either parent during sexual reproduction is a central tenet of genetics and evolutionary biology. Yet, there are many cases where this rule is violated. Such violations limit intraspecific gene flow and can facilitate the formation of genetic barriers, a first step in speciation. Biased transmission of alleles, or segregation distortion, can result from a number of biological processes including epistatic interactions between incompatible loci, gametic selection, and meiotic drive. Examples of these phenomena have been identified in many species, implying that they are universal, but comprehensive species-wide studies of segregation distortion are lacking. We have performed a species-wide screen for distorted allele frequencies in over 500 segregating populations of Arabidopsis thaliana using reduced-representation genome sequencing. Biased transmission of alleles was evident in up to a quarter of surveyed populations. Most populations exhibited distortion at only one genomic region, with some regions being repeatedly affected in multiple populations. Our results begin to elucidate the species-level architecture of biased transmission of genetic material in A. thaliana, and serve as a springboard for future studies into the basis of intraspecific genetic barriers.

On bioRxiv: Arabidopsis genome assembled with one Nanopore flowcell

Posted on July 05, 2017

Arabidopsis thaliana genome assembly with a single Oxford Nanopore flow cell read more

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

Todd P. Michael, Florian Jupe, Felix Bemm, Stanley T. Motley, Justin P. Sandoval, Olivier Loudet, Detlef Weigel, VJoseph R. Ecker

doi.org/10.1101/149997

While many evolutionary questions can be answered by short read re-sequencing, presence/absence polymorphisms of genes and/or transposons have been largely ignored in large-scale intraspecific evolutionary studies. To enable the rigorous analysis of such variants, multiple high quality and contiguous genome assemblies are essential. Similarly, while genome assemblies based on short reads have made genomics accessible for non-reference species, these assemblies have limitations due to low contiguity. Long-read sequencers and long-read technologies have ushered in a new era of genome sequencing where the lengths of reads exceed those of most repeats. However, because these technologies are not only costly, but also time and compute intensive, it has been unclear how scalable they are. Here we demonstrate a fast and cost effective reference assembly for an Arabidopsis thaliana accession using the USB-sized Oxford Nanopore MinION sequencer and typical consumer computing hardware (4 Cores, 16Gb RAM). We assemble the accession KBS-Mac-74 into 62 contigs with an N50 length of 12.3 Mb covering 100% (119 Mb) of the non-repetitive genome. We demonstrate that the polished KBS-Mac-74 assembly is highly contiguous with BioNano optical genome maps, and of high per-base quality against a likewise polished Pacific Biosciences long-read assembly. The approach we implemented took a total of four days at a cost of less than 1,000 USD for sequencing consumables including instrument depreciation.

 

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Upcoming Events

Aug
19

5th ICBPI 2017


Sep
12

IMPRS PhD Student Symposium

September 11-14
in Göttingen, Germany

Detlef speaking at International Horizons in Molecular Biology Symposium: "Genetics and epigenetics of adaptation to the environment"


Sep
13

MiKo Talk Jochen Wolf

September 13, 3 pm
MPH Lecture Hall

Title: "TBA"