D
Daniel Koenig
Researcher at University of California, Riverside
Publications - 46
Citations - 4892
Daniel Koenig is an academic researcher from University of California, Riverside. The author has contributed to research in topics: Capsella & Population. The author has an hindex of 26, co-authored 46 publications receiving 4313 citations. Previous affiliations of Daniel Koenig include University of California, Davis & University of California.
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Journal ArticleDOI
Whole-genome sequencing of multiple Arabidopsis thaliana populations
Jun Cao,Korbinian Schneeberger,Stephan Ossowski,Stephan Ossowski,Torsten Günther,Sebastian Bender,Joffrey Fitz,Daniel Koenig,Christa Lanz,Oliver Stegle,Christoph Lippert,Xi Wang,Felix Ott,Jonas Müller,Carlos Alonso-Blanco,Karsten M. Borgwardt,Karl Schmid,Detlef Weigel +17 more
TL;DR: The majority of common small-scale polymorphisms as well as many larger insertions and deletions in the A. thaliana pan-genome are described, their effects on gene function, and the patterns of local and global linkage among these variants.
Journal ArticleDOI
Spontaneous epigenetic variation in the Arabidopsis thaliana methylome
Claude Becker,Jörg Hagmann,Jonas Müller,Daniel Koenig,Oliver Stegle,Karsten M. Borgwardt,Detlef Weigel +6 more
TL;DR: Compared genome-wide DNA methylation among 10 A. thaliana lines, differentially methylated sites were farther from transposable elements and showed less association with short interfering RNA expression than invariant positions, which has important implications for the potential contribution of sequence-independent epialleles to plant evolution.
Journal ArticleDOI
The Capsella rubella genome and the genomic consequences of rapid mating system evolution
Tanja Slotte,Tanja Slotte,Khaled M. Hazzouri,Khaled M. Hazzouri,J. Arvid Ågren,Daniel Koenig,Florian Maumus,Ya-Long Guo,Kim A. Steige,Adrian E. Platts,Juan S. Escobar,L. Killian Newman,Wei Wang,Terezie Mandáková,Emilio Vello,Lisa M. Smith,Stefan R. Henz,Joshua G. Steffen,Joshua G. Steffen,Shohei Takuno,Shohei Takuno,Yaniv Brandvain,Graham Coop,Peter Andolfatto,Tina T. Hu,Mathieu Blanchette,Richard M. Clark,Hadi Quesneville,Magnus Nordborg,Brandon S. Gaut,Martin A. Lysak,Jerry Jenkins,Jane Grimwood,Jarrod Chapman,Simon E. Prochnik,Shengqiang Shu,Daniel S. Rokhsar,Daniel S. Rokhsar,Jeremy Schmutz,Detlef Weigel,Stephen I. Wright +40 more
TL;DR: The transition to selfing may be typified by parallel shifts in gene expression, along with a measurable reduction of purifying selection, similar to that seen in Arabidopsis, which self fertilization evolved about 1 million years ago.
Journal ArticleDOI
The genome of the stress-tolerant wild tomato species Solanum pennellii
Anthony Bolger,Federico Scossa,Marie E. Bolger,Christa Lanz,Florian Maumus,Takayuki Tohge,Hadi Quesneville,Saleh Alseekh,Iben Sørensen,Gabriel Lichtenstein,Eric A. Fich,Mariana Conte,Heike Keller,Korbinian Schneeberger,Rainer Schwacke,Itai Ofner,Julia Vrebalov,Yimin Xu,Sonia Osorio,Saulo Alves Aflitos,Elio Schijlen,José M. Jiménez-Gómez,Małgorzata Ryngajłło,Seisuke Kimura,Ravi Kumar,Daniel Koenig,Lauren R. Headland,Julin N. Maloof,Neelima Sinha,Roeland C. H. J. van Ham,René Klein Lankhorst,Linyong Mao,Alexander Vogel,Borjana Arsova,Ralph Panstruga,Zhangjun Fei,Jocelyn K. C. Rose,Dani Zamir,Fernando Carrari,James J. Giovannoni,Detlef Weigel,Björn Usadel,Alisdair R. Fernie +42 more
TL;DR: A high-quality genome assembly of the parents of the IL population of S. pennellii is described, defining candidate genes for stress tolerance and providing evidence that transposable elements had a role in the evolution of these traits.
Journal ArticleDOI
Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato
Daniel Koenig,José M. Jiménez-Gómez,Seisuke Kimura,Daniel Fulop,Daniel H. Chitwood,Lauren R. Headland,Ravi Kumar,Michael F. Covington,Upendra K. Devisetty,An V. Tat,Takayuki Tohge,Anthony Bolger,Korbinian Schneeberger,Stephan Ossowski,Christa Lanz,Guangyan Xiong,Mallorie Taylor-Teeples,Siobhan M. Brady,Markus Pauly,Detlef Weigel,Björn Usadel,Alisdair R. Fernie,Jie Peng,Neelima Sinha,Julin N. Maloof +24 more
TL;DR: High-throughput sequencing is used to identify changes in DNA sequence and gene expression that differentiate cultivated tomato and its wild relatives and identifies hundreds of candidate genes that have evolved new protein sequences or have changed expression levels in response to natural selection in wild tomato relatives.