Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella

Molecular Biology and Evolution
Kim SteigeTanja Slotte

Abstract

The selfing syndrome constitutes a suite of floral and reproductive trait changes that have evolved repeatedly across many evolutionary lineages in response to the shift to selfing. Convergent evolution of the selfing syndrome suggests that these changes are adaptive, yet our understanding of the detailed molecular genetic basis of the selfing syndrome remains limited. Here, we investigate the role of cis-regulatory changes during the recent evolution of the selfing syndrome in Capsella rubella, which split from the outcrosser Capsella grandiflora less than 200 ka. We assess allele-specific expression (ASE) in leaves and flower buds at a total of 18,452 genes in three interspecific F1 C. grandiflora x C. rubella hybrids. Using a hierarchical Bayesian approach that accounts for technical variation using genomic reads, we find evidence for extensive cis-regulatory changes. On average, 44% of the assayed genes show evidence of ASE; however, only 6% show strong allelic expression biases. Flower buds, but not leaves, show an enrichment of cis-regulatory changes in genomic regions responsible for floral and reproductive trait divergence between C. rubella and C. grandiflora. We further detected an excess of heterozygous transposable ...Continue Reading

References

Jul 21, 1998·The Plant Cell·J Doebley, L Lukens
Apr 23, 2002·Nature Reviews. Genetics·Spencer C H Barrett
Apr 28, 2006·Evolution; International Journal of Organic Evolution·Carol GoodwillieKermit Ritland
Feb 17, 2007·Nature Reviews. Genetics·Gregory A Wray
May 12, 2007·Evolution; International Journal of Organic Evolution·Hopi E Hoekstra, Jerry A Coyne
Jul 12, 2008·Evolution; International Journal of Organic Evolution·David L Stern, Virginie Orgogozo
Feb 21, 2009·Proceedings of the National Academy of Sciences of the United States of America·John Paul FoxeStephen I Wright
Feb 25, 2009·Evolution; International Journal of Organic Evolution·Michael A GrilloTao Sang
Mar 25, 2009·Proceedings of the National Academy of Sciences of the United States of America·Ya-Long GuoMikkel H Schierup
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Apr 1, 2010·Genome Research·C Joel McManusPatricia J Wittkopp
Jun 23, 2010·Nature Reviews. Genetics·Tomi Pastinen
Jan 22, 2011·Proceedings of the National Academy of Sciences of the United States of America·Jesse D HollisterBrandon S Gaut
Mar 4, 2011·Proceedings of the National Academy of Sciences of the United States of America·James C SchnableMichael Freeling
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Nov 17, 2011·Molecular Biology and Evolution·Fei HeJuliette de Meaux
Apr 24, 2012·Evolution; International Journal of Organic Evolution·Tanja SlotteStephen I Wright
May 30, 2012·Molecular Biology and Evolution·Fei HeJuliette de Meaux
Jun 30, 2012·Bioinformatics·Liguo WangWei Li
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Feb 15, 2013·PLoS Genetics·Xi WangLisa M Smith
Feb 6, 2014·Proceedings of the National Academy of Sciences of the United States of America·Katharina SchiesslRobert Sablowski
Jul 18, 2014·BMC Genomics·J Ågren AgrenStephen I Wright
Nov 7, 2014·PLoS Genetics·Zachary H LemmonJohn F Doebley
Nov 28, 2014·The Plant Cell·Francisco A CubillosOlivier Loudet

❮ Previous
Next ❯

Citations

Mar 5, 2016·Current Opinion in Plant Biology·Kim A Steige, Tanja Slotte
Nov 13, 2015·PLoS Genetics·Frédéric FyonThomas Lenormand
Jan 18, 2017·Proceedings of the National Academy of Sciences of the United States of America·Kim A SteigeTanja Slotte
Jan 14, 2018·Evolution; International Journal of Organic Evolution·Frédéric Fyon, Thomas Lenormand
Sep 1, 2018·Molecular Ecology·Billie A GouldDavid B Lowry
Oct 26, 2018·American Journal of Botany·Juliette de Meaux
Jun 30, 2019·The New Phytologist·Jörg A BachmannTanja Slotte
Mar 19, 2016·The New Phytologist·Ramesh ArunkumarStephen I Wright

❮ Previous
Next ❯

Datasets Mentioned

BETA
PRJEB9020

Methods Mentioned

BETA
RNAseq
PCR
Assay

Software Mentioned

CutAdapt
PoPoolationTE
bedtools
GATK
custom
R
STAR
R package TopGO
VCFTools
- FREEC

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.