The Effects of Gene Duplication Modes on the Evolution of Regulatory Divergence in Wild and Cultivated Soybean

Flowering phenology as a core domestication trait in soybean

(2020) Zhizhong Gong   Journal of Integrative Plant Biology

Genomic Balance Plays Out in Evolution

(2019) James A. Birchler   PLANT CELL

Artificial selection on GmOLEO1 contributes to the increase in seed oil during soybean domestication

(2019) Dan Zhang et al.   PLoS Genetics

Natural variation and selection in GmSWEET39 affect soybean seed oil content

(2019) Long Miao et al.   NEW PHYTOLOGIST

Evolution and Expression Divergence of the CYP78A Subfamily Genes in Soybean

(2018) Ai-Hua Dai et al.   Genes

Genome-wide patterns of regulatory divergence revealed by introgression lines

(2016) Rafael F. Guerrero et al.   EVOLUTION

Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals

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Transcriptome shock in an interspecific F1 triploid hybrid ofOryzarevealed by RNA sequencing

(2015) Ying Wu et al.   Journal of Integrative Plant Biology

Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization

(2015) Jean-Francois Gout et al.   MOLECULAR BIOLOGY AND EVOLUTION

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Tempo and mode of regulatory evolution in Drosophila

(2014) J. D. Coolon et al.   GENOME RESEARCH

Genome-Wide Disruption of Gene Expression in Allopolyploids but Not Hybrids of Rice Subspecies

(2014) Chunming Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

(2014) Ying-hui Li et al.   NATURE BIOTECHNOLOGY

The Role of cis Regulatory Evolution in Maize Domestication

(2014) Zachary H. Lemmon et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Tracing soybean domestication history: From nucleotide to genome

(2012) Moon Young Kim et al.   BREEDING SCIENCE

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

(2012) A. Goncalves et al.   GENOME RESEARCH

Homoeolog expression bias and expression level dominance in allopolyploid cotton

(2012) M-J Yoo et al.   HEREDITY

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Evolutionary History and Complementary Selective Relaxation of the Duplicated PI Genes in Grasses

(2011) Ruo-Xun Wei et al.   Journal of Integrative Plant Biology

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Regulatory divergence in Drosophila revealed by mRNA-seq

(2010) C. J. McManus et al.   GENOME RESEARCH

Natural selection on cis and trans regulation in yeasts

(2010) J. J. Emerson et al.   GENOME RESEARCH

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

The evolution of gene duplications: classifying and distinguishing between models

(2010) Hideki Innan et al.   NATURE REVIEWS GENETICS

Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome

(2010) M. Y. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes

(2009) Patrick P. Edger et al.   CHROMOSOME RESEARCH

The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution

(2009) James A. Birchler et al.   NEW PHYTOLOGIST

Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution

(2008) Lex Flagel et al.   BMC BIOLOGY

Regulatory changes underlying expression differences within and between Drosophila species

(2008) Patricia J Wittkopp et al.   NATURE GENETICS