Structural and functional divergence of a 1-Mb duplicated region in the soybean (Glycine max) genome and comparison to an orthologous region from Phaseolus vulgaris.
Soybean (Glycine max) has undergone at least two rounds of polyploidization, resulting in a paleopolyploid genome that is a mosaic of homoeologous regions. To determine the structural and functional impact of these duplications, we sequenced two ~1-Mb homoeologous regions of soybean, Gm8 and Gm15, derived from the most recent ~13 million year duplication event and the orthologous region from common bean (Phaseolus vulgaris), Pv5. We observed inversions leading to major structural variation and a bias between the two chromosome segments as Gm15 experienced more gene movement (gene retention rate of 81% in Gm15 versus 91% in Gm8) and a nearly twofold increase in the deletion of long terminal repeat (LTR) retrotransposons via solo LTR formation. Functional analyses of Gm15 and Gm8 revealed decreases in gene expression and synonymous substitution rates for Gm15, for instance, a 38% increase in transcript levels from Gm8 relative to Gm15. Transcriptional divergence of homoeologs was found based on expression patterns among seven tissues and developmental stages. Our results indicate asymmetric evolution between homoeologous regions of soybean as evidenced by structural changes and expression variances of homoeologous genes.
Lin
Jer-Young
JY
Molecular and Evolutionary Genetics, Purdue University, West Lafayette, Indiana 47907, USA.
Stupar
Robert M
RM
Hans
Christian
C
Hyten
David L
DL
Jackson
Scott A
SA
D022202:Chromosomes, Artificial, Bacterial; D004251:DNA Transposable Elements; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D018745:Genome, Plant; D017404:In Situ Hybridization, Fluorescence; D020411:Oligonucleotide Array Sequence Analysis; D027805:Phaseolus / Q000235:genetics; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide; D018626:Retroelements; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000235:genetics*
D004251:DNA Transposable Elements; D018744:DNA, Plant; D018626:Retroelements