Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping

Authors


  • R.J.A.B. uses molecular genetic and bioinformatics approaches to study duplicate gene evolution and the consequences of polyploidy. C.S. uses computational methods to investigate genome architecture and gene expression and alternative splicing, using next generation sequence technologies. W.W. is the manager of the Schnable lab where she conducts research on heterosis and carbon capturing crops. L.G. manages the Genomics Technologies Facility at Iowa State University. G.D.M.’s research focuses on comparative genomics for crop improvement applications. P.S. Schnable’s research focuses on structural and functional analyses of complex plant genomes, primarily maize. He was a co-PI on the maize genome sequencing project P.S. Soltis’ research interests include: plant phylogenetics, polyploidy, gene family evolution, phylogeography and conservation genetics. D.E.S. is interested in angiosperm phylogeny, genome doubling, floral developmental genetics, phylogeography and molecular cytogenetics. W.B.B uses bioinformatics and comparative and functional genomics to investigate plant genome structure and function, gene expression and alternative splicing.

Dr W. Brad Barbazuk, Fax: 352-273-8284; E-mail: bbarbazuk@ufl.edu

Abstract

Tragopogon miscellus (Asteraceae) is an evolutionary model for the study of natural allopolyploidy, but until now has been under-resourced as a genetic model. Using 454 and Illumina expressed sequence tag sequencing of the parental diploid species of T. miscellus, we identified 7782 single nucleotide polymorphisms that differ between the two progenitor genomes present in this allotetraploid. Validation of a sample of 98 of these SNPs in genomic DNA using Sequenom MassARRAY iPlex genotyping confirmed 92 SNP markers at the genomic level that were diagnostic for the two parental genomes. In a transcriptome profile of 2989 SNPs in a single T. miscellus leaf, using Illumina sequencing, 69% of SNPs showed approximately equal expression of both homeologs (duplicate homologous genes derived from different parents), 22% showed apparent differential expression and 8.5% showed apparent silencing of one homeolog in T. miscellus. The majority of cases of homeolog silencing involved the T. dubius SNP homeolog (164/254; 65%) rather than the T. pratensis homeolog (90/254). Sequenom analysis of genomic DNA showed that in a sample of 27 of the homeologs showing apparent silencing, 23 (85%) were because of genomic homeolog loss. These methods could be applied to any organism, allowing efficient and cost-effective generation of genetic markers.

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