The Barbazuk lab
comparative and functional genomics to study genome architecture,
evolution. In order to address these questions, genome sequences and
well-established catalogues of genes and their positions within the
required. As more and more genome data becomes available, the methods
catalogue genes become more robust, and ultimately the questions of
organization, gene interaction and regulation can be addressed. Our lab
with crop (particularly maize and tomato), model (Arabidopsis) and
genomes where we apply comparative analysis and computational methods
investigate gene structure, gene content, gene/genome organization and
We are currently
generation sequencing of transcriptome and genome
sequence data: We
are actively using
next generation sequence data from multiple platforms to examine and
characterize genomes and transcriptomes. We currently have projects
that apply next generation
technologies to investigate gene content, gene structure, expression,
gain/loss, genome architecture and sequence diversity.
Gene Annotation and gene structure: Plant
sequence is the
knowledge infrastructure for the next generation of plant molecular
and crop improvement, and will provide the foundation for crop
products of ongoing and future plant sequencing projects are
large contiguous nucleotide segments for which there is no a priori
of content or function. Therefore, high throughput
that can accurately identify genes within genomic sequence are
necessary for annotating and understanding the maize genome.
with Dr. Michael Brent at Washington University,
are improving gene prediction in
tomato by identifying a comprehensive "training set" of complete and
annotated gene models; and, using these to optimize TWINSCAN. TWINSCAN
next-generation gene discovery tool developed by Michael
Originally designed for human gene prediction, it improves gene
integrating traditional probability models like those underlying
FGENESH with information from the alignments between two genomes.
splicing (AS) creates multiple mRNA transcripts from a single gene.
While AS is known to
contribute to gene
regulation and proteome diversity in animals, the study of its
plants is in its early stages. However,
recently available plant genome and transcript sequence data sets are
a global analysis of AS in many plant species. Results of genome
analysis have revealed differences
between animals and
plants in the frequency of alternative splicing. The proportion of
plant genes that have one
or more alternative transcript isoforms is approximately 20%,
AS in plants is not rare, although this rate is ~1/3 of that observed
human. The majority
of plant AS events
have not been functionally characterized, but evidence suggests that AS
participates in important plant functions including stress response,
impact domestication and trait selection. The increasing availability
of plant genome sequence data
larger comparative analyses that will identify functionally important
plant AS events
based on their evolutionary conservation;
determine the influence of genome duplication on the evolution of AS;
discover plant specific cis
that regulate AS.
Yan Fu, Oliver
Bannach, Hao Chen,
Jan-Hendrik Teune, Axel Schmitz, Gerhard Steger, Liming Xiong, and W. Brad Barbazuk .
Alternative Splicing of
Anciently Exonized 5S
rRNA Regulates Plant Transcription Factor TFIIIA. Genome
Research 2009 19:913-21.
Brad Barbazuk, Yan Fu, Karen
Genome-wide analyses of alternative splicing in plants: Opportunities
Challenges. Genome Research 2008 18:1381-92.
Subramanian S, Fu
Y, Sunkar R, Barbazuk BW, Zhu JK,
Yu O. Novel and nodulation-regulated microRNAs
in soybean roots. BMC Genomics.
Brad Barbazuk, Scott J.
Emrich*, Hsin D. Chen, Li
Li, and Patrick S. Schnable. SNP discovery in maize via 454
J. 2007 51:910-18
Scott J. Emrich, W.
Brad Barbazuk, Li Li and Patrick S. Schnable. Gene discovery
and annotation using LCM-454
transcriptome sequencing. Genome Research 2007
Epub 2006 Nov 9.
Bedell, J. A and Pablo D.
representation sequencing: a success in
maize and a promise for other plant genomes.BioEssays