The B73 Maize Genome-Complexity, Diversity, and Dynamics

Carlos Linares, Joshua Garmizo, Jauregui Lilibeth, Lauren Sanborn, Jovana Obradovic

The B73 Maize Genome-Complexity, Diversity, and Dynamics

Carlos Linares, Joshua Garmizo, Jauregui Lilibeth, Lauren Sanborn, Jovana Obradovic

BACKGROUND

RESULTS

• Maize-Domesticated over approx. the past 10,000 years-Originated in Central America-Has undergone continuous cultivation and selection -Hence, it a model organism for genetic studies

• Maize as a Model Organism-Inheritance & function of genes-Physical linkage between genes and chromosomes-Relationship between cytological crossover & recombination-Origin of nucleolus -Telomeres -Epigenetic splicing-Genomic Imprinting -Transposons

• Maize: A Staple Crop In USA

-12 billion bushels of grain/yr-86 million acres of land-Value = $47 billion/yr

What’s the significance of this?-Maize has been manipulated to maximize yield and cater to the tastes of people in a given region, which is important from a genetic standpoint-Cultivating maize at such large quantities and actively selecting favorable traits alters its genome-Great genome expansion over the yearsexpanded dramatically (to 2.3 gigabases) over the last ~3 million years via a proliferation of long terminal repeat retrotransposons

• B73 RefGen_v1 Maize-Almost 85% of the B73 genome consists of transposable elements-Existence and high abundance of LTR retrotransposons in plants originally discovered in maize-Made up of 855 families of DNA transposable elements that make up 8.6% of the genome

• Regions of the genome with the highest LTR retrotransposon density contained the lowest LTR retrotransposon diversity. These results indicate that the maize genome provides a great number of different niches for the survival and procreation of a great variety of retroelements that have evolved to differentially occupy and exploit this genomic diversity.

•Furthermore, Helitrons in maize seem to continually produce new nonautonomous elements responsible for the duplicative insertion of gene segments into new locations and for the innovative genic diversity.

•The finding that Mu insertions and meiotic recombination sites both concentrate in genomic regions marked with epigenetic marks of open chromatin provides support for the hypothesis that open chromatin enhances rates of both Mu insertion and meiotic recombination.

•The B73 maize reference sequence promises to advance basic research and to facilitate efforts to meet the world’s growing needs for food, feed, energy, and industrial feed stocks in an era of global climate change. 

CONCLUSION/DISCUSSION

P < .027 P < .007METHODS

* References available upon request

Maize B73 Reference Genome and Gene Families

Fig. 1.Reference chromosome showing contigs, recombination rate, Mu insertions,MF enrichment, repeat coverage and genedensity, along with rice and sorghum syntenies.

Fig 3. Taken from Anderson et al. 2006 A Model depicting highest gene density at the ends of chromosomes, lowest surrounding the centromeres supporting meiotic rates of recombination

Diagrams

Utilizing BACS and whole genome shotgun sequencing, B73 reference genome version 1 found to be 85% transposable elements consisting of 855 families Majority LTR retrotransposons exhibiting family-specific, non uniform distributions along the chromosome Most complex is Mutator (Mu) family, insertion sites colocalize with gene rich regions that have highest rates of meiotic recombination, also correlate with poorly methylated regions 8 families of Helitrons that are uniquely active within gene rich regions Total of 32, 540 protein encoding genes and 150 microRNA genes predicted from assembled BAC contig

Core set of 8,494 families shared between maize, rice, sorghum, and Arabidopsis Exon sizes similar but maize’s introns larger due to repeating units Rice and sorghum genomes helped define maize’s duplicate regions Effective due to resemblance to maize’s ancestral subgenomes and low numbers of interchromosomal rearrangement since the lineage split Genes retained as duplicates significantly enriched for transcription factors

Unlike most plant genomes, around 95% of genes are methylated and these regions are heavily condensed during interphase, poorly methylated regions correlate with Mu insertions

Maize centromeres, delineated on the basis of their centromere-specific histone H3, contained variable amounts of tandem CentC satellite repeat and centromeric retrotransposon elements (CRMS) Regional centromeres are dynamic loci causing centromere-specific histone H3 domains shift over time as a result of recombinants created by CRMs

Epigenetic marks, such as hypomethylation and histone modifications, guide rates of meiotic recombination Rates highest at the ends of reference chromosomes and low in the regions surrounding the centromere corresponding to pattern of gene density Also key to the contribution of genomic imprinting on gene expression in maize hybrids

Uneven gene losses between duplicated regions, associated with many chromosomal breaks and fusions, involved in returning to a diploid state from ancient allotetraploid

Utilizing BACS and whole genome shotgun sequencing, B73 reference genome version 1 found to be 85% transposable elements consisting of 855 families Majority LTR retrotransposons exhibiting family-specific, non uniform distributions along the chromosome Most complex is Mutator (Mu) family, insertion sites colocalize with gene rich regions that have highest rates of meiotic recombination, also correlate with poorly methylated regions 8 families of Helitrons that are uniquely active within gene rich regions • Total of 32, 540 protein encoding genes and 150 microRNA genes predicted from assembled BAC contig • Core set of 8,494 families shared between maize, rice, sorghum, and Arabidopsis Exon sizes similar but maize’s introns larger due to repeating units Rice and sorghum genomes helped define maize’s duplicate regions Effective due to resemblance to maize’s ancestral subgenomes and low numbers of interchromosomal rearrangement since the lineage split Genes retained as duplicates significantly enriched for transcription factors • Unlike most plant genomes, around 95% of genes are methylated and these regions are heavily condensed during interphase, poorly methylated regions correlate with Mu insertions • Maize centromeres, delineated on the basis of their centromere-specific histone H3, contained variable amounts of tandem CentC satellite repeat and centromeric retrotransposon elements (CRMS) Regional centromeres are dynamic loci causing centromere-specific histone H3 domains shift over time as a result of recombinants created by CRMs  • Epigenetic marks, such as hypomethylation and histone modifications, guide rates of meiotic recombination Rates highest at the ends of reference chromosomes and low in the regions surrounding the centromere corresponding to pattern of gene density Also key to the contribution of genomic imprinting on gene expression in maize hybrids

• Uneven gene losses between duplicated regions, associated with many chromosomal breaks and fusions, involved in returning to a diploid state from ancient allotetraploid

•With a size approximating that of the human genome, the maize genome ( 2.3 gigabases) ranks among the largest plant genomes that have been sequenced.  The size of the maize genome was achieved via a proliferation of long terminal repeat(LTR) retrotransposons over the last 3 million years.

•Although TEs are a major component of all studied plant genomes, and are the most significant contributors to their genome structure and evolution, their properties and reasons for existence are not well understood. In this study, over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes.

•Comprehensive sequence analysis of the maize genome now permits detailed discovery and description of transposable elements (TEs) in this complex nuclear environment.

1. L. K. Anderson, A. Lai, S. M. Stack, C. Rizzon, B. S. Gaut, "Uneven distribution of expressed sequence tag loci on maize pachytene chromosomes," Genome Research 16, 115 (2006).

2. P. S. Schnable et al., "The B73 Maize Genome: Complexity, Diversity, and Dynamics," Science 326, 1112 (2009).