The B73 Maize Genome: Complexity, Diversity, and Dynamics

Abstract

We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.

Plant genomics: sowing the seeds of success

“…Despite the sequencing of the maize genome in 2009 [6], comparatively little is known about the high levels of genetic diversity that exist between the many maize inbred lines. To address this, Romay et al [7] perform genotyping-by-sequencing of 681,257 SNP markers in the 2,815 maize accessions in the USA national maize inbred seed bank.…”

Current challenges in de novo plant genome sequencing and assembly

“…The first free-living organisms were sequenced less than 20 years ago, starting with simple microbial genomes [7], and increasing in complexity to the first eukaryotic genomes [8], the first multicellular species [9], and then on to plant genomes, including Arabidopsis thaliana (thale cress) [10], Oryza sativa (rice) [11], Carica papaya (papaya) [12] and Zea mays (maize) in 2009 [13], using first-generation capillary sequencing. Since then many others have been sequenced leveraging second-generation sequencing, including Fragaria vesca (strawberry) [14], Solanum lycopersicum (tomato) [15] and Cajanus cajan (pigeonpea) [16], and dozens more are nearing completion [17].…”

“…This increase in sequenced plant genomes has largely been driven by technological improvements: whereas the first generation of automated DNA sequencing instruments could sequence thousands of base pairs per day, current state-of-the-art second-generation sequencing instruments can sequence many billions of bases per day for hundreds or thousands of dollars per gigabase instead of millions or billions of dollars per gigabase [18]. These technologies have been applied to study thousands of genomes across the tree of life, enabling rich annotation of their gene networks [19], the development of comparative genomics approaches to infer evolutionary and domestication forces [13], the cataloging of genomic markers to optimize plant breeding [20], and numerous other studies that use the genome sequence as the backbone of the analysis [21]. …”

“…In addition they can have much higher ploidy, which is estimated to occur in up to 80% of all plant species [29], and higher rates of heterozygosity and repeats [30] than their counterparts in other kingdoms. Furthermore, the gene content in plants can be very complex, as shown by the presence of large gene families and abundant pseudogenes with nearly identical sequences derived from recent whole genome duplication events and transposon activity [13]. Plants tend to have high copy chloroplasts and mitochondria organelles, which complicate assembly of their remnants in the nuclear genome and skew coverage levels [12].…”

“…Instead of large contigs and scaffolds spanning large chromosome regions seen in recent vertebrate genome assemblies [31], there is a greater chance to assemble the sequencing reads into isolated gene islands among the background of high copy repeats [13]. Furthermore, the gene sequences may not always be correct, considering that nearly identical gene families are notoriously difficult to assemble and may collapse into a mosaic sequence without necessarily representing any member of the family [32].…”