A GeneTrek analysis of the maize genome

Abstract

Analysis of the sequences of 74 randomly selected BACs demonstrated that the maize nuclear genome contains Ϸ37,000 candidate genes with homologues in other plant species. An additional Ϸ5,500 predicted genes are severely truncated and probably pseudogenes. The distribution of genes is uneven, with Ϸ30% of BACs containing no genes. BAC gene density varies from 0 to 7.9 per 100 kb, whereas most gene islands contain only one gene. The average number of genes per gene island is 1.7. Only 72% of these genes show collinearity with the rice genome. Particular LTR retrotransposon families (e.g., Gyma) are enriched on gene-free BACs, most of which do not come from pericentromeres or other large heterochromatic regions. Gene-containing BACs are relatively enriched in different families of LTR retrotransposons (e.g., Ji). Two major bursts of LTR retrotransposon activity in the last 2 million years are responsible for the large size of the maize genome, but only the more recent of these is well represented in gene-containing BACs, suggesting that LTR retrotransposons are more efficiently removed in these domains. The results demonstrate that sample sequencing and careful annotation of a few randomly selected BACs can provide a robust description of a complex plant genome.gene distribution ͉ gene number ͉ genome annotation ͉ repetitive DNA ͉ sample sequencing W hole-genome sequence analysis has revolutionized the field of plant genetics. A sequenced plant genome provides the full list of genetic elements and also the context in which these elements function. The near-complete sequence of Arabidopsis thaliana (1) enabled the Arabidopsis 2010 project, which proposes to characterize the function of all of the genes in the genome (2). In addition, comparative analysis of the genomes of two or more species with known evolutionary relatedness is a powerful way to identify functional elements, to transfer knowledge from well studied model organisms to related plants, and to infer the mechanisms of genome evolution. For example, comparative analysis of orthologous regions from multiple cereals, including maize, rice, sorghum and wheat, has provided abundant information about the timing, nature and mechanisms of small rearrangements within those genomes (3-7).

The dynamics of LTR retrotransposon accumulation across 25 million years of panicoid grass evolution

“…Efficient and detailed analysis of repetitive DNA content SSA allows analysis of the major repetitive components of a genome without the huge cost of deeply sequencing the entire genome (Brenner et al, 1993;Devos et al, 2005;Liu et al, 2007). Because we are interested in the precise subfamilies of any repeats that were found, the short reads associated with 'next generation' sequencing (Mardis, 2008) were judged to be inappropriate.…”

“…Hence, any full-genome analysis in the panicoids requires analyses of multiple species, but this is expensive at the full-genome level with current genome sequencing technologies. Sample sequence analysis (SSA) (Brenner et al, 1993;Devos et al, 2005;Liu et al, 2007) uses statistical analysis of a small and randomly chosen set of DNA molecules to provide an alternative to full-genome studies. Because full-genome analysis usually under-represents repetitive DNAs (due to challenges in their assembly), a randomly chosen set of DNAs contributing to an SSA can provide a more accurate description of the repetitive DNAs than even a 'completed' genome sequence .…”

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

“…Specifically, all of the six most abundant LTR-retro families that we investigated exhibit high overall levels of internal DNA methylation and H3K9me2 in B73 aerial tissues, as well as spreading of these heterochromatic modifications into adjacent regions of ;1 to 2 kb (Eichten et al, 2012). Nonetheless, members of many of the highly abundant LTR-retro families are closely interspersed with genes in the euchromatic arms of maize chromosomes (SanMiguel et al, 1996;Liu et al, 2007;Baucom et al, 2009). Interestingly, in our data we found that two of these highly abundant LTR-retro families, RLC Ji, and Opie, were significantly enriched in E, EM, and M regions, and a third family, RLG Huck, was significantly enriched in E and M regions.…”

Controlling elements are wild cards in the epigenomic deck

“…Waves of replication have formed families of mostly fragmentary or otherwise degenerate retroelements (1,2). Epigenetic silencing suppresses retrotransposon activity, keeping them from wreaking genetic and epigenetic havoc in their hosts (3,4), but active suppression must be maintained (2).…”

“…T he genomes of multicellular eukaryotes are loaded with retrotransposons, parasites that propagate by transcription of their genomes, reverse transcription, and insertion of a new copy into the host genome (1,2). Waves of replication have formed families of mostly fragmentary or otherwise degenerate retroelements (1,2).…”