Although allelic sequences can vary extensively, it is generally assumed that each gene in one individual will have an allelic counterpart in another individual of the same species. We report here that this assumption does not hold true in maize. We have sequenced over 100 kb from the bz genomic region of two different maize lines and have found dramatic differences between them. First, the retrotransposon clusters, which comprise most of the repetitive DNA in maize, differ markedly in make-up and location relative to the genes in the bz region. Second, and more importantly, the genes themselves differ between the two lines, demonstrating that genetic microcolinearity can be violated within the same species. Our finding has bearing on the underlying genetic basis of hybrid vigor in maize, and possibly other organisms, and on the measurement of genetic distances.
(1, 2), a line that had been used extensively in genetic analyses, with that of the unrelated standard inbred B73 (3) revealed unexpected differences between them. First, retrotransposon clusters, which make up the bulk of the maize genome (4-6), differed in composition and location relative to the genes in the region so that the two sequences could be aligned only at the genes they had in common. Second, and most strikingly, some genes present in McC were absent from B73, indicating that genetic colinearity was violated within the species. Noncolinear haplotypes were also found in a comparison of the genomic intervals containing the z1C zein gene cluster in B73 and BSSS53, inbred lines derived from the same synthetic population (7). The lengths of the z1C regions in the two inbreds varied by 50% because of differences in the number of zein and other genes and in the sizes of the retrotransposon clusters flanking them. Similar extensive nonhomologies were reported between the allelic regions of inbreds B73 and Mo17 at three additional chromosomal locations in the genome (8). That study established that more than one-third of the predicted genes were present in just one inbred at the loci examined, although many of the unshared genes appeared to be truncated. The observation that genes not shared between inbreds violate the maize-rice colinearity usually displayed by shared genes prompted the authors to speculate that unshared genes originated from insertions of a yet-unknown nature rather than deletions.High intraspecific haplotype variability is not restricted to maize, having been recently described in barley, another species with a large amount of repetitive DNA. A comparison of the Rph7 locus in two barley cultivars established that colinearity was restricted to Ͻ35% of the two sequences, principally because of differences in retrotransposon blocks (9). Interestingly, a gene encoding a truncated helicase was present in only one of the two cultivars. On the other hand, no cases of gene acquisition or loss were found in a comparison of two different orthologous regions between rice subspecies (10, 11). This finding suggests that the type of variation detected in maize and barley may not be a general feature of plant genomes. The functional significance of the ''plus-minus'' type of variation is also unclear, because the genes that vary among accessions of the same species are present in multiple copies (3), and many of them are clearly pseudogenes or gene fragments (8, 9). Independent of its generality or functional significance, the described variation raises an important question: How did it arise? Evidence presented here indicates that the apparent intraspecific violations of genetic colinearity in maize and, probably, barley, arise from the movement of genes or gene fragments by Helitrons, a recently discovered type of eukaryotic transposon (12).Helitrons were found by computational analysis of genomic sequences from Arabidopsis, rice, and Caenorhabditis elegans (12) and were later reported to be the caus...
The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have sequenced and de novo assembled a W22 reference genome using short-read sequencing technologies. We show that significant structural heterogeneity exists in comparison to the B73 reference genome at multiple scales, from transposon composition and copy number variation to single-nucleotide polymorphisms. The generation of this reference genome enables accurate placement of thousands of Mutator (Mu) and Dissociation (Ds) transposable element insertions for reverse and forward genetics studies. Annotation of the genome has been achieved using RNA-seq analysis, differential nuclease sensitivity profiling and bisulfite sequencing to map open reading frames, open chromatin sites and DNA methylation profiles, respectively. Collectively, the resources developed here integrate W22 as a community reference genome for functional genomics and provide a foundation for the maize pan-genome.
The FATTY ACID ELONGATION1 (FAE1) gene of Arabidopsis is required for the synthesis of very long chain fatty acids in the seed. The product of the FAE1 gene is presumed to be a condensing enzyme that extends the chain length of fatty acids from C18 to C20 and C22. We report here the cloning of FAE1 by directed transposon tagging with the maize element Activator (Ac). An unstable fae1 mutant was isolated in a line carrying Ac linked to the FAE1 locus on chromosome 4. Cosegregation and reversion analyses established that the new mutant was tagged by Ac. A DNA fragment flanking Ac was cloned by inverse polymerase chain reaction and used to isolate FAE1 genomic clones and a cDNA clone from a library made from immature siliques. The predicted amino acid sequence of the FAE1 protein shares homology with those of other condensing enzymes (chalcone synthase, stilbene synthases, and beta-ketoacyl-acyl carrier protein synthase III), supporting the notion that FAE1 is the structural gene for a synthase or condensing enzyme. FAE1 is expressed in developing seed, but not in leaves, as expected from the effect of the fae1 mutation on the fatty acid compositions of those tissues.
Transposons make up the bulk of eukaryotic genomes, but are difficult to annotate because they evolve rapidly. Most of the unannotated portion of sequenced genomes is probably made up of various divergent transposons that have yet to be categorized. Helitrons are unusual rolling circle eukaryotic transposons that often capture gene sequences, making them of considerable evolutionary importance. Unlike other DNA transposons, Helitrons do not end in inverted repeats or create target site duplications, so they are particularly challenging to identify. Here we present HelitronScanner, a two-layered local combinational variable (LCV) tool for generalized Helitron identification that represents a major improvement over previous identification programs based on DNA sequence or structure. HelitronScanner identified 64,654 Helitrons from a wide range of plant genomes in a highly automated way. We tested HelitronScanner's predictive ability in maize, a species with highly heterogeneous Helitron elements. LCV scores for the 5′ and 3′ termini of the predicted Helitrons provide a primary confidence level and element copy number provides a secondary one. Newly identified Helitrons were validated by PCR assays or by in silico comparative analysis of insertion site polymorphism among multiple accessions. Many new Helitrons were identified in model species, such as maize, rice, and Arabidopsis, and in a variety of organisms where Helitrons had not been reported previously to our knowledge, leading to a major upward reassessment of their abundance in plant genomes. HelitronScanner promises to be a valuable tool in future comparative and evolutionary studies of this major transposon superfamily.A lthough transposable elements constitute the bulk of most sequenced eukaryotic genomes, their annotation has been hindered by their rapid evolutionary divergence. It is conceivable that a large fraction of the unannotated genome of most eukaryotes is made up of as yet unrecognized transposons. To date, elements have been assigned to a superfamily largely on the basis of terminal sequence homology to other elements that still encode vestiges of that superfamily's transposase (1). Helitrons are particularly challenging to identify because, unlike other DNA transposons, they do not end in inverted repeats or create target site duplications. These novel eukaryotic transposons were discovered only recently from a comparative bioinformatic analysis of several plant and animal genomes (2). Helitrons have attracted widespread attention because their remarkable ability to capture gene sequences, and intergenic regions containing potential regulatory elements, makes them of considerable potential evolutionary importance (3-10). Among carefully studied genomes, Helitron content has been estimated to be approximately 2% in Arabidopsis and maize (2, 11, 12) and 4.23% in silkworm (9). However, these values are most likely underestimates because Helitrons are hard to detect computationally given their lack of classical transposon structural features. As...
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