Natural GMOs Part 152. Why biologists expect a lot of random DNA shuffling in any crop variety -- it's what you get in nature on a grande scale.

Organization of eight bz haplotypes (particular variant chromosome versions). Each haplotype is identified by the name of the genetic line, followed by the size of the cloned NotI fragment, in parentheses. The locations of the NotI sites at the proximal and distal ends are marked by Ns on the left and right, respectively. Genes are shown as pentagons pointing in the direction of transcription; exons are in bronze and introns in yellow. There are eight genes in the region: bz, stc1, rpl35A, tac6058, hypro1, znf, tac7077, and uce2 (21). The same symbols are used for gene fragments carried by helitrons (Hels), which are represented as bidirectional arrows below the line for each haplotype. The vacant sites for HelA and HelB in each haplotype are provided as reference points and marked with short vertical strokes. Dashed lines represent deletions. Retrotransposons are indicated by solid triangles of different colors. DNA transposons and TAFTs, which are probably also DNA transposons, are indicated by open triangles in red and orange, respectively. Small insertions are indicated in light blue and are numbered as indicated in Table 3. Only the genes have been drawn to scale. (Q. Wang, H. K. Dooner, Proc. Natl. Acad. Sci. U.S.A. 103, 17644 (2006). )

For an introductory background to the activities of parasitic DNA in plant chromosomes see

• Natural GMOs Part 5. Jumping genes cause mutations.

• Natural GMOs Part 16b: GMOs and Movement of genes between species. "About half the chromosomal DNA of humans, animals and plants is sourced from ...mobile DNA."

• The New Genetics Framework: Natural Genetic Engineering is commonplace in conventional food crops and important for their vigour.

In this post we report a fine over-view short summary written by Nina Fedoroff and just appearing at Science magazine, in a wonderful article on Transposable Elements, Epigenetics, and Genome Evolution:

THE CONTEMPORARY PLANT GENOME LANDSCAPE

"Despite the multiplicity of plant epigenetic silencing mechanisms, the fingerprints of transposition and recombination are evident at every level of plant genome structure, organization, and evolution. Maize genes are clustered in small groups separated by long, uninterrupted stretches of DNA consisting of retrotransposons (101, 102). Almost 85% of the contemporary 2.3-Gb maize (Zea mays or corn) genome comprises transposons, more than 75% of which are long terminal repeat (LTR) retrotransposons (21). Its roughly 40,000 genes, averaging about 3.3 kb in length, form small islands in a sea of more than a million transposons and retrotransposons belonging to almost 1300 different gene families.

In addition to forming very large blocks, retrotransposons exhibit a tendency to home to different neighborhoods. In maize, for example, gypsy and copia elements are over- and underrepresented in pericentromeric regions, respectively (21, 103). Within a retro transposon block, younger elements are progressively nested within older elements, as illustrated in Fig. 6 for a short region near the maize adh1 gene (21, 102, 103). Such targeting can occur through the interaction of retrotransposon-specific proteins and chromatin proteins, which are themselves preferentially associated with certain types of sequences. An example is provided by the interactions of yeast Sir4p, a structural protein of heterochromatin, with a 6-amino acid motif of the Ty5 integrase protein that targets insertion into telomeric heterochromatin (104,105). An Arabidopsis lyrata centromeric retrotransposon was reported to insert preferentially into centromeres in A. thaliana (106). Because the centromeric sequences are quite different in the two species, targeting is likely to involve an interaction with the highly conserved centromere-specific structural proteins.

Unlike retrotransposons, which replicate through an RNA intermediate and reinsert DNA copies, DNA transposons move by a cut-and-paste mechanism, generally excising from just one newly replicated sister chromatid and reinserting into a site either nearby on the same chromosome or elsewhere in the genome (107). Because a copy of the transposon is retained at the donor site, such transposition events commonly give rise to additional transposon copies. DNA transposons account for a much smaller fraction of the plant genome than retrotransposons, are generally present in fewer copies, and tend to be associated with genic regions, some even inserting preferentially into genes (108). Mu transposons in maize favor recombinationally active regions of the genome (109), whereas Helitrons accumulate near but not inside each other (110). Such clustering may reflect the propensity of some TEs to move to nearby sites, long documented for the Ac/Ds(Activator/Dissociation) transposon family of maize (111)..."

@ Transposable Elements, Epigenetics, and Genome Evolution:

Citations include:

Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus
Q. Wang, H. K. Dooner, Proc. Natl. Acad. Sci. U.S.A. 103, 17644 (2006).

Abstract
Maize is probably the most diverse of all crop species. Unexpectedly large differences among haplotypes were first revealed in a comparison of the bz genomic regions of two different inbred lines, McC and B73. Retrotransposon clusters, which comprise most of the repetitive DNA in maize, varied markedly in makeup, and location relative to the genes in the region and genic sequences, later shown to be carried by two helitron transposons, also differed between the inbreds. Thus, the allelic bz regions of these Corn Belt inbreds shared only a minority of the total sequence. To investigate further the variation caused by retrotransposons, helitrons, and other insertions, we have analyzed the organization of the bz genomic region in five additional cultivars selected because of their geographic and genetic diversity: the inbreds A188, CML258, and I137TN, and the land races Coroico and NalTel. This vertical comparison has revealed the existence of several new helitrons, new retrotransposons, members of every superfamily of DNA transposons, numerous miniature elements, and novel insertions flanked at either end by TA repeats, which we call TAFTs (TA-flanked transposons). The extent of variation in the region is remarkable. In pairwise comparisons of eight bz haplotypes, the percentage of shared sequences ranges from 25% to 84%. Chimeric haplotypes were identified that combine retrotransposon clusters found in different haplotypes. We propose that recombination in the common gene space greatly amplifies the variability produced by the retrotransposition explosion in the maize ancestry, creating the heterogeneity in genome organization found in modern maize.

HighWire Press-hosted articles citing this Wang, and Dooner  article:

• Transposable Elements, Epigenetics, and Genome Evolution Science 2012 338 (6108) 758-767 Full Text Full Text (PDF)
• Gene Capture by Helitron Transposons Reshuffles the Transcriptome of MaizeGenetics 2012 190 (3) 965-975Abstract Full Text Full Text (PDF)
• Genome-Wide Characterization of the HD-ZIP IV Transcription Factor Family in Maize: Preferential Expression in the Epidermis Plant Physiol. 2011 157 (2) 790-803 Abstract Full Text Full Text (PDF)
• Genome Size and Transposable Element Content as Determined by High-Throughput Sequencing in Maize and Zea luxurians Genome Biol Evol 2011 3 (0) 219-229 Abstract Full Text Full Text (PDF)
• Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor Genome Res 2010 20 (12) 1689-1699 Abstract Full Text Full Text (PDF)
• The polychromatic Helitron landscape of the maize genome Proc. Natl. Acad. Sci. USA 2009 106 (47) 19916-19921 Abstract Full Text Full Text (PDF)
• A cornucopia of Helitrons shapes the maize genome Proc. Natl. Acad. Sci. USA 2009 106 (47) 19747-19748 Full Text Full Text (PDF)
• Distribution, diversity, evolution, and survival of Helitrons in the maize genome Proc. Natl. Acad. Sci. USA 2009 106 (47) 19922-19927 Abstract Full Text Full Text (PDF)
• Structure-based discovery and description of plant and animal Helitrons Proc. Natl. Acad. Sci. USA 2009 106 (31) 12832-12837 Abstract Full Text Full Text (PDF)
• Inaugural Article: Haplotype structure strongly affects recombination in a maize genetic interval polymorphic for Helitron and retrotransposon insertions Proc. Natl. Acad. Sci. USA 2009 106 (21) 8410-8416 Abstract Full Text Full Text (PDF)
• Excision of Helitron Transposons in Maize Genetics 2009 Vol182 (1) 399-402 Abstract Full Text Full Text (PDF)
• Too many ends: aberrant transposition Genes Dev. 2009 Vol23 (9) 1032-1036 Abstract Full Text Full Text (PDF)
• The Functional Role of Pack-MULEs in Rice Inferred from Purifying Selection and Expression ProfilePlant Cell 2009 Vol21 (1) 25-38 Abstract Full Text Full Text (PDF)
• Macrotransposition and Other Complex Chromosomal Restructuring in Maize by Closely Linked Transposons in Direct OrientationPlant Cell 2008 Vol20 (8) 2019-2032 Abstract Full Text Full Text (PDF)
• Retrotransposon Polymorphisms Affect Genic Recombination in Maize Plant Cell 2008 Vol20 (2) 247 Full Text Full Text (PDF)
• Maize Genome Structure Variation: Interplay between Retrotransposon Polymorphisms and Genic RecombinationPlant Cell 2008 Vol20 (2) 249-258 Abstract Full Text Full Text (PDF)
• Allele-Specific Expression Patterns Reveal Biases and Embryo-Specific Parent-of-Origin Effects in Hybrid MaizePlant Cell 2007 Vol19 (8) 2391-2402 Abstract Full Text Full Text (PDF)
• Predicting the Size of the Progeny Mapping Population Required to Positionally Clone a Gene Genetics 2007 Vol176 (4) 2035-2054 Abstract Full Text Full Text (PDF)
• Allelic variation and heterosis in maize: How do two halves make more than a whole? Genome Res 2007 17 (3) 264-275 Abstract Full Text Full Text (PDF)