Utility of Different Gene Enrichment Approaches Toward Identifying and Sequencing the Maize Gene Space

Springer, Nathan M.; Xu, Xiequn; Barbazuk, W. Brad

doi:10.1104/pp.104.043323

Cited by 46 publications

(48 citation statements)

References 25 publications

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“…About 91.5% of all genes were detected by at least one GSS tag. A previous comparison of CF and MF with a set of 78 full-length cDNAs also showed that 95% of the cDNAs are tagged by at least one sequence read (Springer et al 2004). However, total nucleotide coverage of the full-length cDNAs approached 75%, although this obviously included only exons.…”

Section: Dna Methylation Of the Maize Regionsmentioning

confidence: 99%

Uneven chromosome contraction and expansion in the maize genome

Bruggmann¹,

Bharti²,

Gundlach³

et al. 2006

Genome Res.

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112

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Maize (Zea mays or corn), both a major food source and an important cytogenetic model, evolved from a tetraploid that arose about 4.8 million years ago (Mya). As a result, maize has extensive duplicated regions within its genome. We have sequenced the two copies of one such region, generating 7.8 Mb of sequence spanning 17.4 cM of the short arm of chromosome 1 and 6.6 Mb (25.6 cM) from the long arm of chromosome 9. Rice, which did not undergo a similar whole genome duplication event, has only one orthologous region (4.9 Mb) on the short arm of chromosome 3, and can be used as reference for the maize homoeologous regions. Alignment of the three regions allowed identification of syntenic blocks, and indicated that the maize regions have undergone differential contraction in genic and intergenic regions and expansion by the insertion of retrotransposable elements. Approximately 9% of the predicted genes in each duplicated region are completely missing in the rice genome, and almost 20% have moved to other genomic locations. Predicted genes within these regions tend to be larger in maize than in rice, primarily because of the presence of predicted genes in maize with larger introns. Interestingly, the general gene methylation patterns in the maize homoeologous regions do not appear to have changed with contraction or expansion of their chromosomes. In addition, no differences in methylation of single genes and tandemly repeated gene copies have been detected. These results, therefore, provide new insights into the diploidization of polyploid species.

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Section: Dna Methylation Of the Maize Regionsmentioning

confidence: 99%

Uneven chromosome contraction and expansion in the maize genome

Bruggmann¹,

Bharti²,

Gundlach³

et al. 2006

Genome Res.

Self Cite

112

116

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“…For example, the localization of markers flanking the BAC contigs by FISH will be an effective strategy to estimate the gaps between contigs. The Assembled Zea mays (AZM) sequences are the assembly of methylation filtered and high Cot sequence reads representing 95% of genic sequences in the maize genome, and many of them have been anchored to genetic map and BAC contigs (Springer et al, 2004). Thus, AZM sequences can be used as FISH probes for representing BAC clones or single-copy genes.…”

Section: Applications Of Hr Gene Fishmentioning

confidence: 99%

High-Resolution Single-Copy Gene Fluorescence in Situ Hybridization and Its Use in the Construction of a Cytogenetic Map of Maize Chromosome 9

2006

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High-resolution cytogenetic maps provide important biological information on genome organization and function, as they correlate genetic distance with cytological structures, and are an invaluable complement to physical sequence data. The most direct way to generate a cytogenetic map is to localize genetically mapped genes onto chromosomes by fluorescence in situ hybridization (FISH). Detection of single-copy genes on plant chromosomes has been difficult. In this study, we developed a squash FISH procedure allowing successful detection of single-copy genes on maize (Zea mays) pachytene chromosomes. Using this method, the shortest probe that can be detected is 3.1 kb, and two sequences separated by ;100 kb can be resolved. To show the robust nature of this protocol, we localized nine genetically mapped single-copy genes on chromosome 9 in one FISH experiment. Integration of existing information from genetic maps and the BAC contigbased physical map with the cytological structure of chromosome 9 provides a comprehensive cross-referenced cytogenetic map and shows the dramatic reduction of recombination in the pericentromeric heterochromatic region. To establish a feasible mapping system for maize, we also developed a probe cocktail for unambiguous identification of the 10 maize pachytene chromosomes. These results provide a starting point toward constructing a high-resolution integrated cytogenetic map of maize.

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“…Gene contigs can be ordered by using end sequences of methylation-spanning linker library clones, which consist of blocks of repetitive DNA flanked on either side by genic regions (8), by superimposing the contigs on a lowredundancy sequence of the entire genome or anchoring them to a genetic map. It is estimated that the gene discovery ability of these combined technologies is significantly Ͼ95% (9). Alternative strategies are based on the fact that genes are not evenly distributed over a genome (10)(11)(12)(13).…”

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Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat

Devos

Pontaroli

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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The current view of wheat genome composition is that genes are compartmentalized into gene-rich and gene-poor regions. This model can be tested by analyzing randomly selected bacterial artificial chromosome (BAC) clones for gene content, followed by placement of these BACs onto physical and genetic maps. Map localization could be difficult for BACs that consist entirely of repeated elements. We therefore developed a technique where repeat junctions are used to generate unique markers. Four BAC clones from hexaploid wheat variety Chinese Spring were randomly selected and sequenced at 4-to 6-fold redundancy. About 50% of the BAC sequences corresponded to previously identified repeats, mainly LTR-retrotransposons, whereas most of the remaining DNA consisted of sequences with unknown origin or function. The average gene content was <1%, although each BAC contained one or two identified genes. Repeat boundaries were amplified and used to map each clone to a chromosome arm. Extrapolation from wheat-rice comparative knowledge suggests that three of the four BAC clones originate from ''gene-rich'' regions of the wheat genome. Nevertheless, because these BACs carry only a single gene (two BACs) or two genes (one BAC), the predicted gene density is Ϸ1 gene per 75 kb, which is considerably lower than previously estimated gene densities (one gene per 5-20 kb) for gene-rich regions in wheat. This analysis of randomly selected wheat BAC clones suggests that genes are more evenly distributed in wheat than previously believed and substantiates the need for large-scale random BAC sequencing to determine wheat genome organization.gene density ͉ genome organization ͉ repeat boundaries ͉ repeat markers ͉ Triticum aestivum

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Utility of Different Gene Enrichment Approaches Toward Identifying and Sequencing the Maize Gene Space

Cited by 46 publications

References 25 publications

Uneven chromosome contraction and expansion in the maize genome

Uneven chromosome contraction and expansion in the maize genome

High-Resolution Single-Copy Gene Fluorescence in Situ Hybridization and Its Use in the Construction of a Cytogenetic Map of Maize Chromosome 9

Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat

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