Gene identification in a complex chromosomal continuum by local genomic cross‐referencing

Avramova, Zoya; Tikhonov, Alexander P.; SanMiguel, Phillip; Jin, Young Kwan; Liu, Chang-Nong; Woo, Sung Sick; Wing, Rod A.; Bennetzen, Jeffrey L.

doi:10.1046/j.1365-313x.1996.10061163.x

Cited by 62 publications

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“…This genus-wide vertical comparative sequence data set was compared with a 600,118-bp reference sequence containing the Adh1 locus (OsAdh1RefSeq) from the short arm of chromosome 11 of O. sativa ssp japonica (pseudo molecule build 4; Rice Annotation Project, 2008). The Adh1 region was selected because it has been used as a model locus for comparative genomics across many plant species Clegg, 1991, 1993;Avramova et al, 1996;Sang et al, 1997;Tikhonov et al, 1999;Tarchini et al, 2000;Hass et al, 2003;Ilic et al, 2003;Grover et al, 2007).…”

Section: A Genus-wide Vertical Comparative Sequence Data Setmentioning

confidence: 99%

Dynamic Evolution ofOryzaGenomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set

et al. 2008

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Oryza (23 species; 10 genome types) contains the world's most important food crop — rice. Although the rice genome serves as an essential tool for biological research, little is known about the evolution of the other Oryza genome types. They contain a historical record of genomic changes that led to diversification of this genus around the world as well as an untapped reservoir of agriculturally important traits. To investigate the evolution of the collective Oryza genome, we sequenced and compared nine orthologous genomic regions encompassing the Adh1-Adh2 genes (from six diploid genome types) with the rice reference sequence. Our analysis revealed the architectural complexities and dynamic evolution of this region that have occurred over the past ∼15 million years. Of the 46 intact genes and four pseudogenes in the japonica genome, 38 (76%) fell into eight multigene families. Analysis of the evolutionary history of each family revealed independent and lineage-specific gain and loss of gene family members as frequent causes of synteny disruption. Transposable elements were shown to mediate massive replacement of intergenic space (>95%), gene disruption, and gene/gene fragment movement. Three cases of long-range structural variation (inversions/deletions) spanning several hundred kilobases were identified that contributed significantly to genome diversification.

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Section: A Genus-wide Vertical Comparative Sequence Data Setmentioning

confidence: 99%

Dynamic Evolution ofOryzaGenomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set

et al. 2008

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“…Nonetheless, Calypso and Cyclops-2 Gag have conserved finger motifs characteristic of nucleocapsid proteins, and all three elements have a conserved domain near the Gag N terminus. Gag averages 675 amino acid residues (measured from the first methionine to the active site of protease), which is larger than most classic plant Ty3/gypsy element Gag proteins (e.g., Reina, 482 aa; Avramova et al 1996). If the endogenous retroviruses are in- Figure 8 Transcription termination sites of Arabidopsis thaliana Athila group elements.…”

Section: Shared Features Among Plant Endogenous Retrovirusesmentioning

confidence: 99%

Athila4 of Arabidopsis and Calypso of Soybean Define a Lineage of Endogenous Plant Retroviruses

2001

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The Athila retroelements of Arabidopsis thaliana encode a putative envelope gene, suggesting that they are infectious retroviruses. Because most insertions are highly degenerate, we undertook a comprehensive analysis of the A. thaliana genome sequence to discern their conserved features. One family (Athila4) was identified whose members are largely intact and share >94% nucleotide identity. As a basis for comparison, related elements (the Calypso elements) were characterized from soybean. Consensus Calypso and Athila4 elements are 12–14 kb in length and have long terminal repeats of 1.3–1.8 kb. Gag and Pol are encoded on a single open reading frame (ORF) of 1801 (Calypso) and 1911 (Athila4) amino acids. Following the Gag-Pol ORF are noncoding regions of ∼0.7 and 2 kb, which, respectively, flank the env-like gene. The env-like ORF begins with a putative splice acceptor site and encodes a protein with a predicted central transmembrane domain, similar to retroviral env genes. RNA of Athila elements was detected in an A. thaliana strain with decreased DNA methylation (ddm1). Additionally, a PCR survey identified related reverse transcriptases in diverse angiosperm genomes. Their ubiquitous nature and the potential for horizontal transfer by infection implicates these endogenous retroviruses as important vehicles for plant genome evolution

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“…Third, sorghum is closely related to corn, one of the best plant genetic systems, from which it diverged only 15-20 million years ago (Doebley et al 1990). Genome sequencing, mapping, and related analyses indicate that although noncoding sequences in sorghum and maize have diverged significantly, gene order and gene sequences in these two species are highly conserved making comparative analysis useful (Avramova et al 1996;Tikhonov et al 1999). Finally, several sorghum genetic maps have been constructed (Chittenden et al 1994;Boivin et al 1999;Peng et al 1999), and a high-quality sorghum BAC library was available as a starting point for the construction of a physical map (Woo et al 1994).…”

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A High-throughput AFLP-based Method for Constructing Integrated Genetic and Physical Maps: Progress Toward a Sorghum Genome Map

Klein¹,

Klein²,

Cartinhour³

et al. 2000

Genome Res.

186

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Sorghum is an important target for plant genomic mapping because of its adaptation to harsh environments, diverse germplasm collection, and value for comparing the genomes of grass species such as corn and rice. The construction of an integrated genetic and physical map of the sorghum genome (750 Mbp) is a primary goal of our sorghum genome project. To help accomplish this task, we have developed a new high-throughput PCR-based method for building BAC contigs and locating BAC clones on the sorghum genetic map. This task involved pooling 24,576 sorghum BAC clones (∼4× genome equivalents) in six different matrices to create 184 pools of BAC DNA. DNA fragments from each pool were amplified using amplified fragment length polymorphism (AFLP) technology, resolved on a LI-COR dual-dye DNA sequencing system, and analyzed using Bionumerics software. On average, each set of AFLP primers amplified 28 single-copy DNA markers that were useful for identifying overlapping BAC clones. Data from 32 different AFLP primer combinations identified ∼2400 BACs and ordered ∼700 BAC contigs. Analysis of a sorghum RIL mapping population using the same primer pairs located ∼200 of the BAC contigs on the sorghum genetic map. Restriction endonuclease fingerprinting of the entire collection of sorghum BAC clones was applied to test and extend the contigs constructed using this PCR-based methodology. Analysis of the fingerprint data allowed for the identification of 3366 contigs each containing an average of 5 BACs. BACs in ∼65% of the contigs aligned by AFLP analysis had sufficient overlap to be confirmed by DNA fingerprint analysis. In addition, 30% of the overlapping BACs aligned by AFLP analysis provided information for merging contigs and singletons that could not be joined using fingerprint data alone. Thus, the combination of fingerprinting and AFLP-based contig assembly and mapping provides a reliable, high-throughput method for building an integrated genetic and physical map of the sorghum genome.[The sequence data described in this paper have been submitted to the GenBank data library under accession no. AF218263.]Integrated genetic and physical genome maps are extremely valuable for map-based gene isolation, comparative genome analysis, and as sources of sequenceready clones for genome sequencing projects. Various methods have been developed for assembling physical maps of complex genomes. One of the best characterized approaches uses restriction enzymes to generate large numbers of DNA fragments from genomic subclones (Brenner and Livak 1989;Gregory et al. 1997;Marra et al. 1997). These DNA fingerprints are compared to identify related clones, and to assemble overlapping clones in contigs. The utility of fingerprinting for ordering a complex genome is limited, however, due to variation in DNA migration from gel to gel, the presence of repetitive DNAs, unusual distribution of restriction sites and skewed clone representation. Moreover, fingerprinting, unless combined with other methods, does not link genomic clones directly to gen...

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Gene identification in a complex chromosomal continuum by local genomic cross‐referencing

Cited by 62 publications

References 0 publications

Dynamic Evolution ofOryzaGenomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set

Dynamic Evolution ofOryzaGenomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set

Athila4 of Arabidopsis and Calypso of Soybean Define a Lineage of Endogenous Plant Retroviruses

A High-throughput AFLP-based Method for Constructing Integrated Genetic and Physical Maps: Progress Toward a Sorghum Genome Map

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