Integration of Cot Analysis, DNA Cloning, and High-Throughput Sequencing Facilitates Genome Characterization and Gene Discovery

Peterson, Daniel G.; Schulze, Stefan; Sciara, E.B.; Lee, Scott A.; Bowers, John E.; Nagel, Alexander; Jiang, Ning; Tibbitts, Deanne; Wessler, Susan R.; Paterson, Andrew H.

doi:10.1101/gr.226102

Cited by 177 publications

(158 citation statements)

References 65 publications

(79 reference statements)

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“…However, the Huck element is only a middle-repetitive DNA in S. bicolor (Peterson et al, 2002) and was not seen at all in our sugarcane data set (data not shown). This element is absent from the rice (Oryza sativa) genome, even at an e-value of 1E-01.…”

Section: Resultsmentioning

confidence: 88%

“…This element is absent from the rice (Oryza sativa) genome, even at an e-value of 1E-01. Leviathan is a shared most abundant family among the S. propinquum and Saccharum species, but has a much lower copy number in S. bicolor (Peterson et al, 2002). Leviathan is a middle-repetitive DNA in B73 maize, but none of the element is intact (that is, with two alignable LTRs), so this TE has not been active for a very long time, and thus was missed with the intact element discovery pipeline applied by Baucom et al (2009).…”

Section: Resultsmentioning

confidence: 99%

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

2013

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Sample sequence analysis was employed to investigate the repetitive DNAs that were most responsible for the evolved variation in genome content across seven panicoid grasses with 45-fold variation in genome size and different histories of polyploidy. In all cases, the most abundant repeats were LTR retrotransposons, but the particular families that had become dominant were found to be different in the Pennisetum, Saccharum, Sorghum and Zea lineages. One element family, Huck, has been very active in all of the studied species over the last few million years. This suggests the transmittal of an active or quiescent autonomous set of Huck elements to this lineage at the founding of the panicoids. Similarly, independent recent activity of Ji and Opie elements in Zea and of Leviathan elements in Sorghum and Saccharum species suggests that members of these families with exceptional activation potential were present in the genome(s) of the founders of these lineages. In a detailed analysis of the Zea lineage, the combined action of several families of LTR retrotransposons were observed to have approximately doubled the genome size of Zea luxurians relative to Zea mays and Zea diploperennis in just the last few million years. One of the LTR retrotransposon amplification bursts in Zea may have been initiated by polyploidy, but the great majority of transposable element activations are not. Instead, the results suggest random activation of a few or many LTR retrotransposons families in particular lineages over evolutionary time, with some families especially prone to future activation and hyper-amplification.

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Section: Resultsmentioning

confidence: 88%

Section: Resultsmentioning

confidence: 99%

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

2013

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“…Four LTRretrotransposon families (Ji, Opie, Huck, and Zeon-1) account for 32% of the Ϸ2,500-Mb maize genome (22), and one family (IRRE) accounts for Ϸ10% of the Ϸ10,000-Mb genome of Iris brevicaulis (37). Even the relatively small sorghum genome (Ϸ700 Mb) contains a high copy number retrotransposon family (Retrosor6, Ϸ6,000-7,000 copies) that accounts for Ϸ6% of the genome (38). In contrast, massive amplification of one or more retrotransposon family has not occurred in B. oleracea; the most abundant family contains only Ϸ140 copies (BoCP IXc).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea

Zhang

Wessler

2004

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

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Transposable elements (TEs) are the major component of plant genomes where they contribute significantly to the >1,000-fold genome size variation. To understand the dynamics of TE-mediated genome expansion, we have undertaken a comparative analysis of the TEs in two related organisms: the weed Arabidopsis thaliana (125 megabases) and Brassica oleracea (Ϸ600 megabases), a species with many crop plants. Comparison of the whole genome sequence of A. thaliana with a partial draft of B. oleracea has permitted an estimation of the patterns of TE amplification, diversification, and loss that has occurred in related species since their divergence from a common ancestor. Although we find that nearly all TE lineages are shared, the number of elements in each lineage is almost always greater in B. oleracea. Class 1 (retro) elements are the most abundant TE class in both species with LTR and non-LTR elements comprising the largest fraction of each genome. However, several families of class 2 (DNA) elements have amplified to very high copy number in B. oleracea where they have contributed significantly to genome expansion. Taken together, the results of this analysis indicate that amplification of both class 1 and class 2 TEs is responsible, in part, for B. oleracea genome expansion since divergence from a common ancestor with A. thaliana. In addition, the observation that B. oleracea and A. thaliana share virtually all TE lineages makes it unlikely that wholesale removal of TEs is responsible for the compact genome of A. thaliana.

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“…In regions of the maize genome with lower gene density, comparative gene-island sequencing would be even more efficient. Highthroughput sequencing strategies are currently under development that selectively target gene-rich, low-copy, hypomethylated regions of the genome (Rabinowicz et al, 1999;Peterson et al, 2002). Because the gene-island sequencing method can be tar-geted to genomic regions of special interest or low representation, it should be a useful complementary approach to genome-wide sequencing projects.…”

Section: Comparative Sequence Analysis By Gene-island Sequencingmentioning

confidence: 99%

Targeted Analysis of Orthologous Phytochrome A Regions of the Sorghum, Maize, and Rice Genomes using Comparative Gene-Island Sequencing

et al. 2002

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A "gene-island" sequencing strategy has been developed that expedites the targeted acquisition of orthologous gene sequences from related species for comparative genome analysis. A 152-kb bacterial artificial chromosome (BAC) clone from sorghum (Sorghum bicolor) encoding phytochrome A (PHYA) was fully sequenced, revealing 16 open reading frames with a gene density similar to many regions of the rice (Oryza sativa) genome. The sequences of genes in the orthologous region of the maize (Zea mays) and rice genomes were obtained using the gene-island sequencing method. BAC clones containing the orthologous maize and rice PHYA genes were identified, sheared, subcloned, and probed with the sorghum PHYAcontaining BAC DNA. Sequence analysis revealed that approximately 75% of the cross-hybridizing subclones contained sequences orthologous to those within the sorghum PHYA BAC and less than 25% contained repetitive and/or BAC vector DNA sequences. The complete sequence of four genes, including up to 1 kb of their promoter regions, was identified in the maize PHYA BAC. Nine orthologous gene sequences were identified in the rice PHYA BAC. Sequence comparison of the orthologous sorghum and maize genes aided in the identification of exons and conserved regulatory sequences flanking each open reading frame. Within genomic regions where micro-colinearity of genes is absolutely conserved, gene-island sequencing is a particularly useful tool for comparative analysis of genomes between related species.Many species within the grass family Poaceae provide staple grain and forage supplies for humans and animals and thus are of great economic and humanitarian importance. Members of the grass family are found in wide ranging areas of the world, demonstrating adaptability to diverse environmental conditions. Although genome sizes can vary greatly in the grasses (e.g. 420 Mb and 16,000 Mb for rice [Oryza sativa] and hexaploid wheat [Triticum aestivum], respectively [Arumuganathan and Earle, 1991]), recombinational mapping studies using common DNA markers indicate that gene order is generally conserved within long physical intervals between family members (Hulbert et al., 1990; Ahn and Tanksley, 1993;Van Deynze et al., 1998;Goff et al., 2002). This information has been used to construct comparative genetic maps among many grass species (for review, see Gale, 1997, 2000;Gale and Devos, 1998). The large variation in genome size observed in the grass family is attributable in part to differences in ploidy and to variation in the abundance of repetitive elements, primarily retrotransposons, located between low copy number genic regions in the genome (SanMiguel et al., 1996). In maize (Zea mays), retrotransposons are estimated to make up 50% to 80% of the genome (SanMiguel and Bennetzen, 1998). The repetitive sequences have little apparent sequence conservation among species (Hulbert et al., 1990; Bennetzen et al., 1994;Chen et al., 1998).Because of their widespread economic importance and genetic resources, rice and maize have been focal poin...

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Integration of Cot Analysis, DNA Cloning, and High-Throughput Sequencing Facilitates Genome Characterization and Gene Discovery

Cited by 177 publications

References 65 publications

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

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

Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea

Targeted Analysis of Orthologous Phytochrome A Regions of the Sorghum, Maize, and Rice Genomes using Comparative Gene-Island Sequencing

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