The contribution of short repeats of low sequence complexity to large conifer genomes

Schmidt, Allison L.; Doudrick, R. L.; Heslop-Harrison, J. S.; Schmidt, Thomas

doi:10.1007/s001220051442

Cited by 58 publications

(60 citation statements)

References 28 publications

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“…A probe derived from the Arabidopsis -type telomere sequence detects not only the terminal-telomeric domain, but also interstitial and centromeric domains in pine species (Fuchs et al, 1995;Hizume et al, 2000Hizume et al, , 2002Schmidt et al, 2000;Shibata et al, 2005). The interstitial and centromeric domains that exhibit the telomeric sequences correspond to DAPI positive bands, and therefore to AT-rich domains (Schmidt et al, 2000;Hizume et al, 2002;Shibata et al, 2005). On the contrary in angiosperm forest trees, telomeric sequences are restricted to the terminal chromosome domains (Tuskan et al, 2006).…”

Section: Distribution and Evolution Of Chromosome Landmarksmentioning

confidence: 99%

“…The entire chromosome complement has been unambiguously identified in Pinus thunbergii, Pinus nigra (Hizume et al, 2002), and in Pinus taeda (Islam-Faridi et al, 2007), using a multicolor FISH approach with a telomere repeat sequence. A probe derived from the Arabidopsis -type telomere sequence detects not only the terminal-telomeric domain, but also interstitial and centromeric domains in pine species (Fuchs et al, 1995;Hizume et al, 2000Hizume et al, , 2002Schmidt et al, 2000;Shibata et al, 2005). The interstitial and centromeric domains that exhibit the telomeric sequences correspond to DAPI positive bands, and therefore to AT-rich domains (Schmidt et al, 2000;Hizume et al, 2002;Shibata et al, 2005).…”

Section: Distribution and Evolution Of Chromosome Landmarksmentioning

confidence: 99%

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Molecular cytogenetics of forest trees

Ribeiro

Barão

Viegas³

et al. 2008

Cytogenet Genome Res

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The economic and ecological importance of forest trees, as well as their unique biological features, has recently raised the level of interest in studies on their genomes, including sequencing of the entire poplar genome. However, cytogenetic studies have not moved in parallel with developments in genomics. This is especially true for hardwood species characterized by small genomes and relatively high numbers of small chromosomes. Molecular cytogenetic studies have mainly been focused on coniferous species, owing to the larger size of their chromosomes, and have been applied exclusively for chromosome identification and comparative karyotyping in an attempt to understand genome evolution and phylogenetic relationships. In this context, rRNA genes physical mapped by FISH reveal particularly useful chromosomal landmarks with variable distribution patterns between species. Here we present a contribution of DNA markers used for chromosome analysis, which already allowed a deeper characterization and understanding of the processes underlying genome diversity of forest trees. The use of advanced cytogenetic techniques and other potential important methods for genome analysis of forest trees is also discussed.

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Section: Distribution and Evolution Of Chromosome Landmarksmentioning

confidence: 99%

Section: Distribution and Evolution Of Chromosome Landmarksmentioning

confidence: 99%

Molecular cytogenetics of forest trees

Ribeiro

Barão

Viegas³

et al. 2008

Cytogenet Genome Res

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“…Full-genome sequencing is a challenge in conifers due to their large genome sizes and the high proportion of repeated sequences (Kamm et al 1996;Kossack and Kinlaw 1999;Schmidt et al 2000;Ahuja and Neale 2005). Genome sizes of conifers range from 6500 Mb to ~37,000 Mb.…”

Section: Application Of Genomics In Forest Treesmentioning

confidence: 99%

Genomics, Domestication, and Evolution of Forest Trees

Sederoff

Myburg²,

Kirst³

2009

Cold Spring Harbor Symposia on Quantitative Biology

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“…Although 75% of the pine genome corresponds to highly repeated sequences, there is 25% of low-to single-copy DNA. Pine sequencing has revealed a high number of repeats including retrotransposons (Friesen et al, 2001 and listed references), simple sequence repeats (Schmidt et al, 2000) and complex gene families resulting from duplication events (Kinlaw and Neale, 1997).…”

Section: Pine Genome Structure Some Notes On Pine Genomementioning

confidence: 99%

Genomics applied to the study of adaptation in pine species

et al. 2005

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This manuscript provides an overview on the use of genomics to study pine adaptation to environmental conditions, such as drought or photoperiod. We briefly discuss molecular tools that permit to acquire a comprehensive view of pine genome, such as cytogenetic and genetic linkage maps. We will also discuss the application of two complementary strategies to dissect complex adaptive traits based on linkage disequilibrium between neutral molecular markers and quantitative trait loci: QTL mapping and association analysis. An important step in these studies is the identification of candidate genes involved in the response of pine trees to environmental variation using functional genomic approaches.Key words: Pinus, genetic maps, QTLs, association mapping, ESTs. Resumen Aplicaciones de la genómica al estudio de la adaptación de los pinosEste artículo constituye una revisión de las aplicaciones de la genómica en el estudio de la adaptación de los pinos a diferentes condiciones medioambientales, tales como la sequía o el fotoperíodo. Discutiremos brevemente las herramientas moleculares desarrolladas para adquirir una visión integrada del genoma de pino como por ejemplo la proporcionada por los mapas citológicos y genéticos. También discutiremos la aplicación de dos estrategias complementarias para diseccionar caracteres cuantitativos complejos, basadas en el desequilibrio de ligamiento entre marcadores moleculares neutrales y los loci que causan variación cuantitativa: mapeo de QTLs y estudios de asociación. Otro aspecto importante en estos estudios es la identificación de genes candidatos involucrados en la respuesta de los pinos a variaciones ambientales empleando estrategias de genómica funcional.

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The contribution of short repeats of low sequence complexity to large conifer genomes

Cited by 58 publications

References 28 publications

Molecular cytogenetics of forest trees

Molecular cytogenetics of forest trees

Genomics, Domestication, and Evolution of Forest Trees

Genomics applied to the study of adaptation in pine species

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