Literature DB >> 21987187

Exploring giant plant genomes with next-generation sequencing technology.

Laura J Kelly1, Ilia J Leitch.   

Abstract

Genome size in plants is characterised by its extraordinary range. Although it appears that the majority of plants have small genomes, in several lineages genome size has reached giant proportions. The recent advent of next-generation sequencing (NGS) methods has for the first time made detailed analysis of even the largest of plant genomes a possibility. In this review, we highlight investigations that have utilised NGS for the study of plants with large genomes, as well as describing ongoing work that aims to harness the power of these technologies to gain insights into their evolution. In addition, we emphasise some areas of research where the use of NGS has the potential to generate significant advances in our current understanding of how plant genomes evolve. Finally, we discuss some of the future developments in sequencing technology that may further improve our ability to explore the content and evolutionary dynamics of the very largest genomes.

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Year:  2011        PMID: 21987187     DOI: 10.1007/s10577-011-9246-z

Source DB:  PubMed          Journal:  Chromosome Res        ISSN: 0967-3849            Impact factor:   5.239


  65 in total

1.  Nuclear DNA content and genome size of trout and human.

Authors:  J Dolezel; J Bartos; H Voglmayr; J Greilhuber
Journal:  Cytometry A       Date:  2003-02       Impact factor: 4.355

2.  Assembly of large genomes using second-generation sequencing.

Authors:  Michael C Schatz; Arthur L Delcher; Steven L Salzberg
Journal:  Genome Res       Date:  2010-05-27       Impact factor: 9.043

3.  Diverse retrotransposon families and an AT-rich satellite DNA revealed in giant genomes of Fritillaria lilies.

Authors:  Katerina Ambrozová; Terezie Mandáková; Petr Bures; Pavel Neumann; Ilia J Leitch; Andrea Koblízková; Jirí Macas; Martin A Lysak
Journal:  Ann Bot       Date:  2010-12-14       Impact factor: 4.357

4.  Estimation of nuclear DNA content in plants using flow cytometry.

Authors:  Jaroslav Dolezel; Johann Greilhuber; Jan Suda
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

5.  Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

Authors:  Zhixi Tian; Carene Rizzon; Jianchang Du; Liucun Zhu; Jeffrey L Bennetzen; Scott A Jackson; Brandon S Gaut; Jianxin Ma
Journal:  Genome Res       Date:  2009-09-29       Impact factor: 9.043

6.  Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses.

Authors:  Kankshita Swaminathan; Magdy S Alabady; Kranthi Varala; Emanuele De Paoli; Isaac Ho; Dan S Rokhsar; Aru K Arumuganathan; Ray Ming; Pamela J Green; Blake C Meyers; Stephen P Moose; Matthew E Hudson
Journal:  Genome Biol       Date:  2010-02-03       Impact factor: 13.583

7.  Small RNAs, DNA methylation and transposable elements in wheat.

Authors:  Dario Cantu; Leonardo S Vanzetti; Adam Sumner; Martin Dubcovsky; Marta Matvienko; Assaf Distelfeld; Richard W Michelmore; Jorge Dubcovsky
Journal:  BMC Genomics       Date:  2010-06-29       Impact factor: 3.969

8.  Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data.

Authors:  Petr Novák; Pavel Neumann; Jirí Macas
Journal:  BMC Bioinformatics       Date:  2010-07-15       Impact factor: 3.169

9.  Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis.

Authors:  Katrien M Devos; James K M Brown; Jeffrey L Bennetzen
Journal:  Genome Res       Date:  2002-07       Impact factor: 9.043

10.  Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula.

Authors:  Jirí Macas; Pavel Neumann; Alice Navrátilová
Journal:  BMC Genomics       Date:  2007-11-21       Impact factor: 3.969

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  21 in total

1.  Next-generation sequencing reveals the impact of repetitive DNA across phylogenetically closely related genomes of Orobanchaceae.

Authors:  Mathieu Piednoël; Andre J Aberer; Gerald M Schneeweiss; Jiri Macas; Petr Novak; Heidrun Gundlach; Eva M Temsch; Susanne S Renner
Journal:  Mol Biol Evol       Date:  2012-06-21       Impact factor: 16.240

2.  What's in a genome? The C-value enigma and the evolution of eukaryotic genome content.

Authors:  Tyler A Elliott; T Ryan Gregory
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2015-09-26       Impact factor: 6.237

3.  Genome size and chromosome number in velvet worms (Onychophora).

Authors:  Nicholas W Jeffery; Ivo S Oliveira; T Ryan Gregory; David M Rowell; Georg Mayer
Journal:  Genetica       Date:  2013-01-11       Impact factor: 1.082

4.  CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize.

Authors:  Jonathan I Gent; Nathanael A Ellis; Lin Guo; Alex E Harkess; Yingyin Yao; Xiaoyu Zhang; R Kelly Dawe
Journal:  Genome Res       Date:  2012-12-26       Impact factor: 9.043

5.  Transposon fingerprinting using low coverage whole genome shotgun sequencing in cacao (Theobroma cacao L.) and related species.

Authors:  Saemundur Sveinsson; Navdeep Gill; Nolan C Kane; Quentin Cronk
Journal:  BMC Genomics       Date:  2013-07-24       Impact factor: 3.969

6.  The karyotype, genome survey, and assembly of Mud artemisia (Artemisia selengensis).

Authors:  Heping Wan; Qingying Wei; Qiangqiang Ji; Hong Lan; Xigang Dai; Weida Chen; Yuanhuo Dong; Changli Zeng
Journal:  Mol Biol Rep       Date:  2021-07-23       Impact factor: 2.316

7.  Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride.

Authors:  Marta Matvienko; Alexander Kozik; Lutz Froenicke; Dean Lavelle; Belinda Martineau; Bertrand Perroud; Richard Michelmore
Journal:  PLoS One       Date:  2013-02-08       Impact factor: 3.240

8.  Characterization of the basal angiosperm Aristolochia fimbriata: a potential experimental system for genetic studies.

Authors:  Barbara J Bliss; Stefan Wanke; Abdelali Barakat; Saravanaraj Ayyampalayam; Norman Wickett; P Kerr Wall; Yuannian Jiao; Lena Landherr; Paula E Ralph; Yi Hu; Christoph Neinhuis; Jim Leebens-Mack; Kathiravetpilla Arumuganathan; Sandra W Clifton; Siela N Maximova; Hong Ma; Claude W dePamphilis
Journal:  BMC Plant Biol       Date:  2013-01-24       Impact factor: 4.215

9.  LTR-retrotransposons in R. exoculata and other crustaceans: the outstanding success of GalEa-like copia elements.

Authors:  Mathieu Piednoël; Tifenn Donnart; Caroline Esnault; Paula Graça; Dominique Higuet; Eric Bonnivard
Journal:  PLoS One       Date:  2013-03-04       Impact factor: 3.240

10.  Isolation and characterization of reverse transcriptase fragments of LTR retrotransposons from the genome of Chenopodium quinoa (Amaranthaceae).

Authors:  Bozena Kolano; Edyta Bednara; Hanna Weiss-Schneeweiss
Journal:  Plant Cell Rep       Date:  2013-06-11       Impact factor: 4.570

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