The impact of third generation genomic technologies on plant genome assembly.
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TLDR
Since the introduction of next generation sequencing, plant genome assembly projects do not need to rely on dedicated research facilities or community-wide consortia anymore, even individual research groups can sequence and assemble the genomes they are interested in.About:
This article is published in Current Opinion in Plant Biology.The article was published on 2017-04-01 and is currently open access. It has received 170 citations till now. The article focuses on the topics: Hybrid genome assembly & Sequence assembly.read more
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Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps
Caroline Belser,Benjamin Istace,Erwan Denis,Marion Dubarry,Franc-Christophe Baurens,Cyril Falentin,Mathieu Genete,Wahiba Berrabah,Anne-Marie Chèvre,Régine Delourme,Gwenaëlle Deniot,Philippe Duffé,Stefan Engelen,Arnaud Lemainque,Maria J. Manzanares-Dauleux,Guillaume Martin,Jérôme Morice,Benjamin Noel,Xavier Vekemans,Angélique D'Hont,Mathieu Rousseau-Gueutin,Valérie Barbe,Corinne Cruaud,Patrick Wincker,Jean-Marc Aury +24 more
TL;DR: A strategy based on long reads (MinION or PromethION sequencers) and optical maps (Saphyr system) that can produce chromosome-level assemblies is described and demonstrated applicability by generating high-quality genome sequences for two new dicotyledon morphotypes.
Journal ArticleDOI
RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms.
Zhaodong Hao,Zhaodong Hao,Dekang Lv,Ying Ge,Jisen Shi,Dolf Weijers,Guangchuang Yu,Jinhui Chen +7 more
TL;DR: The visualization of genome-wide data mapping and comparison allow users to quickly establish a clear impression of the chromosomal distribution pattern, thus making RIdeogram a useful tool for any researchers working with omics.
Journal ArticleDOI
SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies.
TL;DR: SyRI is presented, a pairwise whole-genome comparison tool for chromosome-level assemblies that starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearrange regions.
Journal ArticleDOI
De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing.
Maximilian Schmidt,Alexander Vogel,Alisandra K. Denton,Benjamin Istace,Alexandra Wormit,Henri van de Geest,Marie E. Bolger,Saleh Alseekh,Janina Maß,Christian Pfaff,Ulrich Schurr,Roger T. Chetelat,Florian Maumus,Jean-Marc Aury,Sergey Koren,Alisdair R. Fernie,Daniel Zamir,Anthony Bolger,Bjoern Usadel,Bjoern Usadel +19 more
TL;DR: The generation of a comprehensive nanopore sequencing data set with a median read length of 11,979 bp for a self-compatible accession of the wild tomato species Solanum pennellii indicates that such long read sequencing data can be used to affordably sequence and assemble gigabase-sized plant genomes.
Journal ArticleDOI
Plant Phenotyping: Past, Present, and Future
Roland Pieruschka,U. Schurr +1 more
TL;DR: The technological advancement that laid the foundation for the development of phenotyping centers is sketched and the upcoming challenges for further advancement of plant phenotypes specifically with respect to standardization of data acquisition and reusability are evaluated.
References
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Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing
Sasan Amini,Dmitry Pushkarev,Lena Christiansen,Emrah Kostem,Thomas Royce,Casey Turk,Natasha Pignatelli,Andrew Adey,Jacob O. Kitzman,Kandaswamy Vijayan,Mostafa Ronaghi,Jay Shendure,Kevin L. Gunderson,Frank J. Steemers +13 more
TL;DR: An approach for genome-wide haplotyping based on contiguity-preserving transposition (CPT-seq) and combinatorial indexing that could enable haplotype resolution to become routine in human genome sequencing.
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Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements
Rajiv C. McCoy,Ryan W. Taylor,Timothy A. Blauwkamp,Joanna L. Kelley,Michael Kertesz,Dmitry Pushkarev,Dmitri A. Petrov,Anna-Sophie Fiston-Lavier +7 more
TL;DR: A novel Illumina technology called TruSeq synthetic long-reads is applied, which enables placement of individual TE copies in their proper genomic locations as well as accurate reconstruction of TE sequences, and offers a powerful approach to improve de novo assemblies of whole genomes.
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A hybrid approach for the automated finishing of bacterial genomes
Ali Bashir,Aaron Klammer,William P. Robins,Chen-Shan Chin,Dale R. Webster,Ellen E. Paxinos,David Hsu,Meredith Ashby,Susana Wang,Paul Peluso,Robert Sebra,Jon M. Sorenson,James H. Bullard,Jackie Yen,Marie Valdovino,Emilia Mollova,Khai Luong,Steven Lin,Brianna Lamay,Amruta Joshi,Lori A. Rowe,Michael Frace,Cheryl L. Tarr,Maryann Turnsek,Brigid M. Davis,Andrew Kasarskis,John J. Mekalanos,Matthew K. Waldor,Matthew K. Waldor,Eric E. Schadt,Eric E. Schadt +30 more
TL;DR: This work combines sequencing data from second- and third-generation DNA sequencing technologies to assemble the two-chromosome genome of a recent Haitian cholera outbreak strain into two nearly finished contigs at >99.9% accuracy and provides the next generation of rapid microbial identification and full-genome assembly.
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Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing
Chen-Shan Chin,Paul Peluso,Fritz J. Sedlazeck,Maria Nattestad,Gregory T. Concepcion,Alicia Clum,Christopher Dunn,Ronan C. O'Malley,Rosa Figueroa-Balderas,Abraham Morales-Cruz,Grant R. Cramer,Massimo Delledonne,Chongyuan Luo,Joseph R. Ecker,Dario Cantu,David R. Rank,Michael C. Schatz +16 more
TL;DR: The FALCON-based assemblies were substantially more contiguous and complete than alternate short or long-read approaches, and enabled the study of haplotype structures and heterozygosities between the homologous chromosomes, including identifying widespread heterozygous structural variations within the coding sequences.
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Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63.
Jianwei Zhang,Ling-Ling Chen,Feng Xing,David Kudrna,Wen Yao,Dario Copetti,Ting Mu,Weiming Li,Jiaming Song,Weibo Xie,Seunghee Lee,Jayson Talag,Lin Shao,Yue An,Chun Liu Zhang,Yidan Ouyang,Shuai Sun,Wen-Biao Jiao,Fang Lv,Bogu Du,Meizhong Luo,Carlos Ernesto Maldonado,Jose Luis Goicoechea,Lizhong Xiong,Changyin Wu,Yongzhong Xing,Dao-Xiu Zhou,Sibin Yu,Yu Zhao,Gongwei Wang,Yeisoo Yu,Yijie Luo,Zhi Wei Zhou,Beatriz Elena Padilla Hurtado,Ann Danowitz,Rod A. Wing,Qifa Zhang +36 more
TL;DR: High-quality genome sequences for two elite rice varieties, Zhenshan 97 and Minghui 63, representing the two groups of indica rice and the parents of a leading rice hybrid are generated, uncovering extensive structural differences between the two genomes and complementarity in their hybrid transcriptome.