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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Journal ArticleDOI
When Scientists Turn Against Science:Exceptionally Flawed Analysis of Plant Breeding Technologies
TL;DR: Kesavan and Swaminathan as discussed by the authors have written three articles in 2018 dealing with the issues of food and nutritional security, sustainable agriculture and climate change, and provided in their own words a 'proactive analysis' of the available breeding technologies to meet these challenges.
Posted ContentDOI
Reconstructing The Gigabase Plant Genome Of Solanum pennellii 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,Alisdair R. Fernie,Dani Zamir,Anthony Bolger,Bjoern Usadel +17 more
TL;DR: The generation of a comprehensive nanopore sequencing dataset with a median fragment size of 11,979 bp for the wild tomato species Solanum pennellii and it is shown that such long read sequencing data can be used to affordably sequence and assemble Gbase sized diploid plant genomes.
Book ChapterDOI
Mathematical Modeling Approaches in Plant Metabolomics.
TL;DR: In this chapter, a general introduction to mathematical modeling is presented and discussed in context of plant metabolism, with particular focus on the suitability of mathematical approaches to functionally integrate plant metabolomics data in a metabolic network and combine it with other biochemical or physiological parameters.
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Broadening the horizon of crop research: a decade of advancements in plant molecular genetics to divulge phenotype governing genes
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The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites’ Biosynthesis
TL;DR: In this paper , the authors introduce the medicinal plant genome and the application of multi-omics tools for identifying genes related to the biosynthesis pathway of secondary metabolites, and explore comparative genomics and polyploidy for gene family analysis in medicinal plants.
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TL;DR: The sequence of the maize genome reveals it to be the most complex genome known to date and the correlation of methylation-poor regions with Mu transposon insertions and recombination and how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state is reported.
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Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
Chen-Shan Chin,David Alexander,Patrick Marks,Aaron Klammer,James P Drake,Cheryl Heiner,Alicia Clum,Alex Copeland,John Huddleston,Evan E. Eichler,Stephen Turner,Jonas Korlach +11 more
TL;DR: This work presents a hierarchical genome-assembly process (HGAP) for high-quality de novo microbial genome assemblies using only a single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing.
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The map-based sequence of the rice genome
Takashi Matsumoto,Jianzhong Wu,Hiroyuki Kanamori,Yuichi Katayose,Masaki Fujisawa,Nobukazu Namiki,Hiroshi Mizuno,Kimiko Yamamoto,Baltazar A. Antonio,Tomoya Baba,Katsumi Sakata,Yoshiaki Nagamura,Hiroyoshi Aoki,Koji Arikawa,Kohei Arita,Takahito Bito,Yoshino Chiden,Nahoko Fujitsuka,Rie Fukunaka,Masao Hamada,Chizuko Harada,Akiko Hayashi,Saori Hijishita,Mikiko Honda,Satomi Hosokawa,Yoko Ichikawa,Atsuko Idonuma,Masumi Iijima,Michiko Ikeda,Maiko Ikeno,Kazue Ito,Sachie Ito,Tomoko Ito,Yuichi Ito,Yukiyo Ito,Aki Iwabuchi,Kozue Kamiya,Wataru Karasawa,Kanako Kurita,Satoshi Katagiri,Ari Kikuta,Harumi Kobayashi,Noriko Kobayashi,Kayo Machita,Tomoko Maehara,Masatoshi Masukawa,Tatsumi Mizubayashi,Yoshiyuki Mukai,Hideki Nagasaki,Yuko Nagata,Shinji Naito,Marina Nakashima,Yuko Nakama,Yumi Nakamichi,Mari Nakamura,Ayano Meguro,Manami Negishi,Isamu Ohta,Tomoya Ohta,Masako Okamoto,Nozomi Ono,Shoko Saji,Miyuki Sakaguchi,Kumiko Sakai,Michie Shibata,Takanori Shimokawa,Jianyu Song,Yuka Takazaki,Kimihiro Terasawa,Mika Tsugane,Kumiko Tsuji,Shigenori Ueda,Kazunori Waki,Harumi Yamagata,Mayu Yamamoto,Shinichi Yamamoto,Hiroko Yamane,Shoji Yoshiki,Rie Yoshihara,Kazuko Yukawa,Huisun Zhong,Masahiro Yano,Takuji Sasaki,Qiaoping Yuan,Shu Ouyang,Jia Liu,Kristine Jones,Kristen Gansberger,Kelly Moffat,Jessica Hill,Jayati Bera,Douglas Fadrosh,Shaohua Jin,Shivani Johri,Mary Kim,Larry Overton,Matthew Reardon,Tamara Tsitrin,Hue Vuong,Bruce Weaver,Anne Ciecko,Luke J. Tallon,Jacqueline Jackson,Grace Pai,Susan Van Aken,T. Utterback,Steve Reidmuller,Tamara Feldblyum,Joseph Hsiao,Victoria Zismann,Stacey E. Iobst,Aymeric R. De Vazeille,C. Robin Buell,Kai Ying,Ying Li,Tingting Lu,Y. Huang,Qiang Zhao,Qi Feng,Lei Zhang,Jingjie Zhu,Qijun Weng,Jie Mu,Yiqi Lu,Danlin Fan,Yilei Liu,Jianping Guan,Yujun Zhang,Shuliang Yu,Xiaohui Liu,Yu Zhang,Guofan Hong,Bin Han,Nathalie Choisne,Nadia Demange,Gisela Orjeda,Sylvie Samain,Laurence Cattolico,Eric Pelletier,Arnaud Couloux,Béatrice Segurens,Patrick Wincker,Angélique D'Hont,Claude Scarpelli,Jean Weissenbach,Marcel Salanoubat,Francis Quetier,Yeisoo Yu,Hyeran Kim,Teri Rambo,Jennifer Currie,Kristi Collura,Meizhong Luo,Tae-Jin Yang,Jetty S.S. Ammiraju,Friedrich Engler,Carol Soderlund,Rod A. Wing,Lance E. Palmer,Melissa De La Bastide,Lori Spiegel,Lidia Nascimento,Theresa Zutavern,A. O'Shaughnessy,Sujit Dike,Neilay Dedhia,R. Preston,Vivekanand Balija,W. Richard McCombie,Teh Yuan Chow,Hong-Hwa Chen,Mei-Chu Chung,Ching San Chen,J. F. Shaw,Hong Pang Wu,Kwang-Jen Hsiao,Ya Ting Chao,Mu Kuei Chu,Chia Hsiung Cheng,Ai Ling Hour,Pei Fang Lee,Shu Jen Lin,Yao-Cheng Lin,John Yu Liou,Shu Mei Liu,Yue-Ie C. Hsing,Saurabh Raghuvanshi,Amitabh Mohanty,Arvind K. Bharti,Arvind K. Bharti,Anupama Gaur,Vipin Gupta,Dibyendu Kumar,Vydianathan Ravi,Shubha Vij,Anita Kapur,Parul Khurana,Paramjit Khurana,Jitendra P. Khurana,Akhilesh K. Tyagi,Kishor Gaikwad,Alok Singh,Vivek Dalal,Subodh K. Srivastava,Anupam Dixit,Ajit K. Pal,Irfan Ahmad Ghazi,Mahavir Yadav,A. Pandit,Atul Bhargava,K. Sureshbabu,Kamlesh Batra,Tilak Raj Sharma,Trilochan Mohapatra,Nagendra K. Singh,Joachim Messing,Amy Bronzino Nelson,Galina Fuks,Steve Kavchok,Gladys Keizer,Eric Linton Victor Llaca,Rentao Song,Bahattin Tanyolac,Steve Young,Kim Yul Ho,Jang Ho Hahn,G. Sangsakoo,Apichart Vanavichit,Luiz Anderson Teixeira de Mattos,Paulo Dejalma Zimmer,Gaspar Malone,Odir Antônio Dellagostin,Antonio Costa de Oliveira,Michael W. Bevan,Ian Bancroft,Patrick Minx,Holly Cordum,Richard K. Wilson,Zhukuan Cheng,Weiwei Jin,Jiming Jiang,Sally A. Leong,Hisakazu Iwama,Takashi Gojobori,Takeshi Itoh,Takeshi Itoh,Yoshihito Niimura,Yasuyuki Fujii,Takuya Habara,Hiroaki Sakai,Hiroaki Sakai,Yoshiharu Sato,Gregory Wilson,Kiran Kumar,Susan R. McCouch,Nikoleta Juretic,Douglas R. Hoen,Stephen I. Wright,Richard Bruskiewich,Thomas E. Bureau,Akio Miyao,Hirohiko Hirochika,Tomotaro Nishikawa,Koh Ichi Kadowaki,Masahiro Sugiura,Benjamin Burr +265 more
TL;DR: A map-based, finished quality sequence that covers 95% of the 389 Mb rice genome, including virtually all of the euchromatin and two complete centromeres, and finds evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes.