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The Banana (Musa acuminata) genome and the evolution of monocotyledonous plants : W401
Angélique D'Hont,Patrick Wincker +1 more
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TLDR
D'Hont et al. as discussed by the authors reported the first monocotyledon high-continuity whole-genome sequence reported outside Poales, which represents an essential bridge for comparative genome analysis in plants.Abstract:
Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the Zingiberales order, a sister group to the well-studied Poales. We sequenced and assembled the 520 Mb genome of a doubled-haploid of the accession 'Pahang'. This accession belongs to the Musa acuminata species (AA genome) malaccensis subspecies. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it sheds new light on the monocotyledon lineage, reveals Poaceae specific features and has led to the discovery of conserved noncoding sequences predating monocotyledon-eudicotyledon divergence. The complete list of authors involved in this work can be found in D'Hont et al. Nature. 2012 Aug 9; 488(7410):213-7 (Resume d'auteur)read more
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UpSetR: an R package for the visualization of intersecting sets and their properties
TL;DR: UpSetR is an open source R package that employs a scalable matrix‐based visualization to show intersections of sets, their size, and other properties, and is released under the MIT License.
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InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams
Henry Heberle,Gabriela Vaz Meirelles,Felipe Rodrigues da Silva,Guilherme P. Telles,Rosane Minghim +4 more
TL;DR: InteractiVenn is a more flexible tool for interacting with Venn diagrams including up to six sets that offers a clean interface for Venn diagram construction and enables analysis of set unions while preserving the shape of the diagram.
Journal ArticleDOI
UpSet: Visualization of Intersecting Sets.
TL;DR: This paper introduces UpSet, a novel visualization technique for the quantitative analysis of sets, their intersections, and aggregates of intersections, focused on creating task-driven aggregates, communicating the size and properties of aggregates and intersection, and a duality between the visualization of the elements in a dataset and their set membership.
Journal ArticleDOI
Evolution of Gene Duplication in Plants.
TL;DR: This review surveys the current knowledge about gene duplication, including gene duplication mechanisms, the potential fates of duplicate genes, models explaining duplicate gene retention, the properties that distinguish duplicate from singleton genes, and the evolutionary impact of gene duplication.
Journal ArticleDOI
Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species
Seungill Kim,Minkyu Park,Seon-In Yeom,Yong-Min Kim,Je Min Lee,Hyun-Ah Lee,Eunyoung Seo,Jaeyoung Choi,Kyeongchae Cheong,Ki-Tae Kim,Kyongyong Jung,Gir-Won Lee,Sang-Keun Oh,Chungyun Bae,Saet-Byul Kim,Hyeyoung Lee,Shin Young Kim,Myung-Shin Kim,Byoung-Cheorl Kang,Yeong Deuk Jo,Hee Bum Yang,Hee-Jin Jeong,Won-Hee Kang,Jin Kyung Kwon,Chanseok Shin,Jae Yun Lim,June Hyun Park,Jin Hoe Huh,June Sik Kim,Byung-Dong Kim,Oded Cohen,Ilan Paran,Mi Chung Suh,Saet Buyl Lee,Yeon Ki Kim,Younhee Shin,Seung-Jae Noh,Junhyung Park,Young Sam Seo,Suk-Yoon Kwon,Hyun A Kim,Jeong Mee Park,Hyunjin Kim,Sang Bong Choi,Paul W. Bosland,Gregory Reeves,Sung Hwan Jo,Bong Woo Lee,Hyung-Taeg Cho,Hee-Seung Choi,Min-Soo Lee,Yeisoo Yu,Yang Do Choi,Beom Seok Park,Allen Van Deynze,Hamid Ashrafi,Theresa Hill,Woo Taek Kim,Hyun Sook Pai,Hee-Kyung Ahn,Inhwa Yeam,James J. Giovannoni,James J. Giovannoni,Jocelyn K. C. Rose,Iben Sørensen,Sang Jik Lee,Ryan W. Kim,Ik-Young Choi,Beom-Soon Choi,Jong-Sung Lim,Yong-Hwan Lee,Doil Choi +71 more
TL;DR: The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements.
References
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