Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
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TLDR
This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.Abstract:
The flowering plant Arabidopsis thaliana is an important model system for identifying genes and determining their functions. Here we report the analysis of the genomic sequence of Arabidopsis. The sequenced regions cover 115.4 megabases of the 125-megabase genome and extend into centromeric regions. The evolution of Arabidopsis involved a whole-genome duplication, followed by subsequent gene loss and extensive local gene duplications, giving rise to a dynamic genome enriched by lateral gene transfer from a cyanobacterial-like ancestor of the plastid. The genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of Drosophila and Caenorhabditis elegans--the other sequenced multicellular eukaryotes. Arabidopsis has many families of new proteins but also lacks several common protein families, indicating that the sets of common proteins have undergone differential expansion and contraction in the three multicellular eukaryotes. This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.read more
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The Arabidopsis thaliana mobilome and its impact at the species level
Leandro Quadrana,Amanda Bortolini Silveira,George F. Mayhew,Chantal LeBlanc,Robert A. Martienssen,Robert A. Martienssen,Jeffrey A. Jeddeloh,Vincent Colot +7 more
TL;DR: It is shown that loci controlling adaptive responses to the environment are the most frequent transposition targets observed and the importance of transposition as a recurrent generator of large-effect alleles is demonstrated.
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Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana
Takeshi Itoh,Takeshi Itoh,Tsuyoshi Tanaka,Roberto A. Barrero,Chisato Yamasaki,Yasuyuki Fujii,Phillip Hilton,Baltazar A. Antonio,Hideo Aono,Rolf Apweiler,Richard Bruskiewich,Thomas E. Bureau,Frances A. Burr,Antonio Costa de Oliveira,Galina Fuks,Takuya Habara,Georg Haberer,Bin Han,Erimi Harada,Aiko T. Hiraki,Hirohiko Hirochika,Douglas R. Hoen,Hiroki Hokari,Satomi Hosokawa,Yue-Ie C. Hsing,Hiroshi Ikawa,Kazuho Ikeo,Tadashi Imanishi,Tadashi Imanishi,Yukiyo Ito,Pankaj Jaiswal,Masako Kanno,Yoshihiro Kawahara,Yoshihiro Kawahara,Toshiyuki Kawamura,Hiroaki Kawashima,Jitendra P. Khurana,Shoshi Kikuchi,Setsuko Komatsu,Kanako O. Koyanagi,Hiromi Kubooka,Damien Lieberherr,Yao-Cheng Lin,David M. Lonsdale,Takashi Matsumoto,Akihiro Matsuya,W. Richard McCombie,Joachim Messing,Akio Miyao,Nicola Mulder,Yoshiaki Nagamura,Jongmin Nam,Jongmin Nam,Nobukazu Namiki,Hisataka Numa,Shin Nurimoto,Claire O'Donovan,Hajime Ohyanagi,Toshihisa Okido,Satoshi Oota,Naoki Osato,Lance E. Palmer,Lance E. Palmer,Francis Quetier,Saurabh Raghuvanshi,Naomi Saichi,Hiroaki Sakai,Hiroaki Sakai,Yasumichi Sakai,Katsumi Sakata,Tetsuya Sakurai,Fumihiko Sato,Yoshiharu Sato,Heiko Schoof,Heiko Schoof,Motoaki Seki,Michie Shibata,Yuji Shimizu,Kazuo Shinozaki,Yuji Shinso,Nagendra K. Singh,Brian Smith-White,Jun-ichi Takeda,Motohiko Tanino,Tatiana Tatusova,Supat Thongjuea,Fusano Todokoro,Mika Tsugane,Akhilesh K. Tyagi,Apichart Vanavichit,Aihui Wang,Rod A. Wing,Kaori Yamaguchi,Mayu Yamamoto,Naoyuki Yamamoto,Yeisoo Yu,Hao Zhang,Qiang Zhao,Kenichi Higo,Benjamin Burr,Takashi Gojobori,Takuji Sasaki +101 more
TL;DR: The results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene.
Journal ArticleDOI
BASL Controls Asymmetric Cell Division in Arabidopsis
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Journal ArticleDOI
FLAGdb/FST: a database of mapped flanking insertion sites (FSTs) of Arabidopsis thaliana T-DNA transformants.
Franck Samson,Véronique Brunaud,Sandrine Balzergue,Bertrand Dubreucq,Loïc Lepiniec,Georges Pelletier,Michel Caboche,Alain Lecharny +7 more
TL;DR: A large collection of T-DNA insertion transformants of Arabidopsis thaliana has been generated at the Institute of Agronomic Research, Versailles, France and the main scope of FLAGdb/FST is to help biologists to find the FSTs that interrupt the genes in which they are interested.
Journal ArticleDOI
A triptych of the evolution of plant transposable elements.
TL;DR: The three major forces that govern the accumulation of TEs are discussed, corresponding to the three panels of a triptych - transposition, deletion of TE DNA, and the population processes that determine the ultimate evolutionary fate of TE insertions.
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TL;DR: The nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome is determined using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map.
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