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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Assessing genome assembly quality using the LTR Assembly Index (LAI).
TL;DR: A reference-free genome metric called LTR Assembly Index (LAI) that evaluates assembly continuity using LTR-RTs is proposed that can facilitate iterative assembly improvement with assembler selection and identify low-quality genomic regions.
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Epigenetic variation in Arabidopsis disease resistance
TL;DR: It is shown that an Arabidopsis thaliana R-gene cluster is also subject to epigenetic variation, and a heritable but metastable epigenetic variant bal that overexpresses the R-like gene At4g16890 from a gene cluster on Chromosome 4 is described.
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Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana
TL;DR: A new computational method was developed to predict and identify cis-encoded NATs in Arabidopsis and found 1,340 potential NAT pairs that could not otherwise be identified by using one of the two datasets only.
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Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane.
André Luiz Vettore,André Luiz Vettore,Felipe Rodrigues da Silva,Felipe Rodrigues da Silva,Edson L. Kemper,Edson L. Kemper,Glaucia Mendes Souza,Aline Maria Da Silva,Maria Inês Tiraboschi Ferro,Flávio Henrique-Silva,E. A. Giglioti,Manoel Victor Franco Lemos,Luiz Lehmann Coutinho,Marina P. Nobrega,Helaine Carrer,Suzelei C. França,Maurício Bacci,Maria Helena S. Goldman,Suely Lopes Gomes,Luiz R. Nunes,Luis Eduardo Aranha Camargo,Walter José Siqueira,Marie-Anne Van Sluys,Otavio Henrique Thiemann,Eiko E. Kuramae,Roberto Vicente Santelli,Celso Luis Marino,M. L. P. N. Targon,Jesus Aparecido Ferro,Henrique C.S. Silveira,Danyelle C. Marini,Eliana Gertrudes de Macedo Lemos,Claudia Barros Monteiro-Vitorello,José Humberto M. Tambor,Dirce Maria Carraro,Patrícia G. Roberto,Vanderlei G. Martins,Gustavo H. Goldman,Regina Costa de Oliveira,Daniela Truffi,Carlos Augusto Colombo,Magdalena Rossi,P. G. Araujo,Susana Andrea Sculaccio,Aline F. Angella,Marleide M. A. Lima,Vicente E. De Rosa,Fábio Siviero,Virginia E. Coscrato,Marcos A. Machado,Laurent Grivet,Sônia Marli Zingaretti Di Mauro,Francisco G. Nobrega,Carlos Frederico Martins Menck,Marília D. V. Braga,Guilherme P. Telles,Frank A.A. Cara,Guilherme Pedrosa,João Meidanis,Paulo Arruda +59 more
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Journal ArticleDOI
Mechanisms and rates of genome expansion and contraction in flowering plants
TL;DR: Current data suggest that unequal recombination can slow the growth in genome size caused by retrotransposon amplification, but that illegitimate recombination and other deletion processes may be primarily responsible for the removal of non-essential DNA from small genome plants.
References
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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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