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The TIGR Rice Genome Annotation Resource: improvements and new features
TLDR
Through incorporation of multiple transcript and proteomic expression data sets, the Institute for Genomic Research has been able to annotate 24 799 genes (31 739 gene models), representing ∼50% of the total gene models, as expressed in the rice genome.
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The Tree of Life and a New Classification of Bony Fishes
TLDR
A comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages and the order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first time as a monophyletic group in the global phylogeny.
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Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis
TLDR
Alternative splicing is widespread in both rice and Arabidopsis and these species share many common features, indicating that many isoforms will presumably have negative consequences for protein structure and function, suggesting that their biological role involves post-transcriptional regulation of gene expression.
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Dramatic amplification of a rice transposable element during recent domestication
TLDR
The discovery of rice strains where a miniature inverted-repeat transposable element (mPing) has amplified from ≈50 to ≈1,000 copies in four rice strains represents a potentially valuable source of population diversity in self-fertilizing plants like rice.
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Pike and salmon as sister taxa: detailed intraclade resolution and divergence time estimation of Esociformes + Salmoniformes based on whole mitochondrial genome sequences.
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Are flatfishes (Pleuronectiformes) monophyletic?
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Identification and Characterization of Lineage-Specific Genes within the Poaceae1[W][OA]
Using the rice (Oryza sativa) sp. japonica genome annotation, along with genomic sequence and clustered transcript assemblies from 184 species in the plant kingdom, we have identified a set of 861…
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Horizontal Transfer and Death of a Fungal Secondary Metabolic Gene Cluster
TLDR
It is discovered that the unrelated fungus Botrytis cinerea contains a cluster of five genes that is highly similar in sequence and gene order to the Fusarium bikaverin cluster, suggesting that horizontal transfer of wholesale metabolic gene clusters might also be contributing novel regulation.
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Sex-dependent dominance maintains migration supergene in rainbow trout
TLDR
The results constitute the first example of sex-dependent dominance across a large autosomal supergene, a novel mechanism for sexual conflict resolution capable of protecting polygenic sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutation load of heteromorphic sex chromosomes.
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Engineering Pathogen Resistance in Crop Plants
TLDR
The diseases caused by plant viruses are being thwarted through the initiation of endogenous RNA silencing mechanisms, and many of these strategies show great promise, some limitations, and exciting opportunities to develop many new tools for combating plant pests.
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