Gene Family Evolution Reflects Adaptation to Soil Environmental Stressors in the Genome of the CollembolanOrchesella cincta

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

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Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes

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Collembolan Transcriptomes Highlight Molecular Evolution of Hexapods and Provide Clues on the Adaptation to Terrestrial Life

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By-products resulting from lignocellulose pretreatment and their inhibitory effect on fermentations for (bio)chemicals and fuels

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Trimmomatic: a flexible trimmer for Illumina sequence data

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Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

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Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

The Hox genes Ultrabithorax and abdominal-A specify three different types of abdominalappendage in the springtail Orchesella cincta (Collembola)

(2014) Barbora Konopova et al.   EvoDevo

Kraken: ultrafast metagenomic sequence classification using exact alignments

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Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

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Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

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Pfam: the protein families database

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The genome of Mesobuthus martensii reveals a unique adaptation model of arthropods

(2013) Zhijian Cao et al.   Nature Communications

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

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HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies

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MITOS: Improved de novo metazoan mitochondrial genome annotation

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Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

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Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

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Biochemical Diversification through Foreign Gene Expression in Bdelloid Rotifers

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MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

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Efficient de novo assembly of large genomes using compressed data structures

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The evolutionary origin of orphan genes

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iPath2.0: interactive pathway explorer

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The Ecoresponsive Genome of Daphnia pulex

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The significance of genome-wide transcriptional regulation in the evolution of stress tolerance

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The dynamic genome of Hydra

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Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids

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trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

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Adaptive differences in gene expression associated with heavy metal tolerance in the soil arthropodOrchesella cincta

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Comparative Population Analysis of Metallothionein Promoter Alleles Suggests Stress-induced Microevolution in the Field

(2008) Thierry K. S. Janssens et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism

(2008) Christoph Dieterich et al.   NATURE GENETICS

SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny

(2008) Derek Wilson et al.   NUCLEIC ACIDS RESEARCH