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Patterns of putative gene loss suggest rampant developmental system drift in nematodes

https://doi.org/10.1101/627620
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Outgoing claims: the papers this work cites, builds on, or argues with.

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BEDTools: The Swiss‐Army Tool for Genome Feature Analysis
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A Morphogenetic Approach to the Origin and Basic Organization of the Tetrapod Limb
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Comparative Genomics of Gene Loss and Gain in Caenorhabditis and Other Nematodes
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Developmental System Drift
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RNAi analysis of genes expressed in the ovary of Caenorhabditis elegans
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Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi
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Functional genomic analysis of C. elegans chromosome I by systematic RNA interference
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Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III
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Systematic functional analysis of the Caenorhabditis elegans genome using RNAi
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Genetic changes associated with floral adaptation restrict future evolutionary potential
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A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila
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TFE3 transcriptionally activates hepatic IRS-2, participates in insulin signaling and ameliorates diabetes
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Evolution by gene loss
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Biology and genome of a newly discovered sibling species of Caenorhabditis elegans
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Developmental system drift and flexibility in evolutionary trajectories
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Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss
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Bacterial genome size reduction by experimental evolution
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Profile hidden Markov models.
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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
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Divergence Times in Caenorhabditis and Drosophila Inferred from Direct Estimates of the Neutral Mutation Rate
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WormBase 2016: expanding to enable helminth genomic research
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The Pfam protein families database: towards a more sustainable future
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Genomic basis of recombination suppression in the hybrid between Caenorhabditis briggsae and C. nigoni
inferredcites →https://doi.org/10.1101/181107openalex-snapshot
Dramatic evolution of body length due to post-embryonic changes in cell size in a newly discovered close relative of C. elegans
inferredcites →https://doi.org/10.1101/398446openalex-snapshot
Comparative genomics of ten new Caenorhabditis species
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Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes
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Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
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The time-resolved transcriptome of C. elegans
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Single Gene–Mediated Shift in Pollinator Attraction in Petunia
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Independent origins of self‐compatibility in Arabidopsis thaliana
inferredcites →https://doi.org/10.1126/science.1090432openalex-snapshot
Ecological Adaptation During Incipient Speciation Revealed by Precise Gene Replacement
inferredcites →https://doi.org/10.1126/science.1165917openalex-snapshot
Divergent Evolution of Duplicate Genes Leads to Genetic Incompatibilities Within A. thaliana
inferredcites →https://doi.org/10.1126/science.1189015openalex-snapshot
Genotype to Phenotype: A Complex Problem
inferredcites →https://doi.org/10.1126/science.1196914openalex-snapshot
Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project
inferredcites →https://doi.org/10.1126/science.1215040openalex-snapshot
A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes
inferredcites →https://doi.org/10.1126/science.1248384openalex-snapshot
Leaf Shape Evolution Through Duplication, Regulatory Diversification, and Loss of a Homeobox Gene
inferredcites →https://doi.org/10.1126/science.285.5429.901openalex-snapshot
Functional Characterization of the S. cerevisiae Genome by Gene Deletion and Parallel Analysis
inferredcites →https://doi.org/10.1126/science.aan0621openalex-snapshot
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inferredcites →https://doi.org/10.1126/science.aao0827openalex-snapshot
Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins
inferredcites →https://doi.org/10.1146/annurev-med-100708-204735openalex-snapshot
Structural Variation in the Human Genome and its Role in Disease
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2105-12-32openalex-snapshot
Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community
inferredcites →https://doi.org/10.1186/1471-2148-11-339openalex-snapshot
A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits
inferredcites →https://doi.org/10.1186/s12864-017-3860-xopenalex-snapshot
Genome analysis of Diploscapter coronatus: insights into molecular peculiarities of a nematode with parthenogenetic reproduction
inferredcites →https://doi.org/10.1186/s12898-017-0150-zopenalex-snapshot
Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes
inferredcites →https://doi.org/10.1186/s12898-018-0182-zopenalex-snapshot
Field studies reveal a close relative of C. elegans thrives in the fresh figs of Ficus septica and disperses on its Ceratosolen pollinating wasps
inferredcites →https://doi.org/10.1186/s13059-015-0721-2openalex-snapshot
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
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Caenorhabditis monodelphis sp. n.: defining the stem morphology and genomics of the genus Caenorhabditis
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The Conditional Nature of Genetic Interactions: The Consequences of Wild-Type Backgrounds on Mutational Interactions in a Genome-Wide Modifier Screen
inferredcites →https://doi.org/10.1371/journal.pgen.1004077openalex-snapshot
Comparative RNAi Screens in C. elegans and C. briggsae Reveal the Impact of Developmental System Drift on Gene Function
inferredcites →https://doi.org/10.1371/journal.pgen.1005323openalex-snapshot
Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes
inferredcites →https://doi.org/10.1371/journal.pone.0029811openalex-snapshot
Evolution of Susceptibility to Ingested Double-Stranded RNAs in Caenorhabditis Nematodes
inferredcites →https://doi.org/10.1371/journal.pone.0094723openalex-snapshot
A Streamlined System for Species Diagnosis in Caenorhabditis (Nematoda: Rhabditidae) with Name Designations for 15 Distinct Biological Species
inferredcites →https://doi.org/10.1534/g3.117.300281openalex-snapshot
Rapid Gene Family Evolution of a Nematode Sperm Protein Despite Sequence Hyper-conservation
inferredcites →https://doi.org/10.1534/genetics.115.176099openalex-snapshot
A Transparent Window into Biology: A Primer on Caenorhabditis elegans
inferredcites →https://doi.org/10.1534/genetics.116.196493openalex-snapshot
Molecular Population Genetics
inferredcites →https://doi.org/10.1534/genetics.118.300243openalex-snapshot
From “the Worm” to “the Worms” and Back Again: The Evolutionary Developmental Biology of Nematodes
inferredcites →https://doi.org/10.2174/138920212803251391openalex-snapshot
Genome-Wide RNAi Longevity Screens in Caenorhabditis elegans
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Modern Applied Statistics with S-Plus.
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Wild worm embryogenesis harbors ubiquitous polygenic modifier variation

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inferred← citeshttps://doi.org/10.1111/1755-0998.13752openalex-snapshot
The Aphelenchoides genomes reveal substantial horizontal gene transfers in the last common ancestor of free‐living and major plant‐parasitic nematodes
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