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ORFans in Mitochondrial Genomes of Marine Polychaete Polydora

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1006/jmbi.2000.4315openalex-snapshot

Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen

inferredcites →https://doi.org/10.1007/978-3-319-24277-4openalex-snapshot

ggplot2

inferredcites →https://doi.org/10.1007/pl00006321openalex-snapshot

Mitochondrial DNA of the coral sarcophyton glaucum contains a gene for a homologue of bacterial muts: A possible case of gene transfer from the nucleus to the mitochondrion

inferredcites →https://doi.org/10.1007/s00227-013-2214-8openalex-snapshot

Shell-boring versus tube-dwelling: is the mode of life fixed or flexible? Two cases in spionid polychaetes (Annelida, Spionidae)

inferredcites →https://doi.org/10.1007/s12526-016-0515-0openalex-snapshot

First report of the polychaete Polydora hoplura (Annelida: Spionidae) from North and South America and Asian Pacific

inferredcites →https://doi.org/10.1016/0022-2836(82)90515-0openalex-snapshot

A simple method for displaying the hydropathic character of a protein

inferredcites →https://doi.org/10.1016/0305-1978(93)90053-topenalex-snapshot

Genetic differences between two sibling species of the Polydora ciliata complex (Polychaeta: Spionidae)

inferredcites →https://doi.org/10.1016/j.crmeth.2021.100014openalex-snapshot

Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations

inferredcites →https://doi.org/10.1016/j.cub.2017.10.051openalex-snapshot

A New Lineage of Eukaryotes Illuminates Early Mitochondrial Genome Reduction

inferredcites →https://doi.org/10.1016/j.gene.2007.07.006openalex-snapshot

The mitochondrial genome of Pocillopora (Cnidaria: Scleractinia) contains two variable regions: The putative D-loop and a novel ORF of unknown function

inferredcites →https://doi.org/10.1016/j.gene.2016.08.050openalex-snapshot

Syllidae mitochondrial gene order is unusually variable for Annelida

inferredcites →https://doi.org/10.1016/j.jmb.2004.05.028openalex-snapshot

Improved Prediction of Signal Peptides: SignalP 3.0

inferredcites →https://doi.org/10.1016/j.jmb.2017.12.007openalex-snapshot

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

inferredcites →https://doi.org/10.1016/j.tig.2007.05.011openalex-snapshot

The unusual system of doubly uniparental inheritance of mtDNA: isn’t one enough?

inferredcites →https://doi.org/10.1016/j.ympev.2015.08.008openalex-snapshot

Evolution of mitochondrial gene order in Annelida

inferredcites →https://doi.org/10.1017/s0025315406013099openalex-snapshot

The morphology of two sibling sympatric Polydora species (Polychaeta: Spionidae) from the Sea of Japan

inferredcites →https://doi.org/10.1017/s002531541600093xopenalex-snapshot

And then there was one:Polydora uncinataandPolydora hoplura(Annelida: Spionidae), the problematic polydorid pest species represent a single species

inferredcites →https://doi.org/10.1038/375109b0openalex-snapshot

A coral mitochondrial mutS gene

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nrg2482openalex-snapshot

Turning a hobby into a job: How duplicated genes find new functions

inferredcites →https://doi.org/10.1038/s41586-018-0059-5openalex-snapshot

Deep mitochondrial origin outside the sampled alphaproteobacteria

inferredcites →https://doi.org/10.1038/s41598-017-04094-wopenalex-snapshot

Multiple introns in a deep-sea Annelid (Decemunciger: Ampharetidae) mitochondrial genome

inferredcites →https://doi.org/10.1038/s41598-021-92994-3openalex-snapshot

Mitochondrial genomes of two Polydora (Spionidae) species provide further evidence that mitochondrial architecture in the Sedentaria (Annelida) is not conserved

inferredcites →https://doi.org/10.1038/s41598-022-08103-5openalex-snapshot

Mitogenome of a stink worm (Annelida: Travisiidae) includes degenerate group II intron that is also found in five congeneric species

inferredcites →https://doi.org/10.1038/srep12072openalex-snapshot

The making of a branching annelid: an analysis of complete mitochondrial genome and ribosomal data of Ramisyllis multicaudata

inferredcites →https://doi.org/10.1073/pnas.91.16.7463openalex-snapshot

An unusual type of mitochondrial DNA inheritance in the blue mussel Mytilus.

inferredcites →https://doi.org/10.1080/00222938000770351openalex-snapshot

Variations in some morphological characteristics ofPolydora ciliata(Johnston)

inferredcites →https://doi.org/10.1080/23802359.2022.2047116openalex-snapshot

Complete mitochondrial genome of the abalone shell-boring Polydora hoplura (Polychaeta, Spionidae)

inferredcites →https://doi.org/10.1093/bioinformatics/btp033openalex-snapshot

Jalview Version 2—a multiple sequence alignment editor and analysis workbench

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/btt701openalex-snapshot

RNASurface: fast and accurate detection of locally optimal potentially structured RNA segments

inferredcites →https://doi.org/10.1093/bioinformatics/btu031openalex-snapshot

InterProScan 5: genome-scale protein function classification

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/bioinformatics/btu393openalex-snapshot

circlize implements and enhances circular visualization in R

inferredcites →https://doi.org/10.1093/gbe/evt101openalex-snapshot

A Comparative Analysis of Mitochondrial ORFans: New Clues on Their Origin and Role in Species with Doubly Uniparental Inheritance of Mitochondria

inferredcites →https://doi.org/10.1093/gbe/evv224openalex-snapshot

The Utility of Genome Skimming for Phylogenomic Analyses as Demonstrated for Glycerid Relationships (Annelida, Glyceridae)

inferredcites →https://doi.org/10.1093/gbe/evw195openalex-snapshot

Animal Mitochondrial DNA as We Do Not Know It: mt-Genome Organization and Evolution in Nonbilaterian Lineages

inferredcites →https://doi.org/10.1093/gigascience/giab008openalex-snapshot

Twelve years of SAMtools and BCFtools

inferredcites →https://doi.org/10.1093/molbev/msab120openalex-snapshot

MEGA11: Molecular Evolutionary Genetics Analysis Version 11

inferredcites →https://doi.org/10.1093/molbev/msi108openalex-snapshot

Mitochondrial Genomes of Two Demosponges Provide Insights into An Early Stage of Animal Evolution

inferredcites →https://doi.org/10.1093/molbev/msj025openalex-snapshot

A Hotspot of Gene Order Rearrangement by Tandem Duplication and Random Loss in the Vertebrate Mitochondrial Genome

inferredcites →https://doi.org/10.1093/molbev/msm070openalex-snapshot

Glass Sponges and Bilaterian Animals Share Derived Mitochondrial Genomic Features: A Common Ancestry or Parallel Evolution?

inferredcites →https://doi.org/10.1093/molbev/msp318openalex-snapshot

Evolution of Caenorhabditis Mitochondrial Genome Pseudogenes and Caenorhabditis briggsae Natural Isolates

inferredcites →https://doi.org/10.1093/molbev/mst197openalex-snapshot

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

inferredcites →https://doi.org/10.1093/nar/gkp368openalex-snapshot

@TOME-2: a new pipeline for comparative modeling of protein-ligand complexes

inferredcites →https://doi.org/10.1093/nar/gky448openalex-snapshot

HMMER web server: 2018 update

inferredcites →https://doi.org/10.1093/nar/gkz173openalex-snapshot

MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004068openalex-snapshot

Complete mtDNA Sequences of Two Millipedes Suggest a New Model for Mitochondrial Gene Rearrangements: Duplication and Nonrandom Loss

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040410openalex-snapshot

Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.

inferredcites →https://doi.org/10.1098/rsbl.2022.0122openalex-snapshot

The longest mitochondrial protein in metazoans is encoded by the male-transmitted mitogenome of the bivalve Scrobicularia plana

inferredcites →https://doi.org/10.1098/rstb.2020.0159openalex-snapshot

Molluscan mitochondrial genomes break the rules

inferredcites →https://doi.org/10.1101/gr.241299.118openalex-snapshot

Plasmid detection and assembly in genomic and metagenomic data sets

inferredcites →https://doi.org/10.1111/j.1096-3642.1986.tb01808.xopenalex-snapshot

Morphological variation in Polydora ciliata complex (Polychaeta: Annelida)

inferredcites →https://doi.org/10.1186/1471-2105-5-113openalex-snapshot

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

inferredcites →https://doi.org/10.1186/s12862-018-1186-1openalex-snapshot

Extensive mitochondrial gene rearrangements in Ctenophora: insights from benthic Platyctenida

inferredcites →https://doi.org/10.1186/s12862-019-1554-5openalex-snapshot

Variability of mitochondrial ORFans hints at possible differences in the system of doubly uniparental inheritance of mitochondria among families of freshwater mussels (Bivalvia: Unionida)

inferredcites →https://doi.org/10.1186/s12864-016-2986-6openalex-snapshot

In silico analyses of mitochondrial ORFans in freshwater mussels (Bivalvia: Unionoida) provide a framework for future studies of their origin and function

inferredcites →https://doi.org/10.1371/journal.pone.0001488openalex-snapshot

Group II Introns Break New Boundaries: Presence in a Bilaterian's Genome

inferredcites →https://doi.org/10.1371/journal.pone.0022594openalex-snapshot

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

inferredcites →https://doi.org/10.1385/1-59259-890-0:571openalex-snapshot

Protein Identification and Analysis Tools on the ExPASy Server

inferredcites →https://doi.org/10.1534/genetics.109.110700openalex-snapshot

Comparative Mitochondrial Genomics of Freshwater Mussels (Bivalvia: Unionoida) With Doubly Uniparental Inheritance of mtDNA: Gender-Specific Open Reading Frames and Putative Origins of Replication

inferredcites →https://doi.org/10.21105/joss.00905openalex-snapshot

Python Implementation of Codon Adaptation Index

inferredcites →https://doi.org/10.21105/joss.01686openalex-snapshot

Welcome to the Tidyverse

inferredcites →https://doi.org/10.32614/cran.package.dplyropenalex-snapshot

dplyr: A Grammar of Data Manipulation

inferredcites →https://doi.org/10.7717/peerj.8356openalex-snapshot

Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.11646/zootaxa.5529.2.2zenodo-depositor-declared

A twin of Polydora hoplura (Annelida: Spionidae) from the Arabian (Persian) Gulf, with review of primers used for barcoding of Spionidae

inferred← citeshttps://doi.org/10.1007/s11033-024-09270-6openalex-snapshot

Comparative mitogenomics of Brachiopods reveals conservatism in articulate species and unusualness in inarticulate species

inferred← citeshttps://doi.org/10.1093/9780197790847.003.0017openalex-snapshot

From Sediment to Shells

inferred← citeshttps://doi.org/10.1134/s0006297925603296openalex-snapshot

Mechanisms of Intracellular Selection of Mitochondrial DNA

inferred← citeshttps://doi.org/10.21203/rs.3.rs-7724154/v1openalex-snapshot

The partial mitochondrial genome of the enigmatic Bermuda fireworm Odontosyllis enopla Verrill, 1900 and its phylogenetic implications

inferred← citeshttps://doi.org/10.3390/life16091391openalex-snapshot

Organellar Genome Analysis of the Red Alga Rhodymenia intricata (Rhodophyta, Florideophyceae) and Its Phylogenetic Analysis

inferred← citeshttps://doi.org/10.3724/1000-3207.2025.2025.0243openalex-snapshot

COMPARATIVE ANALYSIS OF THE F AND M-TYPE MITOCHONDRIAL GENOME ARCHITECTURE AND EVOLUTION IN LEPIDODESMA LANGUILATI (BIVALVIA: UNIONIDAE) UNDER DOUBLY UNIPARENTAL INHERITANCE

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