ArticlePeerJ2013
Whole genome phylogeny for 21 Drosophila species using predicted 2b-RAD fragments.
Article in PeerJ, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
33 citing papers in PubMed, 114 citations in OpenAlex.
- Genome composition and GC content influence loci distribution in reduced representation genomic studies.BMC genomics · 2024Article
- Genetic variation in disease resistance in Drosophila spp. is mitigated in Drosophila sechellia by specialization to a toxic host.Scientific reports · 2023Article
- Article
- Telomeric retrotransposons show propensity to form G-quadruplexes in various eukaryotic species.Mobile DNA · 2023Article
- 2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics.Ecology and evolution · 2023Article
- Phylogenomic analyses of the genus Drosophila reveals genomic signals of climate adaptation.Molecular ecology resources · 2022Article
- Insights into the Divergence of ChineseBiology · 2022Article
- Genetic Linkage and Physical Mapping for an Oyster Mushroom (Applied and environmental microbiology · 2021Article
- Article
- The UDP-Glycosyltransferase Family inFrontiers in physiology · 2021Article
- Genome Wide Analysis for Growth at Two Growth Stages in A New Fast-Growing Common Carp Strain (Cyprinus carpio L.).Scientific reports · 2020Article
- "What You Need, Baby, I Got It": Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila.Biology · 2020Review
- Review
- Conservation of gene architecture and domains amidst sequence divergence in theJournal of genetics · 2020Article
- Analysis of genome-wide SNPs based on 2b-RAD sequencing of pooled samples reveals signature of selection in different populations ofJournal of biosciences · 2019Article
- Evolutionary history and classification of Micropia retroelements in Drosophilidae species.PloS one · 2019Article
- Identification and characterization of novel conserved RNA structures in Drosophila.BMC genomics · 2018Article
- A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci.BMC genomics · 2018Article
- Evidence for Introgression Among Three Species of theFrontiers in genetics · 2018Article
- Combined QTL and Genome Scan Analyses With the Help of 2b-RAD Identify Growth-Associated Genetic Markers in a New Fast-Growing Carp Strain.Frontiers in genetics · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Type IIB restriction endonucleases are site-specific endonucleases that cut both strands of double-stranded DNA upstream and downstream of their recognition sequences. These restriction enzymes have recognition sequences that are generally interrupted and range from 5 to 7 bases long. They produce DNA fragments which are uniformly small, ranging from 21 to 33 base pairs in length (without cohesive ends). The fragments are generated from throughout the entire length of a genomic DNA providing an excellent fractional representation of the genome. In this study we simulated restriction enzyme digestions on 21 sequenced genomes of various Drosophila species using the predicted targets of 16 Type IIB restriction enzymes to effectively produce a large and arbitrary selection of loci from these genomes. The fragments were then used to compare organisms and to calculate the distance between genomes in pair-wise combination by counting the number of shared fragments between the two genomes. Phylogenetic trees were then generated for each enzyme using this distance measure and the consensus was calculated. The consensus tree obtained agrees well with the currently accepted tree for the Drosophila species. We conclude that multi-locus sub-genomic representation combined with next generation sequencing, especially for individuals and species without previous genome characterization, can accelerate studies of comparative genomics and the building of accurate phylogenetic trees.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.