ArticleBMC evolutionary biology2008
Phylogenetic and chromosomal analyses of multiple gene families syntenic with vertebrate Hox clusters.
Article in BMC evolutionary biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 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
23 citing papers in PubMed, 58 citations in OpenAlex.
- A shared ancient enhancer element differentially regulates the bric-a-brac tandem gene duplicates in the developing Drosophila leg.PLoS genetics · 2022Article
- Reconstruction of the Carbohydrate 6-O Sulfotransferase Gene Family Evolution in Vertebrates Reveals Novel Member, CHST16, Lost in Amniotes.Genome biology and evolution · 2020Article
- Phylogenetic analyses of human 1/2/8/20 paralogons suggest segmental duplications during animal evolution.3 Biotech · 2019Article
- Evolution of vertebrate nicotinic acetylcholine receptors.BMC evolutionary biology · 2019Article
- IGF-Binding Proteins: Why Do They Exist and Why Are There So Many?Frontiers in endocrinology · 2018Review
- Somatotropic Axis Regulation Unravels the Differential Effects of Nutritional and Environmental Factors in Growth Performance of Marine Farmed Fishes.Frontiers in endocrinology · 2018Review
- Insulin-Like Growth Factor-Binding Proteins of Teleost Fishes.Frontiers in endocrinology · 2018Review
- Evolution and expression of the phosphodiesterase 6 genes unveils vertebrate novelty to control photosensitivity.BMC evolutionary biology · 2016Article
- Lamprey IGF-Binding Protein-3 Has IGF-Dependent and -Independent Actions.Frontiers in endocrinology · 2016Article
- Nrf2 and Nrf2-related proteins in development and developmental toxicity: Insights from studies in zebrafish (Danio rerio).Free radical biology & medicine · 2015Review
- Clustering of mammalian Hox genes with other H3K27me3 targets within an active nuclear domain.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Identification, characterization and feeding response of peptide YYb (PYYb) gene in grass carp (Ctenopharyngodon idellus).Fish physiology and biochemistry · 2014Article
- A clinical and molecular review of ubiquitous glucose-6-phosphatase deficiency caused by G6PC3 mutations.Orphanet journal of rare diseases · 2013Review
- Nrf2b, novel zebrafish paralog of oxidant-responsive transcription factor NF-E2-related factor 2 (NRF2).The Journal of biological chemistry · 2012Article
- Evolution of the vertebrate paralemmin gene family: ancient origin of gene duplicates suggests distinct functions.PloS one · 2012Article
- Silencing, positive selection and parallel evolution: busy history of primate cytochromes C.PloS one · 2011Article
- Piecemeal or big bangs: correlating the vertebrate evolution with proposed models of gene expansion events.Nature reviews. Genetics · 2010Article
- 2R or not 2R is not the question anymore.Nature reviews. Genetics · 2010Article
- Identification of the zebrafish ventral habenula as a homolog of the mammalian lateral habenula.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2010Article
- Evolution of developmental regulation in the vertebrate FgfD subfamily.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEver since the theory about two rounds of genome duplication (2R) in the vertebrate lineage was proposed, the Hox gene clusters have served as the prime example of quadruplicate paralogy in mammalian genomes. In teleost fishes, the observation of additional Hox clusters absent in other vertebrate lineages suggested a third tetraploidization (3R). Because the Hox clusters occupy a quite limited part of each chromosome, and are special in having position-dependent regulation within the multi-gene cluster, studies of syntenic gene families are needed to determine the extent of the duplicated chromosome segments. We have analyzed in detail 14 gene families that are syntenic with the Hox clusters to see if their phylogenies are compatible with the Hox duplications and the 2R/3R scenario. Our starting point was the gene family for the NPY family of peptides located near the Hox clusters in the pufferfish Takifugu rubripes, the zebrafish Danio rerio, and human.
resultsSeven of the gene families have members on at least three of the human Hox chromosomes and two families are present on all four. Using both neighbor-joining and quartet-puzzling maximum likelihood methods we found that 13 families have a phylogeny that supports duplications coinciding with the Hox cluster duplications. One additional family also has a topology consistent with 2R but due to lack of urochordate or cephalochordate sequences the time window when these duplications could have occurred is wider. All but two gene families also show teleost-specific duplicates.
conclusionBased on this analysis we conclude that the Hox cluster duplications involved a large number of adjacent gene families, supporting expansion of these families in the 2R, as well as in the teleost 3R tetraploidization. The gene duplicates presumably provided raw material in early vertebrate evolution for neofunctionalization and subfunctionalization.
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.