Evidence map›Paper›PMID 25503521›Full record

ArticlePloS one2014

Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC.

Weerachai Jaratlerdsiri, Janine Deakin, Ricardo M Godinez, Xueyan Shan, Daniel G Peterson, Sylvain Marthey, Eric Lyons, Fiona M McCarthy, Sally R Isberg, Damien P Higgins and 5 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed
2.5field-weighted citation impact, top 10% of its field
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

11 citing papers in PubMed, 50 citations in OpenAlex.

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  8. Alternative haplotypes of antigen processing genes in zebrafish diverged early in vertebrate evolution.Proceedings of the National Academy of Sciences of the United States of America · 2016
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors at 7 institutions in 4 countries.

Weerachai JaratlerdsiriFaculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia.
Janine DeakinEvolution Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia; Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory 2601, Australia.
Ricardo M GodinezDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, United States of America; Department of Genetics, Harvard Medical School, 77 Louis Pasteur Ave., Boston, Massachusetts 02115, United States of America.
Xueyan ShanDepartment of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39762, United States of America.
Daniel G PetersonInstitute for Genomics, Biocomputing and Biotechnology (IGBB), Mississippi State University, Mississippi State, Mississippi 39762, United States of America.
Sylvain MartheyAnimal Genetics and Integrative Biology, INRA, UMR 1313 Jouy-en-Josas 78352, France.
Eric LyonsSchool of Plant Science, University of Arizona, Tucson, Arizona 85721, United States of America.
Fiona M McCarthySchool of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona 85721, United States of America.
Sally R IsbergFaculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia; Center for Crocodile Research, P.O. Box 329, Noonamah, Northern Territory 0837, Australia.
Damien P HigginsFaculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia.
Amanda Y ChongFaculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia.
John St JohnDepartment of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California 95064, United States of America.
Travis C GlennDepartment of Environmental Health Science, University of Georgia, Athens, Georgia 30602, United States of America.
David A RayDepartment of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39762, United States of America; Institute for Genomics, Biocomputing and Biotechnology (IGBB), Mississippi State University, Mississippi State, Mississippi 39762, United States of America.
Jaime GongoraFaculty of Veterinary Science, University of Sydney, Sydney, New South Wales 2006, Australia.
The University of Sydney · AUMississippi State University · USUniversity of Arizona · USFracture Analysis Consultants (United States) · USInstitut National de la Recherche Agronomique · MAUniversity of California, Santa Cruz · USUniversity of Georgia · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The major histocompatibility complex (MHC) is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes I, II and III) containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians) are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus) and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2-6 times longer) than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (>80% identity) with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs.

Indexed as

GenomicsAlligators and CrocodilesAnimalsChromosomes, Artificial, BacterialContig MappingGenes, MHC Class IGenes, MHC Class IIRetroelementsRetroviridaeSpecies SpecificityRetroelements

Identifiers

PMID25503521
PMCPMC4263668
OpenAlexW2099900473

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.