Unresolved orthology and peculiar coding sequence properties of lamprey genes : the KCNA gene family as test case

Qiu, Huan; Hildebrand, Falk; Kuraku, Shigehiro; Meyer, Axel

Unresolved orthology and peculiar coding sequence properties of lamprey genes : the KCNA gene family as test case

Dateien

1471-2164-12-325--.pdfGröße: 3.1 MBDownloads: 221

Datum

2011

Autor:innen

Qiu, Huan

Hildebrand, Falk

Kuraku, Shigehiro

Meyer, Axel

Open Access-Veröffentlichung

Open Access Gold

Sammlungen

Biologie

Publikationstyp

Zeitschriftenartikel

Publikationsstatus

Published

Erschienen in

BMC Genomics. 2011, 12(1), 325. eISSN 1471-2164. Available under: doi: 10.1186/1471-2164-12-325

Zusammenfassung

Background:
In understanding the evolutionary process of vertebrates, cyclostomes (hagfishes and lamprey) occupy crucial positions. Resolving molecular phylogenetic relationships of cyclostome genes with gnathostomes (jawed vertebrates) genes is indispensable in deciphering both the species tree and gene trees. However, molecular phylogenetic analyses, especially those including lamprey genes, have produced highly discordant results between gene families. To efficiently scrutinize this problem using partial genome assemblies of early vertebrates, we focused on the potassium voltage-gated channel, shaker-related (KCNA) family, whose members are mostly single-exon.

Results:
Seven sea lamprey KCNA genes as well as six elephant shark genes were identified, and their orthologies to bony vertebrate subgroups were assessed. In contrast to robustly supported orthology of the elephant shark genes to gnathostome subgroups, clear orthology of any sea lamprey gene could not be established. Notably, sea lamprey KCNA sequences displayed unique codon usage pattern and amino acid composition, probably associated with exceptionally high GC-content in their coding regions. This lamprey-specific property of coding sequences was also observed generally for genes outside this gene family.

Conclusions:
Our results suggest that secondary modifications of sequence properties unique to the lamprey lineage may be one of the factors preventing robust orthology assessments of lamprey genes, which deserves further genome-wide validation. The lamprey lineage-specific alteration of protein-coding sequence properties needs to be taken into consideration in tackling the key questions about early vertebrate evolution.

Fachgebiet (DDC)

570 Biowissenschaften, Biologie

Zitieren

ISO 690

QIU, Huan, Falk HILDEBRAND, Shigehiro KURAKU, Axel MEYER, 2011. Unresolved orthology and peculiar coding sequence properties of lamprey genes : the KCNA gene family as test case. In: BMC Genomics. 2011, 12(1), 325. eISSN 1471-2164. Available under: doi: 10.1186/1471-2164-12-325

BibTex

@article{Qiu2011Unres-18928,
  year={2011},
  doi={10.1186/1471-2164-12-325},
  title={Unresolved orthology and peculiar coding sequence properties of lamprey genes : the KCNA gene family as test case},
  number={1},
  volume={12},
  journal={BMC Genomics},
  author={Qiu, Huan and Hildebrand, Falk and Kuraku, Shigehiro and Meyer, Axel},
  note={Article Number: 325}
}

RDF

<rdf:RDF
    xmlns:dcterms="http://purl.org/dc/terms/"
    xmlns:dc="http://purl.org/dc/elements/1.1/"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:bibo="http://purl.org/ontology/bibo/"
    xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#"
    xmlns:foaf="http://xmlns.com/foaf/0.1/"
    xmlns:void="http://rdfs.org/ns/void#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > 
  <rdf:Description rdf:about="https://kops.uni-konstanz.de/server/rdf/resource/123456789/18928">
    <foaf:homepage rdf:resource="http://localhost:8080/"/>
    <dc:contributor>Meyer, Axel</dc:contributor>
    <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/18928/1/1471-2164-12-325--.pdf"/>
    <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2012-04-05T08:28:27Z</dc:date>
    <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2012-04-05T08:28:27Z</dcterms:available>
    <dc:creator>Hildebrand, Falk</dc:creator>
    <dc:rights>terms-of-use</dc:rights>
    <dcterms:issued>2011</dcterms:issued>
    <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/>
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <dc:creator>Meyer, Axel</dc:creator>
    <dcterms:rights rdf:resource="https://rightsstatements.org/page/InC/1.0/"/>
    <dc:contributor>Kuraku, Shigehiro</dc:contributor>
    <dc:contributor>Hildebrand, Falk</dc:contributor>
    <bibo:uri rdf:resource="http://kops.uni-konstanz.de/handle/123456789/18928"/>
    <dcterms:title>Unresolved orthology and peculiar coding sequence properties of lamprey genes : the KCNA gene family as test case</dcterms:title>
    <dc:creator>Kuraku, Shigehiro</dc:creator>
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <dc:contributor>Qiu, Huan</dc:contributor>
    <dcterms:abstract xml:lang="eng">Background:&lt;br /&gt;In understanding the evolutionary process of vertebrates, cyclostomes (hagfishes and lamprey) occupy crucial positions. Resolving molecular phylogenetic relationships of cyclostome genes with gnathostomes (jawed vertebrates) genes is indispensable in deciphering both the species tree and gene trees. However, molecular phylogenetic analyses, especially those including lamprey genes, have produced highly discordant results between gene families. To efficiently scrutinize this problem using partial genome assemblies of early vertebrates, we focused on the potassium voltage-gated channel, shaker-related (KCNA) family, whose members are mostly single-exon.&lt;br /&gt;&lt;br /&gt;Results:&lt;br /&gt;Seven sea lamprey KCNA genes as well as six elephant shark genes were identified, and their orthologies to bony vertebrate subgroups were assessed. In contrast to robustly supported orthology of the elephant shark genes to gnathostome subgroups, clear orthology of any sea lamprey gene could not be established. Notably, sea lamprey KCNA sequences displayed unique codon usage pattern and amino acid composition, probably associated with exceptionally high GC-content in their coding regions. This lamprey-specific property of coding sequences was also observed generally for genes outside this gene family.&lt;br /&gt;&lt;br /&gt;Conclusions:&lt;br /&gt;Our results suggest that secondary modifications of sequence properties unique to the lamprey lineage may be one of the factors preventing robust orthology assessments of lamprey genes, which deserves further genome-wide validation. The lamprey lineage-specific alteration of protein-coding sequence properties needs to be taken into consideration in tackling the key questions about early vertebrate evolution.</dcterms:abstract>
    <dcterms:bibliographicCitation>First publ. in: BMC Genomics ; 12 (2011). - 325</dcterms:bibliographicCitation>
    <dc:language>eng</dc:language>
    <dc:creator>Qiu, Huan</dc:creator>
    <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/18928/1/1471-2164-12-325--.pdf"/>
  </rdf:Description>
</rdf:RDF>

Universitätsbibliographie

Ja