File Download

There are no files associated with this item.

  Links for fulltext
     (May Require Subscription)
Supplementary

Article: Low nucleotide diversity at the pal1 locus in the widely distributed Pinus sylvestris

TitleLow nucleotide diversity at the pal1 locus in the widely distributed Pinus sylvestris
Authors
Issue Date2002
PublisherOxford University Press. The Journal's web site is located at http://mbe.oxfordjournals.org/
Citation
Molecular Biology And Evolution, 2002, v. 19 n. 2, p. 179-188 How to Cite?
AbstractNucleotide polymorphism in Scots pine (Pinus sylvestris) was studied in the gene encoding phenylalanine ammonialyase (Pal, EC 4.3.1.5). Scots pine, like many other pine species, has a large current population size. The observed levels of inbreeding depression suggest that Scots pine may have a high mutation rate to deleterious alleles. Many Scots pine markers such as isozymes, RFLPs, and microsatellites are highly variable. These observations suggest that the levels of nucleotide variation should be higher than those in other plant species. A 2,045-bp fragment of the pal1 locus was sequenced from five megagametophytes each from a different individual from each of four populations, from northern and southern Finland, central Russia, and northern Spain. There were 12 segregating sites in the locus. The synonymous site overall nucleotide diversity was only 0.0049. In order to compare pal1 with other pine genes, sequence was obtained from two alleles of 11 other loci (total length 4,606 bp). For these, the synonymous nucleotide diversity was 0.0056. These estimates are lower than those from other plants. This is most likely because of a low mutation rate, as estimated from between-pine species synonymous site divergence. In other respects, Scots pine has the characteristics of a species with a large effective population. There was no linkage disequilibrium even between closely linked sites. This resulted in high haplotype diversity (14 different haplotypes among 20 sequences). This could also give rise to high per locus diversity at the protein level. Divergence between populations in the main range was low, whereas an isolated Spanish population had slightly lower diversity and higher divergence than the remaining populations.
Persistent Identifierhttp://hdl.handle.net/10722/178763
ISSN
2015 Impact Factor: 13.649
2015 SCImago Journal Rankings: 8.168
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorDvornyk, Ven_US
dc.contributor.authorSirviö, Aen_US
dc.contributor.authorMikkonen, Men_US
dc.contributor.authorSavolainen, Oen_US
dc.date.accessioned2012-12-19T09:49:36Z-
dc.date.available2012-12-19T09:49:36Z-
dc.date.issued2002en_US
dc.identifier.citationMolecular Biology And Evolution, 2002, v. 19 n. 2, p. 179-188en_US
dc.identifier.issn0737-4038en_US
dc.identifier.urihttp://hdl.handle.net/10722/178763-
dc.description.abstractNucleotide polymorphism in Scots pine (Pinus sylvestris) was studied in the gene encoding phenylalanine ammonialyase (Pal, EC 4.3.1.5). Scots pine, like many other pine species, has a large current population size. The observed levels of inbreeding depression suggest that Scots pine may have a high mutation rate to deleterious alleles. Many Scots pine markers such as isozymes, RFLPs, and microsatellites are highly variable. These observations suggest that the levels of nucleotide variation should be higher than those in other plant species. A 2,045-bp fragment of the pal1 locus was sequenced from five megagametophytes each from a different individual from each of four populations, from northern and southern Finland, central Russia, and northern Spain. There were 12 segregating sites in the locus. The synonymous site overall nucleotide diversity was only 0.0049. In order to compare pal1 with other pine genes, sequence was obtained from two alleles of 11 other loci (total length 4,606 bp). For these, the synonymous nucleotide diversity was 0.0056. These estimates are lower than those from other plants. This is most likely because of a low mutation rate, as estimated from between-pine species synonymous site divergence. In other respects, Scots pine has the characteristics of a species with a large effective population. There was no linkage disequilibrium even between closely linked sites. This resulted in high haplotype diversity (14 different haplotypes among 20 sequences). This could also give rise to high per locus diversity at the protein level. Divergence between populations in the main range was low, whereas an isolated Spanish population had slightly lower diversity and higher divergence than the remaining populations.en_US
dc.languageengen_US
dc.publisherOxford University Press. The Journal's web site is located at http://mbe.oxfordjournals.org/en_US
dc.relation.ispartofMolecular Biology and Evolutionen_US
dc.subject.meshAtp-Binding Cassette Transporters - Geneticsen_US
dc.subject.meshCodonen_US
dc.subject.meshDna Primers - Chemistryen_US
dc.subject.meshDna, Plant - Geneticsen_US
dc.subject.meshFungal Proteins - Geneticsen_US
dc.subject.meshGenetic Variationen_US
dc.subject.meshGenetics, Populationen_US
dc.subject.meshIsoenzymes - Geneticsen_US
dc.subject.meshLinkage Disequilibrium - Geneticsen_US
dc.subject.meshMutation - Geneticsen_US
dc.subject.meshPinus - Geneticsen_US
dc.subject.meshPinus Sylvestrisen_US
dc.subject.meshPolymerase Chain Reactionen_US
dc.subject.meshPolymorphism, Geneticen_US
dc.subject.meshRecombination, Geneticen_US
dc.subject.meshSaccharomyces Cerevisiae Proteinsen_US
dc.subject.meshSeeds - Geneticsen_US
dc.titleLow nucleotide diversity at the pal1 locus in the widely distributed Pinus sylvestrisen_US
dc.typeArticleen_US
dc.identifier.emailDvornyk, V: dvornyk@hku.hken_US
dc.identifier.authorityDvornyk, V=rp00693en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.pmid11801746-
dc.identifier.scopuseid_2-s2.0-0036149896en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-0036149896&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume19en_US
dc.identifier.issue2en_US
dc.identifier.spage179en_US
dc.identifier.epage188en_US
dc.identifier.isiWOS:000173711000006-
dc.publisher.placeUnited Statesen_US
dc.identifier.f10001003929-
dc.identifier.scopusauthoridDvornyk, V=6701789786en_US
dc.identifier.scopusauthoridSirviö, A=6505804759en_US
dc.identifier.scopusauthoridMikkonen, M=6603704309en_US
dc.identifier.scopusauthoridSavolainen, O=7003301206en_US

Export via OAI-PMH Interface in XML Formats


OR


Export to Other Non-XML Formats