Evaluation of two approaches to genotyping major histocompatibility complex class I in a passerine-CE-SSCP and 454 pyrosequencing

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11310%2F12%3A10100936" target="_blank" >RIV/00216208:11310/12:10100936 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/68081766:_____/12:00365694

Výsledek na webu

<a href="http://dx.doi.org/10.1111/j.1755-0998.2011.03082.x" target="_blank" >http://dx.doi.org/10.1111/j.1755-0998.2011.03082.x</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1111/j.1755-0998.2011.03082.x" target="_blank" >10.1111/j.1755-0998.2011.03082.x</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Evaluation of two approaches to genotyping major histocompatibility complex class I in a passerine-CE-SSCP and 454 pyrosequencing

Popis výsledku v původním jazyce

MHC is linked to individual fitness and is important in evolutionary ecology and conservation genetics. Gene duplication and positive selection usually lead to high polymorphism in the MHC region, making genotyping of MHC a challenging task. We compare the performance of two methods for MHC class I genotyping in a passerine with highly duplicated MHC class I genes: CE-SSCP analysis and 454 GS FLX Titanium pyrosequencing. According to our findings, the number of MHC alleles detected by CE-SSCP is significantly lower than detected by 454. To resolve discrepancies between the two methods, we cloned and Sanger sequenced a MHC class I amplicon for an individual with high number of alleles. We found perfect congruence between cloning/Sanger sequencing and 454. Thus, in case of multi-locus amplification, CE-SSCP considerably underestimates individual MHC diversity. Numbers of alleles detected by both methods are significantly correlated, although the correlation is weak (r=0.32).

Název v anglickém jazyce

Evaluation of two approaches to genotyping major histocompatibility complex class I in a passerine-CE-SSCP and 454 pyrosequencing

Popis výsledku anglicky

MHC is linked to individual fitness and is important in evolutionary ecology and conservation genetics. Gene duplication and positive selection usually lead to high polymorphism in the MHC region, making genotyping of MHC a challenging task. We compare the performance of two methods for MHC class I genotyping in a passerine with highly duplicated MHC class I genes: CE-SSCP analysis and 454 GS FLX Titanium pyrosequencing. According to our findings, the number of MHC alleles detected by CE-SSCP is significantly lower than detected by 454. To resolve discrepancies between the two methods, we cloned and Sanger sequenced a MHC class I amplicon for an individual with high number of alleles. We found perfect congruence between cloning/Sanger sequencing and 454. Thus, in case of multi-locus amplification, CE-SSCP considerably underestimates individual MHC diversity. Numbers of alleles detected by both methods are significantly correlated, although the correlation is weak (r=0.32).

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

EG - Zoologie

OECD FORD obor

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Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2012

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Molecular Ecology Resources

ISSN

1755-098X

e-ISSN

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Svazek periodika

12

Číslo periodika v rámci svazku

2

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

8

Strana od-do

285-292

Kód UT WoS článku

000299930300011

EID výsledku v databázi Scopus

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