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Amplified fragment length homoplasy: in silico analysis for model and non-model species.

Paris M, Bonnes B, Ficetola GF, Poncet BN, Després L - BMC Genomics (2010)

Bottom Line: In addition, we compared in silico AFLPs to empirical data obtained from three related non-model species (Bacillus thuringiensis ser. israelensis, Arabis alpina and Aedes rusticus).Furthermore, the number of co-migrating fragments in a single peak was dependent on the genome richness in repetitive sequences: we found up to 582 co-migrating fragments in Ae. aegypti.These predictions can be used to tackle current issues in the planning of AFLP studies by limiting homoplasy rate and population genetic estimation bias.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 09, France. margotparis1@gmail.com

ABSTRACT

Background: AFLP markers are widely used in evolutionary genetics and ecology. However the frequent occurrence of non-homologous co-migrating fragments (homoplasy) both at the intra- and inter-individual levels in AFLP data sets is known to skew key parameters in population genetics. Geneticists can take advantage of the growing number of full genome sequences available for model species to study AFLP homoplasy and to predict it in non-model species.

Results: In this study we performed in silico AFLPs on the complete genome of three model species to predict intra-individual homoplasy in a prokaryote (Bacillus thuringiensis ser. konkukian), a plant (Arabidopsis thaliana) and an animal (Aedes aegypti). In addition, we compared in silico AFLPs to empirical data obtained from three related non-model species (Bacillus thuringiensis ser. israelensis, Arabis alpina and Aedes rusticus). Our results show that homoplasy rate sharply increases with the number of peaks per profile. However, for a given number of peaks per profile, genome size or taxonomical range had no effect on homoplasy. Furthermore, the number of co-migrating fragments in a single peak was dependent on the genome richness in repetitive sequences: we found up to 582 co-migrating fragments in Ae. aegypti. Finally, we show that in silico AFLPs can help to accurately predict AFLP profiles in related non-model species.

Conclusions: These predictions can be used to tackle current issues in the planning of AFLP studies by limiting homoplasy rate and population genetic estimation bias. ISIF (In SIlico Fingerprinting) program is freely available at http://www-leca.ujf-grenoble.fr/logiciels.htm.

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Comparison of the in silico (upper panel) and experimental (lower panel) AFLP profiles obtained with the primer combination EcoRI+ATG/MseI+ATG for the model species Arabidopsis thaliana.
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Figure 1: Comparison of the in silico (upper panel) and experimental (lower panel) AFLP profiles obtained with the primer combination EcoRI+ATG/MseI+ATG for the model species Arabidopsis thaliana.

Mentions: In silico AFLPs on A. thaliana using the primer combination EcoRI+ATG/MseI+ATG generated 20 non-identical fragments between 50 and 500 pb; however, due to size homoplasy, this only corresponded to 13 different peak sizes (Figure 1). Experimental AFLP generated a profile with 12 peaks (Figure 1) and the two profiles almost perfectly matched, except for the expected peak at 410 bp that was scored as missing in the experimental profile (Figure 1) because it was below the detection threshold (only 85 rfu in intensity). We repeated the whole AFLP protocol three times, and we found no difference between the three experimental AFLP profiles; the reproducibility rate was 100%. All experimental sequenced fragments obtained by pyrosequencing perfectly matched the sequences of in silico fragments, including the 410 bp fragment.


Amplified fragment length homoplasy: in silico analysis for model and non-model species.

Paris M, Bonnes B, Ficetola GF, Poncet BN, Després L - BMC Genomics (2010)

Comparison of the in silico (upper panel) and experimental (lower panel) AFLP profiles obtained with the primer combination EcoRI+ATG/MseI+ATG for the model species Arabidopsis thaliana.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2875239&req=5

Figure 1: Comparison of the in silico (upper panel) and experimental (lower panel) AFLP profiles obtained with the primer combination EcoRI+ATG/MseI+ATG for the model species Arabidopsis thaliana.
Mentions: In silico AFLPs on A. thaliana using the primer combination EcoRI+ATG/MseI+ATG generated 20 non-identical fragments between 50 and 500 pb; however, due to size homoplasy, this only corresponded to 13 different peak sizes (Figure 1). Experimental AFLP generated a profile with 12 peaks (Figure 1) and the two profiles almost perfectly matched, except for the expected peak at 410 bp that was scored as missing in the experimental profile (Figure 1) because it was below the detection threshold (only 85 rfu in intensity). We repeated the whole AFLP protocol three times, and we found no difference between the three experimental AFLP profiles; the reproducibility rate was 100%. All experimental sequenced fragments obtained by pyrosequencing perfectly matched the sequences of in silico fragments, including the 410 bp fragment.

Bottom Line: In addition, we compared in silico AFLPs to empirical data obtained from three related non-model species (Bacillus thuringiensis ser. israelensis, Arabis alpina and Aedes rusticus).Furthermore, the number of co-migrating fragments in a single peak was dependent on the genome richness in repetitive sequences: we found up to 582 co-migrating fragments in Ae. aegypti.These predictions can be used to tackle current issues in the planning of AFLP studies by limiting homoplasy rate and population genetic estimation bias.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 09, France. margotparis1@gmail.com

ABSTRACT

Background: AFLP markers are widely used in evolutionary genetics and ecology. However the frequent occurrence of non-homologous co-migrating fragments (homoplasy) both at the intra- and inter-individual levels in AFLP data sets is known to skew key parameters in population genetics. Geneticists can take advantage of the growing number of full genome sequences available for model species to study AFLP homoplasy and to predict it in non-model species.

Results: In this study we performed in silico AFLPs on the complete genome of three model species to predict intra-individual homoplasy in a prokaryote (Bacillus thuringiensis ser. konkukian), a plant (Arabidopsis thaliana) and an animal (Aedes aegypti). In addition, we compared in silico AFLPs to empirical data obtained from three related non-model species (Bacillus thuringiensis ser. israelensis, Arabis alpina and Aedes rusticus). Our results show that homoplasy rate sharply increases with the number of peaks per profile. However, for a given number of peaks per profile, genome size or taxonomical range had no effect on homoplasy. Furthermore, the number of co-migrating fragments in a single peak was dependent on the genome richness in repetitive sequences: we found up to 582 co-migrating fragments in Ae. aegypti. Finally, we show that in silico AFLPs can help to accurately predict AFLP profiles in related non-model species.

Conclusions: These predictions can be used to tackle current issues in the planning of AFLP studies by limiting homoplasy rate and population genetic estimation bias. ISIF (In SIlico Fingerprinting) program is freely available at http://www-leca.ujf-grenoble.fr/logiciels.htm.

Show MeSH