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Discovery of Genome-Wide Microsatellite Markers in Scombridae: A Pilot Study on Albacore Tuna.

Nikolic N, Duthoy S, Destombes A, Bodin N, West W, Puech A, Bourjea J - PLoS ONE (2015)

Bottom Line: The number of individuals was insufficient to provide accurate results on differentiation.ThuAla-Hki-01 has a lower number of alleles (9), low heterozygosity (24-27%), low assignment index and significant inbreeding.Finally, the 34 «neutral» and 3 «non-neutral» microsatellites markers were tested on four economically important Scombridae species-Thunnus albacares, Thunnus thynnus, Thunnus obesus, and Acanthocybium solandri.

View Article: PubMed Central - PubMed

Affiliation: IFREMER, Institut Français de Recherche pour l'Exploitation de la Mer, Délégation de La Réunion, Rue Jean Bertho, BP 60, 97 822 Le Port Cedex, La Réunion, France.

ABSTRACT
Recent developments in sequencing technologies and bioinformatics analysis provide a greater amount of DNA sequencing reads at a low cost. Microsatellites are the markers of choice for a variety of population genetic studies, and high quality markers can be discovered in non-model organisms, such as tuna, with these recent developments. Here, we use a high-throughput method to isolate microsatellite markers in albacore tuna, Thunnus alalunga, based on coupling multiplex enrichment and next-generation sequencing on 454 GS-FLX Titanium pyrosequencing. The crucial minimum number of polymorphic markers to infer evolutionary and ecological processes for this species has been described for the first time. We provide 1670 microsatellite design primer pairs, and technical and molecular genetics selection resulting in 43 polymorphic microsatellite markers. On this panel, we characterized 34 random and selectively neutral markers («neutral») and 9 «non-neutral» markers. The variability of «neutral» markers was screened with 136 individuals of albacore tuna from southwest Indian Ocean (42), northwest Indian Ocean (31), South Africa (31), and southeast Atlantic Ocean (32). Power analysis demonstrated that the panel of genetic markers can be applied in diversity and population genetics studies. Global genetic diversity for albacore was high with a mean number of alleles at 16.94; observed heterozygosity 66% and expected heterozygosity 77%. The number of individuals was insufficient to provide accurate results on differentiation. Of the 9 «non-neutral» markers, 3 were linked to a sequence of known function. The one is located to a sequence having an immunity function (ThuAla-Tcell-01) and the other to a sequence having energy allocation function (ThuAla-Hki-01). These two markers were genotyped on the 136 individuals and presented different diversity levels. ThuAla-Tcell-01 has a high number of alleles (20), heterozygosity (87-90%), and assignment index. ThuAla-Hki-01 has a lower number of alleles (9), low heterozygosity (24-27%), low assignment index and significant inbreeding. Finally, the 34 «neutral» and 3 «non-neutral» microsatellites markers were tested on four economically important Scombridae species-Thunnus albacares, Thunnus thynnus, Thunnus obesus, and Acanthocybium solandri.

No MeSH data available.


Number of microsatellites detected within good quality reads for primer design purpose and number of microsatellites with a successfully designed primer pair by motif type.
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pone.0141830.g003: Number of microsatellites detected within good quality reads for primer design purpose and number of microsatellites with a successfully designed primer pair by motif type.

Mentions: A total of 62 628 sequences with 4 285 (7%, Fig 2) unique and consensus sequences containing microsatellite markers were identified (motifs—type of repeat unit—range length of 248–288 bp) from 454 pyrosequencing. Genotyping profile characteristics of 1 670 primer pairs have been designed and described (S2 Table). Out of these sequences, 250 were high quality candidate microsatellite markers (Fig 3) and 225 were successfully designed. As expected, the most commonly found motifs were those used for library enrichment, in particular dinucleotide types AG and AC (37 and 139 microsatellites, respectively), followed by trinucleotides AAG, AAC, and AGG (7, 11, and 5 microsatellites, respectively) (Fig 3). However, although AT was not used as a motif for enrichment, 3 AT microsatellites were identified. Focusing on AG and AC motifs, the average number of repeated motifs was 8 for AG and 11 for AC with a maximum of 21 and 29, respectively (Fig 3). Allelic size range was 106 bp to 302 bp for 43 microsatellite markers (Table 2).


Discovery of Genome-Wide Microsatellite Markers in Scombridae: A Pilot Study on Albacore Tuna.

Nikolic N, Duthoy S, Destombes A, Bodin N, West W, Puech A, Bourjea J - PLoS ONE (2015)

Number of microsatellites detected within good quality reads for primer design purpose and number of microsatellites with a successfully designed primer pair by motif type.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4636268&req=5

pone.0141830.g003: Number of microsatellites detected within good quality reads for primer design purpose and number of microsatellites with a successfully designed primer pair by motif type.
Mentions: A total of 62 628 sequences with 4 285 (7%, Fig 2) unique and consensus sequences containing microsatellite markers were identified (motifs—type of repeat unit—range length of 248–288 bp) from 454 pyrosequencing. Genotyping profile characteristics of 1 670 primer pairs have been designed and described (S2 Table). Out of these sequences, 250 were high quality candidate microsatellite markers (Fig 3) and 225 were successfully designed. As expected, the most commonly found motifs were those used for library enrichment, in particular dinucleotide types AG and AC (37 and 139 microsatellites, respectively), followed by trinucleotides AAG, AAC, and AGG (7, 11, and 5 microsatellites, respectively) (Fig 3). However, although AT was not used as a motif for enrichment, 3 AT microsatellites were identified. Focusing on AG and AC motifs, the average number of repeated motifs was 8 for AG and 11 for AC with a maximum of 21 and 29, respectively (Fig 3). Allelic size range was 106 bp to 302 bp for 43 microsatellite markers (Table 2).

Bottom Line: The number of individuals was insufficient to provide accurate results on differentiation.ThuAla-Hki-01 has a lower number of alleles (9), low heterozygosity (24-27%), low assignment index and significant inbreeding.Finally, the 34 «neutral» and 3 «non-neutral» microsatellites markers were tested on four economically important Scombridae species-Thunnus albacares, Thunnus thynnus, Thunnus obesus, and Acanthocybium solandri.

View Article: PubMed Central - PubMed

Affiliation: IFREMER, Institut Français de Recherche pour l'Exploitation de la Mer, Délégation de La Réunion, Rue Jean Bertho, BP 60, 97 822 Le Port Cedex, La Réunion, France.

ABSTRACT
Recent developments in sequencing technologies and bioinformatics analysis provide a greater amount of DNA sequencing reads at a low cost. Microsatellites are the markers of choice for a variety of population genetic studies, and high quality markers can be discovered in non-model organisms, such as tuna, with these recent developments. Here, we use a high-throughput method to isolate microsatellite markers in albacore tuna, Thunnus alalunga, based on coupling multiplex enrichment and next-generation sequencing on 454 GS-FLX Titanium pyrosequencing. The crucial minimum number of polymorphic markers to infer evolutionary and ecological processes for this species has been described for the first time. We provide 1670 microsatellite design primer pairs, and technical and molecular genetics selection resulting in 43 polymorphic microsatellite markers. On this panel, we characterized 34 random and selectively neutral markers («neutral») and 9 «non-neutral» markers. The variability of «neutral» markers was screened with 136 individuals of albacore tuna from southwest Indian Ocean (42), northwest Indian Ocean (31), South Africa (31), and southeast Atlantic Ocean (32). Power analysis demonstrated that the panel of genetic markers can be applied in diversity and population genetics studies. Global genetic diversity for albacore was high with a mean number of alleles at 16.94; observed heterozygosity 66% and expected heterozygosity 77%. The number of individuals was insufficient to provide accurate results on differentiation. Of the 9 «non-neutral» markers, 3 were linked to a sequence of known function. The one is located to a sequence having an immunity function (ThuAla-Tcell-01) and the other to a sequence having energy allocation function (ThuAla-Hki-01). These two markers were genotyped on the 136 individuals and presented different diversity levels. ThuAla-Tcell-01 has a high number of alleles (20), heterozygosity (87-90%), and assignment index. ThuAla-Hki-01 has a lower number of alleles (9), low heterozygosity (24-27%), low assignment index and significant inbreeding. Finally, the 34 «neutral» and 3 «non-neutral» microsatellites markers were tested on four economically important Scombridae species-Thunnus albacares, Thunnus thynnus, Thunnus obesus, and Acanthocybium solandri.

No MeSH data available.