Development and cross-species transferability of 23 microsatellite markers from the vulnerable Chinese Egret (Egretta eulophotes) using 454 sequencing

Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coralMillepora platyphylla, an important reef-builder of Indo-Pacific reefs.We tested the cross-species amplification of these loci in five other species of the genusMilleporaand analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target speciesM. platyphylla,among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five otherMilleporaspecies revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean speciesM. complanatadue to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species ofMillepora.Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323–0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoanMilleporaspecies creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.

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Isolation and characterization of microsatellite markers for Osmanthus fragrans (Oleaceae) using 454 sequencing technology

Genetics and Molecular Research ◽

10.4238/2015.december.16.15 ◽

2015 ◽

Vol 14 (4) ◽

pp. 17154-17158 ◽

Cited By ~ 3

Author(s):

W.J. Yuan ◽

Y. Li ◽

Y.F. Ma ◽

Y.J. Han ◽

F.D. Shang

Keyword(s):

Microsatellite Markers ◽

454 Sequencing ◽

Sequencing Technology ◽

Osmanthus Fragrans ◽

Isolation And Characterization

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Development of Microsatellite Markers for the Clonal ShrubOrixa japonica(Rutaceae) Using 454 Sequencing

Applications in Plant Sciences ◽

10.3732/apps.1600066 ◽

2016 ◽

Vol 4 (10) ◽

pp. 1600066

Author(s):

Ichiro Tamaki ◽

Suzuki Setsuko ◽

Kyoko Sugai ◽

Nao Yanagisawa

Keyword(s):

Microsatellite Markers ◽

454 Sequencing

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Isolation and characterisation via 454 sequencing of microsatellites from the tawny frogmouth, Podargus strigoides (Class Aves, Family Podargidae)

Australian Journal of Zoology ◽

10.1071/zo12062 ◽

2012 ◽

Vol 60 (2) ◽

pp. 133

Author(s):

Fiona E. Hogan ◽

Marian Weaving ◽

Gregory R. Johnston

Keyword(s):

Population Genetics ◽

Gene Flow ◽

Microsatellite Markers ◽

Reproductive Ecology ◽

454 Sequencing ◽

Urban Environments ◽

Shotgun Sequencing ◽

Target Species ◽

Single Population ◽

Polymorphic Microsatellite

We isolated 24 novel polymorphic microsatellite markers from the tawny frogmouth, a nocturnal bird endemic to Australia, which has successfully adapted to urban environments. Initially, 454 shotgun sequencing was used to identify 733 loci with primers designed. Of these, we trialled 30 in the target species of which all amplified a product of expected size. Subsequently, all 30 of these loci were screened for variation in 25 individuals, from a single population in Melbourne, Victoria, Australia. Twenty-eight loci were polymorphic with observed heterozygosity ranging from 0.03 to 0.96 (mean 0.58) and the number of alleles per locus ranged from 2 to 18 (average of 6.5); we confirmed that 24 loci conformed to Hardy–Weinberg expectations. The 24 loci identified here will be sufficient to unequivocally identify individuals and will be useful in understanding the reproductive ecology, population genetics and the gene flow amongst localities in urban environments where this bird thrives.

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