Microsatellite loci and the complete mitochondrial DNA sequence characterized through next generation sequencing and de novo genome assembly for the critically endangered orange-bellied parrot, Neophema chrysogaster

Miller, Adam, Good, RT, Coleman, RA, Lancaster, ML and Weeks, AR 2013, Microsatellite loci and the complete mitochondrial DNA sequence characterized through next generation sequencing and de novo genome assembly for the critically endangered orange-bellied parrot, Neophema chrysogaster, Molecular biology reports, vol. 40, no. 1, pp. 35-42, doi: 10.1007/s11033-012-1950-z.

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Title Microsatellite loci and the complete mitochondrial DNA sequence characterized through next generation sequencing and de novo genome assembly for the critically endangered orange-bellied parrot, Neophema chrysogaster
Author(s) Miller, Adam
Good, RT
Coleman, RA
Lancaster, ML
Weeks, AR
Journal name Molecular biology reports
Volume number 40
Issue number 1
Start page 35
End page 42
Total pages 8
Publisher Springer
Place of publication Amsterdam, The Netherlands
Publication date 2013-01
ISSN 0301-4851
1573-4978
Keyword(s) Neophema chrysogaster
Microsatellite library development
Mitochondrial genome sequence
Next generation DNA sequencing
De novo genome assembly
Summary A suite of polymorphic microsatellite markers and the complete mitochondrial genome sequence was developed by next generation sequencing (NGS) for the critically endangered orange-bellied parrot, Neophema chrysogaster. A total of 14 polymorphic loci were identified and characterized using DNA extractions representing 40 individuals from Melaleuca, Tasmania, sampled in 2002. We observed moderate genetic variation across most loci (mean number of alleles per locus = 2.79; mean expected heterozygosity = 0.53) with no evidence of individual loci deviating significantly from Hardy-Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, and analyses indicated no evidence of null alleles across loci. De novo and reference-based genome assemblies performed using MIRA were used to assemble the N. chrysogaster mitochondrial genome sequence with mean coverage of 116-fold (range 89 to 142-fold). The mitochondrial genome consists of 18,034 base pairs, and a typical metazoan mitochondrial gene content consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a single large non-coding region (control region). The arrangement of mitochondrial genes is also typical of Avian taxa. The annotation of the mitochondrial genome and the characterization of 14 microsatellite markers provide a valuable resource for future genetic monitoring of wild and captive N. chrysogaster populations. As found previously, NGS provides a rapid, low cost and reliable method for polymorphic nuclear genetic marker development and determining complete mitochondrial genome sequences when only a fraction of a genome is sequenced.
Language eng
DOI 10.1007/s11033-012-1950-z
Field of Research 060411 Population, Ecological and Evolutionary Genetics
050202 Conservation and Biodiversity
Socio Economic Objective 970106 Expanding Knowledge in the Biological Sciences
HERDC Research category C1.1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Copyright notice ©2012, Springer Science+Business Media Dordrecht
Persistent URL http://hdl.handle.net/10536/DRO/DU:30088772

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