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Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes

Gan, Han Ming, Schultz, Mark B. and Austin, Christopher M. 2014, Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes, Genome biology and evolution, vol. 14, pp. 1-8, doi: 10.1186/1471-2148-14-19.

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Title Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes
Author(s) Gan, Han Ming
Schultz, Mark B.
Austin, Christopher M.ORCID iD for Austin, Christopher M. orcid.org/0000-0003-1848-6267
Journal name Genome biology and evolution
Volume number 14
Start page 1
End page 8
Total pages 8
Publisher BioMed Central
Place of publication London, Eng.
Publication date 2014-02-03
ISSN 1759-6653
1471-2148
Keyword(s) Animals
Astacoidea
Australia
Computational Biology
Fresh Water
Gene Order
Gene Rearrangement
Genome, Mitochondrial
Sequence Analysis, DNA
Science & Technology
Life Sciences & Biomedicine
Evolutionary Biology
Genetics & Heredity
Freshwater crayfish
Mitochondrial genome characterization
Bench top sequencing
Engaeus
Parastacidae
COMPLETE MITOCHONDRIAL GENOME
DNA SEQUENCE
CRUSTACEA
DECAPODA
PHYLOGENY
LOBSTER
Summary BACKGROUND: Although it is possible to recover the complete mitogenome directly from shotgun sequencing data, currently reported methods and pipelines are still relatively time consuming and costly. Using a sample of the Australian freshwater crayfish Engaeus lengana, we demonstrate that it is possible to achieve three-day turnaround time (four hours hands-on time) from tissue sample to NCBI-ready submission file through the integration of MiSeq sequencing platform, Nextera sample preparation protocol, MITObim assembly algorithm and MITOS annotation pipeline.

RESULTS: The complete mitochondrial genome of the parastacid freshwater crayfish, Engaeus lengana, was recovered by modest shotgun sequencing (1.2 giga bases) using the Illumina MiSeq benchtop sequencing platform. Genome assembly using the MITObim mitogenome assembler recovered the mitochondrial genome as a single contig with a 97-fold mean coverage (min. = 17; max. = 138). The mitogenome consists of 15,934 base pairs and contains the typical 37 mitochondrial genes and a non-coding AT-rich region. The genome arrangement is similar to the only other published parastacid mitogenome from the Australian genus Cherax.

CONCLUSIONS: We infer that the gene order arrangement found in Cherax destructor is common to Australian crayfish and may be a derived feature of the southern hemisphere family Parastacidae. Further, we report to our knowledge, the simplest and fastest protocol for the recovery and assembly of complete mitochondrial genomes using the MiSeq benchtop sequencer.
Language eng
DOI 10.1186/1471-2148-14-19
Field of Research 060305 Evolution of Developmental Systems
060408 Genomics
0604 Genetics
0603 Evolutionary Biology
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 ©2014, Gan et al.
Free to Read? Yes
Use Rights Creative Commons Attribution licence
Persistent URL http://hdl.handle.net/10536/DRO/DU:30091318

Document type: Journal Article
Collections: School of Life and Environmental Sciences
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Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.