Index-free de novo assembly and deconvolution of mixed mitochondrial genomes.

Genome Biology and Evolution
Bennet J McComishDavid Penny

Abstract

Second-generation sequencing technology has allowed a very large increase in sequencing throughput. In order to make use of this high throughput, we have developed a pipeline for sequencing and de novo assembly of multiple mitochondrial genomes without the costs of indexing. Simulation studies on a mixture of diverse animal mitochondrial genomes showed that mitochondrial genomes could be reassembled from a high coverage of short (35 nt) reads, such as those generated by a second-generation Illumina Genome Analyzer. We then assessed this experimentally with long-range polymerase chain reaction products from mitochondria of a human, a rat, a bird, a frog, an insect, and a mollusc. Comparison with reference genomes was used for deconvolution of the assembled contigs rather than for mapping of sequence reads. As proof of concept, we report the complete mollusc mitochondrial genome of an olive shell (Amalda northlandica). It has a very unusual putative control region, which contains a structure that would probably only be detectable by next-generation sequencing. The general approach has considerable potential, especially when combined with indexed sequencing of different groups of genomes.

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Jun 24, 2011·Journal of Applied Genetics·Chandra Shekhar PareekAndrzej Tretyn
Dec 14, 2012·PloS One·Age BrauerMaido Remm
Jan 4, 2013·PloS One·Chris A CorserDavid Penny
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Oct 18, 2015·Genome Biology and Evolution·Gillian C GibbDavid Penny
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Dec 4, 2010·BMC Evolutionary Biology·Judith H RobinsHoward A Ross
Apr 6, 2021·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Fabrizio GhiselliJeffrey L Boore

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Datasets Mentioned

BETA
AB043889
AB029616
AJ428514
GQ214521
GU570664
GU196685

Methods Mentioned

BETA
genetic modification
PCR
Illumina sequencing

Software Mentioned

SOLiD
Exonerate
R
MySQL
Perl
Illumina
Geneious
Velvet
MFold
Edena

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